2502.13025v1

# Agentic Deep Graph Reasoning Yields Self-Organizing Knowledge Networks **Authors**: - Markus J. Buehler (Laboratory for Atomistic and Molecular Mechanics) - Cambridge, MA 02139, USA > Corresponding author. ## Abstract We present an agentic, autonomous graph expansion framework that iteratively structures and refines knowledge in situ. Unlike conventional knowledge graph construction methods relying on static extraction or single-pass learning, our approach couples a reasoning-native large language model with a continually updated graph representation. At each step, the system actively generates new concepts and relationships, merges them into a global graph, and formulates subsequent prompts based on its evolving structure. Through this feedback-driven loop, the model organizes information into a scale-free network characterized by hub formation, stable modularity, and bridging nodes that link disparate knowledge clusters. Over hundreds of iterations, new nodes and edges continue to appear without saturating, while centrality measures and shortest path distributions evolve to yield increasingly distributed connectivity. Our analysis reveals emergent patterns—such as the rise of highly connected “hub” concepts and the shifting influence of “bridge” nodes—indicating that agentic, self-reinforcing graph construction can yield open-ended, coherent knowledge structures. Applied to materials design problems, we present compositional reasoning experiments by extracting node-specific and synergy-level principles to foster genuinely novel knowledge synthesis, yielding cross-domain ideas that transcend rote summarization and strengthen the framework’s potential for open-ended scientific discovery. We discuss other applications in scientific discovery and outline future directions for enhancing scalability and interpretability. Keywords Artificial Intelligence $·$ Science $·$ Graph Theory $·$ Category Theory $·$ Materials Science $·$ Materiomics $·$ Language Modeling $·$ Reasoning $·$ Isomorphisms $·$ Engineering ## 1 Introduction Scientific inquiry often proceeds through an interplay of incremental refinement and transformative leaps, evoking broader questions of how knowledge evolves under continual reflection and questioning. In many accounts of discovery, sustained progress arises not from isolated insights but from an iterative process in which prior conclusions are revisited, expressed as generalizable ideas, refined, or even reorganized as new evidence and perspectives emerge [1]. Foundational work in category theory has formalized aspects of this recursive structuring, showing how hierarchical representations can unify diverse knowledge domains and enable higher-level abstractions in both the natural and social sciences [2, 3, 4]. Across engineering disciplines including materials science, such iterative integration of information has proven essential in synthesizing deeply interlinked concepts. Recent AI methods, however, often emphasize predictive accuracy and single-step outputs over the layered, self-reflective processes that characterize human problem-solving. Impressive gains in natural language processing, multimodal reasoning [5, 6, 7, 8, 9, 10, 11, 12], and materials science [13, 14, 15, 16, 17], including breakthroughs in molecular biology [18] and protein folding [19, 20, 21], showcase the prowess of large-scale models trained on vast datasets. Yet most of the early systems generate answers in a single pass, sidestepping the symbolic, stepwise reasoning that often underpins scientific exploration. This gap has prompted a line of research into modeling that explicitly incorporates relational modeling, reflection or multi-step inferences [2, 3, 4, 22, 23, 24, 25, 26, 27, 28], hinting at a transition from single-shot pattern recognition to more adaptive synthesis of answers from first principles in ways that more closely resemble compositional mechanisms. Thus, a fundamental challenge now is how can we build scientific AI systems that synthesize information rather than memorizing it. Graphs offer a natural substrate for this kind of iterative knowledge building. By representing concepts and their relationships as a network, it becomes possible to capture higher-order structure—such as hubs, bridging nodes, or densely interconnected communities—that might otherwise remain implicit. This explicit relational format also facilitates systematic expansion: each newly added node or edge can be linked back to existing concepts, reshaping the network and enabling new paths of inference [29, 23, 27]. Moreover, graph-based abstractions can help large language models move beyond memorizing discrete facts; as nodes accumulate and form clusters, emergent properties may reveal cross-domain synergies or overlooked gaps in the knowledge space. Recent work suggests that standard Transformer architectures can be viewed as a form of Graph Isomorphism Network (GIN), where attention operates over relational structures rather than raw token sequences [23]. Under this lens, each attention head effectively tests for isomorphisms in local neighborhoods of the graph, offering a principled way to capture both global and local dependencies. A category-theoretic perspective further bolsters this approach by providing a unified framework for compositional abstractions: nodes and edges can be treated as objects and morphisms, respectively, while higher-level concepts emerge from functorial mappings that preserve relational structure [2, 3, 4]. Taken together, these insights hint at the potential for compositional capabilities in AI systems, where simpler building blocks can be combined and reconfigured to form increasingly sophisticated representations, rather than relying on one-pass computations or static ontologies. By using graph-native modeling and viewing nodes and edges as composable abstractions, such a model may be able to recognize and reapply learned configurations in new contexts—akin to rearranging building blocks to form unanticipated solutions. This compositional approach, strengthened by category-theoretic insights, allows the system to not only interpolate among known scenarios but to extrapolate to genuinely novel configurations. In effect, graph-native attention mechanisms treat interconnected concepts as first-class entities, enabling the discovery of new behaviors or interactions that purely sequence-based methods might otherwise overlook. A fundamental challenge remains: How can we design AI systems that, rather than merely retrieving or matching existing patterns, build and refine their own knowledge structures across iterations. Recent work proposes that graphs can be useful strategies to endow AI models with relational capabilities [29, 23, 27] both within the framework of creating graph-native attention mechanisms and by training models to use graphs as native abstractions during learned reasoning phases. Addressing this challenge requires not only methods for extracting concepts but also mechanisms for dynamically organizing them so that new information reshapes what is already known. By endowing large language models with recursively expanding knowledge graph capabilities, we aim to show how stepwise reasoning can support open-ended discovery and conceptual reorganization. The work presented here explores how such feedback-driven graph construction may lead to emergent, self-organizing behaviors, shedding light on the potential for truly iterative AI approaches that align more closely with the evolving, integrative nature of human scientific inquiry. Earlier work on graph-native reasoning has demonstrated that models explicitly taught how to reason in graphs and abstractions can lead to systems that generalize better and are more interpretable [27]. Here we explore whether we can push this approach toward ever-larger graphs, creating extensive in situ graph reasoning loops where models spend hours or days developing complex relational structures before responding to a task. Within such a vision, several key issues arise: Will repeated expansions naturally preserve the network’s relational cohesion, or risk splintering into disconnected clusters? Does the continuous addition of new concepts and edges maintain meaningful structure, or lead to saturation and redundancy? And to what extent do bridging nodes, which may initially spark interdisciplinary links, remain influential over hundreds of iterations? In the sections ahead, we investigate these questions by analyzing how our recursively expanded knowledge graphs grow and reorganize at scale—quantifying hub formation, modular stability, and the persistence of cross-domain connectors. Our findings suggest that, rather than collapsing under its own complexity, the system retains coherent, open-ended development, pointing to new possibilities for large-scale knowledge formation in AI-driven research for scientific exploration. Iterative Reasoning $i<N$ Define Initial Question (Broad question or specific topic, e.g., "Impact-Resistant Materials") Generate Graph-native Reasoning Tokens <|thinking|> ... <|/thinking|> Parse Graph $G_local^i$ (Extract Nodes and Relations) Merge Extracted Graph with Larger Graph (Append Newly Added Nodes/Edges) $G←G∪G_local^i$ Save and Visualize Final Integrated Graph $G$ Generate New Question Based on Last Extracted Added Nodes/Edges as captured in $G_local^i$ Figure 1: Algorithm used for iterative knowledge extraction and graph refinement. At each iteration $i$ , the model generates reasoning tokens (blue). From the response, a local graph $G_local^i$ is extracted (violet) and merged with the global knowledge graph $G$ (light violet). The evolving graph is stored in multiple formats for visualization and analysis (yellow). Instead of letting the model respond to the task, a follow-up task is generated based on the latest extracted nodes and edges in $G_local^i$ (green), ensuring iterative refinement (orange), so that the model generates yet more reasoning tokens, and as part of that process, new nodes and edges. The process continues until the stopping condition $i<N$ is met, yielding a final structured knowledge graph $G$ (orange). ### 1.1 Knowledge Graph Expansion Approaches Knowledge graphs are one way to organize relational understanding of the world. They have grown from manually curated ontologies decades ago into massive automatically constructed repositories of facts. A variety of methodologies have been developed for expanding knowledge graphs. Early approaches focused on information extraction from text using pattern-based or open-domain extractors. For example, the DIPRE algorithm [30] bootstrapped relational patterns from a few seed examples to extract new facts in a self-reinforcing loop. Similarly, the KnowItAll system [31] introduced an open-ended, autonomous “generate-and-test” paradigm to extract entity facts from the web with minimal supervision. Open Information Extraction methods like TextRunner [32] and ReVerb [33] further enabled unsupervised extraction of subject–predicate–object triples from large text corpora without requiring a predefined schema. These unsupervised techniques expanded knowledge graphs by harvesting new entities and relations from unstructured data, although they often required subsequent mapping of raw extractions to a coherent ontology. In parallel, research on knowledge graph completion has aimed to expand graphs by inferring missing links and attributes. Statistical relational learning and embedding-based models (e.g., translational embeddings like TransE [34]) predict new relationships by generalizing from known graph structures. Such approaches, while not fully unsupervised (they rely on an existing core of facts for training), can autonomously suggest plausible new edges to add to a knowledge graph. Complementary to embeddings, logical rule-mining systems such as AMIE [35] showed that high-confidence Horn rules can be extracted from an existing knowledge base and applied to infer new facts recursively. Traditional link prediction heuristics from network science – for example, preferential attachment and other graph connectivity measures – have also been used as simple unsupervised methods to propose new connections in knowledge networks. Together, these techniques form a broad toolkit for knowledge graph expansion, combining text-derived new content with graph-internal inference to improve a graph’s coverage and completeness. ### 1.2 Recursive and Autonomous Expansion Techniques A notable line of work seeks to make knowledge graphs growth continuous and self-sustaining – essentially achieving never-ending expansion. The NELL project (Never-Ending Language Learner) [36] pioneered this paradigm, with a system that runs 24/7, iteratively extracting new beliefs from the web, integrating them into its knowledge base, and retraining itself to improve extraction competence each day. Over years of operation, NELL has autonomously accumulated millions of facts by coupling multiple learners (for parsing, classification, relation extraction, etc.) in a semi-supervised bootstrapping loop. This recursive approach uses the knowledge learned so far to guide future extractions, gradually expanding coverage while self-correcting errors; notably, NELL can even propose extensions to its ontology as new concepts emerge. Another milestone in autonomous knowledge graph construction was Knowledge Vault [37], which demonstrated web-scale automatic knowledge base population by fusing facts from diverse extractors with probabilistic inference. Knowledge Vault combined extractions from text, tables, page structure, and human annotations with prior knowledge from existing knowledge graphs, yielding a vast collection of candidate facts (on the order of 300 million) each accompanied by a calibrated probability of correctness. This approach showed that an ensemble of extractors, coupled with statistical fusion, can populate a knowledge graph at scales far beyond what manual curation or single-source extraction can achieve. Both NELL and Knowledge Vault illustrate the power of autonomous or weakly-supervised systems that grow a knowledge graph with minimal human intervention, using recursive learning and data fusion to continually expand and refine the knowledge repository. More recent research has explored agent-based and reinforcement learning (RL) frameworks for knowledge graph expansion and reasoning. Instead of one-shot predictions, these methods allow an agent to make multi-hop queries or sequential decisions to discover new facts or paths in the graph. For example, some work [38] employ an agent that learns to navigate a knowledge graph and find multi-step relational paths, effectively learning to reason over the graph to answer queries. Such techniques highlight the potential of autonomous reasoning agents that expand knowledge by exploring connections in a guided manner (using a reward signal for finding correct or novel information). This idea of exploratory graph expansion aligns with concepts in network science, where traversing a network can reveal undiscovered links or communities. It also foreshadowed approaches like Graph-PReFLexOR [27] that treat reasoning as a sequential decision process, marked by special tokens, that can iteratively build and refine a task-specific knowledge graph. Applications of these expansion techniques in science and engineering domains underscore their value for discovery [29]. Automatically constructed knowledge graphs have been used to integrate and navigate scientific literature, enabling hypothesis generation by linking disparate findings. A classic example is Swanson’s manual discovery of a connection between dietary fish oil and Raynaud’s disease, which emerged by linking two disjoint bodies of literature through intermediate concepts [39, 40]. Modern approaches attempt to replicate such cross-domain discovery in an automated way: for instance, mining biomedical literature to propose new drug–disease links, or building materials science knowledge graphs that connect material properties, processes, and applications to suggest novel materials, engineering concepts, or designs [41, 29]. ### 1.3 Relation to Earlier Work and Key Hypothesis The prior work discussed in Section 1.2 provides a foundation for our approach, which draws on the never-ending learning spirit of NELL [36] and the web-scale automation of Knowledge Vault [37] to dynamically grow a knowledge graph in situ as it reasons. Like those systems, it integrates information from diverse sources and uses iterative self-improvement. However, rather than relying on passive extraction or purely probabilistic link prediction, our method pairs on-the-fly logical reasoning with graph expansion within the construct of a graph-native reasoning LLM. This means each newly added node or edge is both informed by and used for the model’s next step of reasoning. Inspired in part by category theory and hierarchical inference, we move beyond static curation by introducing a principled, recursive reasoning loop that helps maintain transparency in how the knowledge graph evolves. In this sense, the work can be seen as a synthesis of existing ideas—continuous learning, flexible extraction, and structured reasoning—geared toward autonomous problem-solving in scientific domains. Despite substantial progress in knowledge graph expansion, many existing methods still depend on predefined ontologies, extensive post-processing, or reinforce only a fixed set of relations. NELL and Knowledge Vault, for instance, demonstrated how large-scale extraction and integration of facts can be automated, but they rely on established schemas or require manual oversight to refine extracted knowledge [36, 37]. Reinforcement learning approaches such as DeepPath [38] can efficiently navigate existing graphs but do not grow them by generating new concepts or hypotheses. By contrast, the work reported here treats reasoning as an active, recursive process that expands a knowledge graph while simultaneously refining its structure. This aligns with scientific and biological discovery processes, where knowledge is not just passively accumulated but also reorganized in light of new insights. Another key distinction is the integration of preference-based objectives, enabling more explicit interpretability of each expansion step. Methods like TransE [34] excel at capturing statistical regularities but lack an internal record of reasoning paths; our approach, in contrast, tracks and justifies each newly added node or relation. This design allows for a transparent, evolving representation that is readily applied to interdisciplinary exploration—such as in biomedicine [39] and materials science [41] —without depending on rigid taxonomies. Hence, this work goes beyond conventional graph expansion by embedding recursive reasoning directly into the construction process, bridging the gap between passive knowledge extraction and active discovery. As we show in subsequent sections, this self-expanding paradigm yields scale-free knowledge graphs in which emergent hubs and bridge nodes enable continuous reorganization, allowing the system to evolve its understanding without exhaustive supervision and paving the way for scalable hypothesis generation and autonomous reasoning. Hypothesis. We hypothesize that recursive graph expansion enables self-organizing knowledge formation, allowing intelligence-like behavior to emerge without predefined ontologies, external supervision, or centralized control. Using a pre-trained model, Graph-PReFLexOR (an autonomous graph-reasoning model trained on a corpus of biological and biologically inspired materials principles) we demonstrate that knowledge graphs can continuously expand in a structured yet open-ended manner, forming scale-free networks with emergent conceptual hubs and interdisciplinary bridge nodes. Our findings suggest that intelligence-like reasoning can arise from recursive self-organization, challenging conventional paradigms and advancing possibilities for autonomous scientific discovery and scalable epistemic reasoning. ## 2 Results and Discussion We present the results of experiments in which the graph-native reasoning model engages in a continuous, recursive process of graph-based reasoning, expanding its knowledge graph representation autonomously over 1,000 iterations. Unlike prior approaches that rely on a small number of just a few recursive reasoning steps, the experiments reported in this paper explore how knowledge formation unfolds in an open-ended manner, generating a dynamically evolving graph. As the system iterates, it formulates new tasks, refines reasoning pathways, and integrates emerging concepts, progressively structuring its own knowledge representation following the simple algorithmic paradigm delineated in Figure 1. The resulting graphs from all iterations form a final integrated knowledge graph, which we analyze for structural and conceptual insights. Figure 2 depicts the final state of the graph, referred to as graph $G_1$ , after the full reasoning process. The recursive graph reasoning process can be conducted in either an open-ended setting or develoepd into a more tailored manner to address a specific domain or flavor in which reasoning steps are carried out (details, see Materials and Methods). In the example explored here, we focus on designing impact-resistant materials. In this specialized scenario, we initiate the model with a concise, topic-specific prompt – e.g., Describe a way to design impact resistant materials, and maintain the iterative process of extracting structured knowledge from the model’s reasoning. We refer to the resulting graph as $G_2$ . Despite the narrower focus, the same core principles apply: each new piece of information from the language model is parsed into nodes and edges, appended to a global graph, and informs the next iteration’s query. In this way, $G_2$ captures a highly directed and domain-specific knowledge space while still exhibiting many of the emergent structural traits—such as hub formation, stable modularity, and growing connectivity—previously seen in the more general graph $G_1$ . Figure 3 shows the final snapshot for $G_2$ . To further examine the emergent structural organization of both graphs, Figures S1 and S2 display the same graphs with nodes and edges colored according to cluster identification, revealing the conceptual groupings that emerge during recursive knowledge expansion. <details> <summary>x2.png Details</summary>  ### Visual Description ## Network Graph: Abstract Connectivity Visualization ### Overview The image displays a complex, abstract network graph visualization rendered in a monochromatic orange color palette against a plain white background. It consists of numerous nodes (points) connected by a dense web of curved edges (lines). The visualization appears to be generated by a force-directed layout algorithm, where connected nodes attract each other and all nodes repel each other, resulting in a clustered, organic structure. There is no accompanying text, labels, axes, titles, or legend present in the image. ### Components * **Nodes:** Represented as circular dots. They vary significantly in size and color intensity (saturation/value). * **Size:** Ranges from very small, faint points to large, prominent circles. The largest node is located in the lower-left quadrant. * **Color:** All nodes are shades of orange. Larger nodes are a deeper, more saturated red-orange, while smaller nodes are a pale, light orange. * **Edges:** Represented as thin, curved lines connecting the nodes. They also vary in opacity and thickness. * **Opacity/Thickness:** Lines connected to larger, more central nodes appear darker and slightly thicker. Lines in peripheral or less dense areas are very faint and thin. The curvature suggests an attempt to minimize line crossings in a dense network. * **Spatial Layout:** The graph is not uniformly distributed. It features distinct clusters and several highly connected central hubs. * **Primary Hub:** A very large, dark red-orange node in the lower-left quadrant acts as a major focal point, with a dense starburst of connections radiating from it. * **Secondary Hubs:** Several medium-sized, darker orange nodes are visible, particularly in the upper-right quadrant and near the center, each serving as a local center for their own cluster of connections. * **Periphery:** The outer edges of the graph are populated by many small, faint nodes with fewer connections, creating a diffuse, cloud-like boundary. ### Detailed Analysis * **Node Hierarchy:** The visualization implies a clear hierarchy or importance metric, likely based on **degree centrality** (number of connections). The size and color intensity of a node are directly correlated with its connectivity. * **Largest Node (Lower-Left):** Approximate diameter is 5-7 times that of the smallest nodes. Its deep red-orange color and the sheer density of edges emanating from it mark it as the most significant entity in this network. * **Medium Nodes (e.g., Upper-Right Cluster):** Several nodes are approximately 2-3 times the diameter of the smallest nodes, colored a standard orange. They form the cores of smaller clusters. * **Small Nodes:** The vast majority of nodes are very small and pale, indicating low connectivity. * **Edge Density:** The density of connections is highest around the major hubs, creating visually opaque regions of overlapping lines. The density decreases markedly towards the periphery of the graph. * **Cluster Identification:** At least three major clusters are discernible: 1. A large, dense cluster anchored by the primary hub in the lower-left. 2. A significant cluster in the upper-right quadrant, centered around 2-3 medium hubs. 3. A more diffuse, less tightly knit cluster in the lower-right area. ### Key Observations 1. **Monochromatic Encoding:** All data is encoded using a single hue (orange) with variations in saturation and lightness. This creates a cohesive visual but makes precise differentiation between many nodes challenging without interactive tools. 2. **Absence of Metadata:** The graph is entirely abstract. There are no labels for nodes, no title, no legend explaining what the nodes or edges represent, and no scale. This limits interpretation to structural analysis only. 3. **Force-Directed Layout Characteristics:** The organic, clustered appearance with curved edges is typical of algorithms like Fruchterman-Reingold or Force Atlas, which prioritize showing community structure and relative importance. 4. **Visual Weight Imbalance:** The composition is heavily weighted towards the lower-left due to the primary hub, creating a strong visual anchor point. ### Interpretation This image is a pure visualization of **network topology and relative node importance**. It demonstrates the following structural principles: * **Scale-Free Network Properties:** The presence of a few highly connected hubs (the large nodes) amidst many poorly connected nodes is characteristic of scale-free networks, common in social networks, biological pathways, and the internet. * **Community Structure:** The clear clustering indicates the network contains communities or modules—groups of nodes more densely connected to each other than to the rest of the network. * **Centrality Visualization:** The design effectively uses pre-attentive visual attributes (size, color intensity) to immediately draw the viewer's eye to the most central nodes, providing an instant understanding of the network's backbone. **Limitations & Missing Information:** The complete lack of semantic labels is the critical limitation. We cannot determine if this represents a social network, a citation network, a neural network, a protein interaction map, or any other type of relational data. The visualization shows *that* structure exists and *what* its relative properties are, but not *what it is*. To derive factual meaning, this graph would need to be paired with a data table mapping node IDs to labels and a description of the edge relationships. </details> Figure 2: Knowledge graph $G_1$ after around 1,000 iterations, under a flexible self-exploration scheme initiated with the prompt Discuss an interesting idea in bio-inspired materials science. We observe the formation of a highly connected graph with multiple hubs and centers. <details> <summary>x3.png Details</summary>  ### Visual Description ## Network Diagram: Centralized Hub-and-Spoke Structure ### Overview The image displays a complex, abstract network diagram or graph visualization against a plain white background. It consists of numerous nodes (dots) connected by thin, curved lines (edges). The structure is highly centralized, with one dominant, brightly colored node acting as a primary hub, from which a dense web of connections radiates outward to form several distinct clusters. There is no textual information, labels, axes, or legends present in the image. ### Components * **Nodes:** Represented as circular dots. They vary in size and color saturation. * **Primary Hub Node:** A single, large, solid **dark red** node located slightly above the geometric center of the main cluster. * **Secondary Nodes:** Numerous smaller nodes in shades of **light orange, peach, and beige**. These are distributed throughout the diagram, with some forming dense local clusters. * **Edges:** Represented as thin, curved lines connecting the nodes. They are predominantly in **light orange and beige** tones, with some lines near the central hub appearing slightly darker or more saturated. The lines are not straight; they follow organic, sweeping curves. * **Spatial Layout:** The network is not uniformly distributed. It features: * A **dense central cluster** surrounding the red hub node. * Several **peripheral clusters** connected to the center by longer, sparser lines. Notable clusters are visible in the **bottom-left**, **bottom-right**, and **upper-left** regions of the diagram. * The overall shape is asymmetrical and organic, resembling a neural network, a root system, or a force-directed graph layout. ### Detailed Analysis * **Node Distribution & Hierarchy:** * The **dark red central node** is the largest and most visually prominent element, indicating it is the primary hub or most connected entity in the network. * Surrounding it is a high-density region of medium-sized **orange nodes**, which are themselves heavily interconnected and also connected to the central hub. * Further out, the nodes become smaller, lighter in color (beige), and less densely connected, forming semi-autonomous clusters. * **Connection (Edge) Patterns:** * **High Density at Core:** The area immediately around the red hub has the highest concentration of edges, creating a near-solid mass of overlapping lines. * **Radial Flow:** Many lines emanate directly from the central hub to nodes in the inner ring and to key nodes in the peripheral clusters. * **Inter-Cluster Connections:** Long, curved lines bridge the gaps between the central mass and the outlying clusters (e.g., a distinct bundle of lines connects the center to the bottom-right cluster). * **Intra-Cluster Connections:** Within each peripheral cluster, nodes are tightly interconnected with short, dense lines, suggesting strong local relationships. ### Key Observations 1. **Clear Central Dominance:** The network has a single, unambiguous focal point (the red node). This is not a decentralized or flat network. 2. **Hierarchical Clustering:** The structure suggests a hierarchy: Primary Hub (red) -> Secondary Hubs (larger orange nodes in the core) -> Peripheral Clusters (groups of smaller beige nodes). 3. **Organic, Non-Geometric Layout:** The use of curved lines and the irregular placement of clusters indicate this is likely a visualization of relational data (e.g., social connections, citation networks, biological pathways) rather than a schematic or technical blueprint. 4. **Absence of Quantitative Data:** There are no numerical values, scales, or labels. The diagram communicates structure and relationship strength (implied by line density and node size) but not precise metrics. ### Interpretation This diagram visually represents a **centralized network system with a strong core-periphery structure**. The dark red node is the critical point of failure or the primary source/influence within the system. The dense web of connections around it indicates intense interaction, communication, or dependency. The peripheral clusters likely represent communities, departments, or specialized subgroups that are internally cohesive but rely on connections to the central hub for integration into the larger network. The long, bridging lines are crucial for overall network cohesion; their removal would isolate the clusters. **What it likely represents:** Without labels, the exact domain is ambiguous, but the pattern is classic for: * A **social network** with a central influencer or organization. * A **computer network** with a main server and clustered clients. * A **biological neural network** or **protein interaction network**. * A **knowledge graph** with a core concept linked to many related ideas. **Notable Anomaly:** The complete lack of text is significant. It suggests the image is either a purely aesthetic visualization, a template, or a figure meant to be accompanied by a detailed caption in an external document. The information is entirely encoded in the topology, color, and density of the graph itself. </details> Figure 3: Visualizatrion of the knowledge graph Graph 2 after around 500 iterations, under a topic-specific self-exploration scheme initiated with the prompt Describe a way to design impact resistant materials. The graph structure features a complex interwoven but highly connected network with multiple centers. Table 1 shows a comparison of network properties for two graphs (graph $G_1$ , see Figure 2 and graph $G_2$ , see Figure 3), each computed at the end of their iterations. The scale-free nature of each graph is determined by fitting the degree distribution to a power-law model using the maximum likelihood estimation method. The analysis involves estimating the power-law exponent ( $α$ ) and the lower bound ( $x_\min$ ), followed by a statistical comparison against an alternative exponential distribution. A log-likelihood ratio (LR) greater than zero and a $p$ -value below 0.05 indicate that the power-law distribution better explains the degree distribution than an exponential fit, suggesting that the network exhibits scale-free behavior. In both graphs, these criteria are met, supporting a scale-free classification. We observe that $G_1$ has a power-law exponent of $α=3.0055$ , whereas $G_2$ has a lower $α=2.6455$ , indicating that Graph 2 has a heavier-tailed degree distribution with a greater presence of high-degree nodes (hubs). The lower bound $x_\min$ is smaller in $G_2$ ( $x_\min=10.0$ ) compared to $G_1$ ( $x_\min=24.0$ ), suggesting that the power-law regime starts at a lower degree value, reinforcing its stronger scale-free characteristics. Other structural properties provide additional insights into the connectivity and organization of these graphs. The average clustering coefficients (0.1363 and 0.1434) indicate moderate levels of local connectivity, with $G_2$ exhibiting slightly higher clustering. The average shortest path lengths (5.1596 and 4.8984) and diameters (17 and 13) suggest that both graphs maintain small-world characteristics, where any node can be reached within a relatively short number of steps. The modularity values (0.6970 and 0.6932) indicate strong community structures in both graphs, implying the presence of well-defined clusters of interconnected nodes. These findings collectively suggest that both graphs exhibit small-world and scale-free properties, with $G_2$ demonstrating a stronger tendency towards scale-free behavior due to its lower exponent and smaller $x_\min$ . Beyond scale-free characteristics, we note that the two graphs exhibit differences in structural properties that influence their connectivity and community organization. We find that $G_1$ , with 3,835 nodes and 11,910 edges, is much larger and more densely connected than $G_2$ , which has 2,180 nodes and 6,290 edges. However, both graphs have similar average degrees (6.2112 and 5.7706), suggesting comparable overall connectivity per node. The number of self-loops is slightly higher in Graph 1 (70 vs. 33), though this does not significantly impact global structure. The clustering coefficients (0.1363 and 0.1434) indicate moderate levels of local connectivity, with Graph 2 exhibiting slightly more pronounced local clustering. The small-world nature of both graphs is evident from their average shortest path lengths (5.1596 and 4.8984) and diameters (17 and 13), implying efficient information flow. Modularity values (0.6970 and 0.6932) suggest both graphs have well-defined community structures, with Graph 1 showing marginally stronger modularity, possibly due to its larger size. Overall, while both graphs display small-world and scale-free properties, $G_2$ appears to have a more cohesive structure with shorter paths and higher clustering, whereas $G_1$ is larger with a slightly stronger community division. | Number of nodes Number of edges Average degree | 3835 11910 6.2112 | 2180 6290 5.7706 | | --- | --- | --- | | Number of self-loops | 70 | 33 | | Average clustering coefficient | 0.1363 | 0.1434 | | Average shortest path length (LCC) | 5.1596 | 4.8984 | | Diameter (LCC) | 17 | 13 | | Modularity (Louvain) | 0.6970 | 0.6932 | | Log-likelihood ratio (LR) | 15.6952 | 39.6937 | | p-value | 0.0250 | 0.0118 | | Power-law exponent ( $α$ ) | 3.0055 | 2.6455 | | Lower bound ( $x_\min$ ) | 24.0 | 10.0 | | Scale-free classification | Yes | Yes | Table 1: Comparison of network properties for two graphs (graph $G_1$ , see Figure 2 and S1 and graph $G_2$ , see Figure 3 and S2), each computed at the end of their iterations. Both graphs exhibit scale-free characteristics, as indicated by the statistically significant preference for a power-law degree distribution over an exponential fit (log-likelihood ratio $LR>0$ and $p<0.05$ ). The power-law exponent ( $α$ ) for $G_1$ is 3.0055, while $G_2$ has a lower exponent of 2.6455, suggesting a heavier-tailed degree distribution. The clustering coefficients (0.1363 and 0.1434) indicate the presence of local connectivity, while the shortest path lengths (5.1596 and 4.8984) and diameters (17 and 13) suggest efficient global reachability. The high modularity values (0.6970 and 0.6932) indicate strong community structure in both graphs. Overall, both networks exhibit hallmark properties of scale-free networks, with $G_2$ showing a more pronounced scale-free behavior due to its lower $α$ and lower $x_\min$ . ### 2.1 Basic Analysis of Recursive Graph Growth We now move on to a detailed analysis of the evolution of the graph as the reasoning process unfolds over thinking iterations. This sheds light into how the iterative process dynamically changes the nature of the graph. The analysis is largely focused on $G_1$ , albeit a few key results are also included for $G_2$ . Detailed methods about how the various quantities are computed are included in Materials and Methods. Figure 4 illustrates the evolution of key structural properties of the recursively generated knowledge graph. The number of nodes and edges both exhibit linear growth with iterations, indicating that the reasoning process systematically expands the graph without saturation. The increase in edges is slightly steeper than that of nodes, suggesting that each new concept introduced is integrated into an increasingly dense network of relationships rather than remaining isolated. This continuous expansion supports the hypothesis that the model enables open-ended knowledge discovery through recursive self-organization. The average degree of the graph steadily increases, stabilizing around six edges per node. This trend signifies that the knowledge graph maintains a balance between exploration and connectivity, ensuring that newly introduced concepts remain well-integrated within the broader structure. Simultaneously, the maximum degree follows a non-linear trajectory, demonstrating that certain nodes become significantly more connected over time. This emergent hub formation is characteristic of scale-free networks and aligns with patterns observed in human knowledge organization, where certain concepts act as central abstractions that facilitate higher-order reasoning. The size of the largest connected component (LCC) grows proportionally with the total number of nodes, reinforcing the observation that the graph remains a unified, traversable structure rather than fragmenting into disconnected subgraphs. This property is crucial for recursive reasoning, as it ensures that the system retains coherence while expanding. The average clustering coefficient initially fluctuates but stabilizes around 0.16, indicating that while localized connections are formed, the graph does not devolve into tightly clustered sub-networks. Instead, it maintains a relatively open structure that enables adaptive reasoning pathways. These findings highlight the self-organizing nature of the recursive reasoning process, wherein hierarchical knowledge formation emerges without the need for predefined ontologies or supervised corrections. The presence of conceptual hubs, increasing relational connectivity, and sustained network coherence suggest that the model autonomously structures knowledge in a manner that mirrors epistemic intelligence. This emergent organization enables the system to navigate complex knowledge spaces efficiently, reinforcing the premise that intelligence-like behavior can arise through recursive, feedback-driven information processing. Further analysis of degree distribution and centrality metrics would provide deeper insights into the exact nature of this evolving graph topology. <details> <summary>x4.png Details</summary>  ### Visual Description \n ## Multi-Panel Line Chart: Network Evolution Metrics ### Overview The image is a composite figure containing six individual line charts, labeled (a) through (f), arranged in a 2x3 grid. Each chart plots a different network metric against a common x-axis, "Iteration," which ranges from 0 to 1000. The charts collectively visualize the evolution of various properties of a network (likely a growing graph) over time or steps. The data is presented as dense scatter plots with connected points, forming thick lines. ### Components/Axes * **Common X-Axis (All Charts):** Label: "Iteration". Scale: Linear, from 0 to 1000 with major tick marks at 0, 200, 400, 600, 800, 1000. * **Subplot (a) - Top Left:** * **Title:** "#Nodes vs. Iteration" * **Y-Axis Label:** "#Nodes" * **Y-Axis Scale:** Linear, from 0 to 4000 with major ticks every 500. * **Data Series Color:** Blue. * **Subplot (b) - Top Center:** * **Title:** "#Edges vs. Iteration" * **Y-Axis Label:** "#Edges" * **Y-Axis Scale:** Linear, from 0 to 12000 with major ticks every 2000. * **Data Series Color:** Orange. * **Subplot (c) - Top Right:** * **Title:** "Avg Degree vs. Iteration" * **Y-Axis Label:** "Avg Degree" * **Y-Axis Scale:** Linear, from 4.0 to 6.0 with major ticks every 0.5. * **Data Series Color:** Green. * **Subplot (d) - Bottom Left:** * **Title:** "Max Degree vs. Iteration" * **Y-Axis Label:** "Max Degree" * **Y-Axis Scale:** Linear, from 0 to 250 with major ticks every 50. * **Data Series Color:** Red. * **Subplot (e) - Bottom Center:** * **Title:** "Largest Comp Size vs. Iteration" * **Y-Axis Label:** "Nodes in LCC" (LCC likely stands for Largest Connected Component). * **Y-Axis Scale:** Linear, from 0 to 2000 with major ticks every 500. * **Data Series Color:** Purple. * **Subplot (f) - Bottom Right:** * **Title:** "Avg Clustering vs. Iteration" * **Y-Axis Label:** "Clustering" * **Y-Axis Scale:** Linear, from 0.12 to 0.28 with major ticks every 0.02. * **Data Series Color:** Teal. ### Detailed Analysis * **Trend Verification & Data Points:** * **(a) #Nodes:** The blue line shows a strong, nearly perfect linear upward trend. Starting near 0 at iteration 0, it reaches approximately 3800 nodes by iteration 1000. * **(b) #Edges:** The orange line also shows a strong, nearly perfect linear upward trend, steeper than the node count. Starting near 0, it reaches approximately 12,000 edges by iteration 1000. * **(c) Avg Degree:** The green line shows an initial sharp drop from ~5.1 to ~4.0 within the first ~50 iterations, followed by a general upward trend with some fluctuations. It rises to approximately 6.2 by iteration 1000. * **(d) Max Degree:** The red line shows a stepwise, generally increasing trend. It starts near 0, has a notable jump around iteration 300-400, and ends at approximately 255 by iteration 1000. * **(e) Largest Comp Size (Nodes in LCC):** The purple line shows a strong, nearly perfect linear upward trend, very similar in shape to the #Nodes plot. It starts near 0 and reaches approximately 2100 nodes in the LCC by iteration 1000. * **(f) Avg Clustering:** The teal line shows a dramatic initial drop from ~0.275 to a minimum of ~0.125 within the first ~50 iterations. It then recovers to a plateau around 0.17-0.18, where it remains relatively stable with minor fluctuations for the remainder of the iterations. ### Key Observations 1. **Linear Growth:** The total number of nodes, edges, and the size of the largest connected component all grow linearly with iteration. This suggests a consistent, rule-based network growth process. 2. **Degree Dynamics:** While the average degree dips initially, it recovers and increases over time, indicating the network becomes more densely connected on average as it grows. The maximum degree increases in a stepwise fashion, suggesting the emergence of occasional "hub" nodes. 3. **Clustering Collapse and Stabilization:** The average clustering coefficient undergoes a severe collapse early in the process, indicating a rapid loss of local triadic closure. It then stabilizes at a lower value (~0.17), suggesting the growing network maintains a consistent, albeit low, level of local clustering after the initial phase. 4. **LCC vs. Total Nodes:** The size of the largest connected component (LCC) tracks very closely with the total number of nodes (compare plots a and e). By iteration 1000, the LCC contains ~2100 of the ~3800 total nodes (~55%), indicating the network is not fully connected but has a single dominant component. ### Interpretation The data depicts the evolution of a growing network under a specific generative model. The linear growth in nodes and edges points to a process where a fixed number of nodes and connections are added per iteration. The early, sharp decline in both average degree and clustering is a critical signature. This pattern is characteristic of models where new nodes initially attach in a way that does not form many triangles (low clustering) and may connect to a limited number of existing nodes (lowering average degree). The subsequent rise in average degree suggests the attachment rules may change or that later nodes connect more broadly. The stabilization of clustering at a low, non-zero value indicates the model produces a network with some, but not excessive, local cohesiveness. The close tracking of the LCC size with total nodes implies the growth process efficiently integrates most new nodes into the main component. Overall, this figure likely analyzes a simulation of a network growth algorithm, highlighting its impact on fundamental topological properties over time. </details> Figure 4: Evolution of basic graph properties over recursive iterations, highlighting the emergence of hierarchical structure, hub formation, and adaptive connectivity, for $G_1$ . Figure S5 illustrates the same analysis of the evolution of key structural properties of the recursively generated knowledge graph for graph $G_2$ , as a comparison. Structural Evolution of the Recursive Knowledge Graph Figure 5 presents the evolution of three key structural properties, including Louvain modularity, average shortest path length, and graph diameter, over iterations. These metrics provide deeper insights into the self-organizing behavior of the graph as it expands through iterative reasoning. The Louvain modularity, depicted in Figure 5 (a), measures the strength of community structure within the graph. Initially, modularity increases sharply, reaching a peak around 0.75 within the first few iterations. This indicates that the early phases of reasoning lead to the rapid formation of well-defined conceptual clusters. As the graph expands, modularity stabilizes at approximately 0.70, suggesting that the system maintains distinct knowledge domains while allowing new interconnections to form. This behavior implies that the model preserves structural coherence, ensuring that the recursive expansion does not collapse existing conceptual groupings. The evolution of the average shortest path length (SPL), shown in Figure 5 (b), provides further evidence of structured self-organization. Initially, the SPL increases sharply before stabilizing around 4.5–5.0. The initial rise reflects the introduction of new nodes that temporarily extend shortest paths before they are effectively integrated into the existing structure. The subsequent stabilization suggests that the recursive process maintains an efficient knowledge representation, ensuring that information remains accessible despite continuous expansion. This property is crucial for reasoning, as it implies that the system does not suffer from runaway growth in path lengths, preserving navigability. The graph diameter, illustrated in Figure 5 (c), exhibits a stepwise increase, eventually stabilizing around 16–18. The staircase-like behavior suggests that the recursive expansion occurs in structured phases, where certain iterations introduce concepts that temporarily extend the longest shortest path before subsequent refinements integrate them more effectively. This bounded expansion indicates that the system autonomously regulates its hierarchical growth, maintaining a balance between depth and connectivity. These findings reveal several emergent properties of the recursive reasoning model. The stabilization of modularity demonstrates the ability to autonomously maintain structured conceptual groupings, resembling human-like hierarchical knowledge formation. The controlled growth of the shortest path length highlights the system’s capacity for efficient information propagation, preventing fragmentation. We note that the bounded expansion of graph diameter suggests that reasoning-driven recursive self-organization is capable of structuring knowledge in a way that mirrors epistemic intelligence, reinforcing the hypothesis that certain forms of intelligent-like behavior can emerge without predefined ontologies. <details> <summary>x5.png Details</summary>  ### Visual Description \n ## Line Charts: Network Metric Evolution Over Iterations ### Overview The image contains three horizontally arranged line charts, labeled (a), (b), and (c), each plotting a different network metric against the number of iterations of an algorithm (likely a community detection or network optimization algorithm). The charts share a common x-axis ("Iteration") ranging from 0 to 1000. Each chart uses a distinct color for its data series and markers. ### Components/Axes * **Common X-Axis (All Charts):** * **Label:** "Iteration" * **Scale:** Linear, from 0 to 1000. * **Major Tick Marks:** 0, 200, 400, 600, 800, 1000. * **Chart (a) - Left:** * **Title:** "Louvain Modularity vs. Iteration" * **Y-Axis Label:** "Modularity" * **Y-Axis Scale:** Linear, from 0.45 to 0.80. * **Data Series Color:** Magenta (bright pink). * **Marker Style:** Solid circles. * **Chart (b) - Center:** * **Title:** "Avg Shortest Path vs. Iteration" * **Y-Axis Label:** "Avg SPL" (presumably Average Shortest Path Length). * **Y-Axis Scale:** Linear, from 2 to 6. * **Data Series Color:** Blue. * **Marker Style:** Solid circles. * **Chart (c) - Right:** * **Title:** "Diameter vs. Iteration" * **Y-Axis Label:** "Diameter" * **Y-Axis Scale:** Linear, from 4 to 18. * **Data Series Color:** Red. * **Marker Style:** Solid circles. ### Detailed Analysis **Chart (a): Louvain Modularity** * **Trend Verification:** The magenta line shows a very sharp, near-vertical increase from a low starting point, peaks early, and then exhibits a gradual, noisy decline over the remaining iterations. * **Data Points (Approximate):** * Iteration 0: Modularity ≈ 0.44. * Rapid increase to a peak: Modularity ≈ 0.80 at approximately iteration 50. * Following the peak, the value fluctuates but trends downward. * By iteration 200: Modularity ≈ 0.75. * By iteration 400: Modularity ≈ 0.72. * By iteration 600: Modularity ≈ 0.71. * By iteration 1000: Modularity ≈ 0.70. **Chart (b): Average Shortest Path Length (Avg SPL)** * **Trend Verification:** The blue line shows a sharp initial increase, a peak, a subsequent decline, and then stabilizes into a plateau with minor fluctuations. * **Data Points (Approximate):** * Iteration 0: Avg SPL ≈ 1.8. * Rapid increase to a peak: Avg SPL ≈ 6.5 at approximately iteration 100. * Decline after the peak. * By iteration 200: Avg SPL ≈ 5.8. * By iteration 400: Avg SPL ≈ 5.4. * From iteration 600 to 1000: The value stabilizes around Avg SPL ≈ 5.2, with very slight downward drift. **Chart (c): Diameter** * **Trend Verification:** The red line shows a stepwise increasing trend. It rises sharply in discrete jumps, plateaus, and then jumps again, reaching a final plateau. * **Data Points (Approximate):** * Iteration 0: Diameter = 4. * Sharp, step-like increases occur in the first ~150 iterations. * Plateaus are visible at Diameter ≈ 10, 14, 15, and 16. * A final jump occurs around iteration 450-500. * From approximately iteration 500 to 1000: The diameter stabilizes at a constant value of 17. ### Key Observations 1. **Phase of Rapid Change:** All three metrics undergo their most significant changes within the first 200 iterations, suggesting an initial, volatile phase of the algorithm. 2. **Divergent Long-Term Trends:** After the initial phase, the metrics diverge. Modularity slowly decreases, Avg SPL stabilizes, and Diameter remains constant at its maximum value. 3. **Stepwise vs. Continuous Change:** The Diameter (c) changes in clear, discrete steps, while Modularity (a) and Avg SPL (b) change more continuously, albeit with noise. 4. **Peak and Decline:** Both Modularity and Avg SPL exhibit a distinct peak early in the process before settling to a lower, stable value. ### Interpretation The data illustrates the evolution of a network's structural properties during an iterative optimization process, likely the Louvain method for community detection. * **Initial Optimization (Iterations 0-~200):** The algorithm rapidly reorganizes the network. Modularity skyrockets, indicating the swift formation of well-defined communities. Concurrently, both the average shortest path length and the network diameter increase sharply. This suggests that as communities form, paths between nodes within the same community shorten, but paths between nodes in different communities may become longer, increasing the overall "spread" of the network. * **Stabilization Phase (Iterations ~200-1000):** The algorithm enters a refinement phase. Modularity slowly decreases, which could indicate a slight merging or redefinition of communities that sacrifices some modularity for other properties. The average shortest path length stabilizes, suggesting the overall efficiency of information flow across the network has reached an equilibrium. The diameter remains fixed at its peak value (17), meaning the longest shortest path in the network no longer changes; the network's overall "size" is locked in. * **Trade-off Revealed:** The plots collectively demonstrate a potential trade-off. Achieving high modularity (strong community structure) early on comes at the cost of increasing the network's diameter and average path length. The final state is a network with a stable, slightly lower modularity, a fixed maximum diameter, and a stable average path length. This could represent a balance between having distinct communities and maintaining reasonable global connectivity. The stepwise increase in diameter is particularly notable, suggesting that specific, discrete rewiring events during the optimization cause sudden jumps in the network's longest path. </details> Figure 5: Evolution of key structural properties in the recursively generated knowledge graph $G_1$ : (a) Louvain modularity, showing stable community formation; (b) average shortest path length, highlighting efficient information propagation; and (c) graph diameter, demonstrating bounded hierarchical expansion. For comparison, Figure S4 presents the evolution of three key structural properties—Louvain modularity, average shortest path length, and graph diameter—over recursive iterations for graph $G_2$ . ### 2.2 Analysis of Advanced Graph Evolution Metrics Figure 6 presents the evolution of six advanced structural metrics over recursive iterations, capturing higher-order properties of the self-expanding knowledge graph. These measures provide insights into network organization, resilience, and connectivity patterns emerging during recursive reasoning. Degree assortativity coefficient is a measure of the tendency of nodes to connect to others with similar degrees. A negative value indicates disassortativity (high-degree nodes connect to low-degree nodes), while a positive value suggests assortativity (nodes prefer connections to similarly connected nodes). The degree assortativity coefficient (Figure 6 (a)) begins with a strongly negative value near $-0.25$ , indicating a disassortative structure where high-degree nodes preferentially connect to low-degree nodes. Over time, assortativity increases and stabilizes around $-0.05$ , suggesting a gradual shift toward a more balanced connectivity structure without fully transitioning to an assortative regime. This trend is consistent with the emergence of hub-like structures, characteristic of scale-free networks, where a few nodes accumulate a disproportionately high number of connections. The global transitivity (Figure 6 (b)), measuring the fraction of closed triplets in the network, exhibits an initial peak near 0.35 before rapidly declining and stabilizing towards 0.10, albeit still decreasing. This suggests that early in the recursive reasoning process, the graph forms tightly clustered regions, likely due to localized conceptual groupings. As iterations progress, interconnections between distant parts of the graph increase, reducing local clustering and favoring long-range connectivity, a hallmark of expanding knowledge networks. The $k$ -core Index defines the largest integer $k$ for which a subgraph exists where all nodes have at least $k$ connections. A higher maximum $k$ -core index suggests a more densely interconnected core. The maximum $k$ -core index (Figure 6 (c)), representing the deepest level of connectivity, increases in discrete steps, reaching a maximum value of 11. This indicates that as the graph expands, an increasingly dense core emerges, reinforcing the formation of highly interconnected substructures. The stepwise progression suggests that specific iterations introduce structural reorganizations that significantly enhance connectivity rather than continuous incremental growth. We observe that the size of the largest $k$ -core (Figure 6 (d)) follows a similar pattern, growing in discrete steps and experiencing a sudden drop around iteration 700 before stabilizing again. This behavior suggests that the graph undergoes structural realignments, possibly due to the introduction of new reasoning pathways that temporarily reduce the dominance of the most connected core before further stabilization. Betweenness Centrality is a measure of how often a node appears on the shortest paths between other nodes. High betweenness suggests a critical role in information flow, while a decrease indicates decentralization and redundancy in pathways. The average betweenness centrality (Figure 6 (e)) initially exhibits high values, indicating that early reasoning iterations rely heavily on specific nodes to mediate information flow. Over time, betweenness declines and stabilizes a bit below 0.01, suggesting that the graph becomes more navigable and distributed, reducing reliance on key bottleneck nodes over more iterations. This trend aligns with the emergence of redundant reasoning pathways, making the system more robust to localized disruptions. Articulation points are nodes whose removal would increase the number of disconnected components in the graph, meaning they serve as key bridges between different knowledge clusters. The number of articulation points (Figure 6 (f)) steadily increases throughout iterations, reaching over 800. This suggests that as the knowledge graph expands, an increasing number of bridging nodes emerge, reflecting a hierarchical structure where key nodes maintain connectivity between distinct regions. Despite this increase, the network remains well connected, indicating that redundant pathways mitigate the risk of fragmentation. A network where the degree distribution follows a power-law, meaning most nodes have few connections, but a small number (hubs) have many (supporting the notion of a scale-free network). Our findings provide evidence that the recursive graph reasoning process spontaneously organizes into a hierarchical, scale-free structure, balancing local clustering, global connectivity, and efficient navigability. The noted trends in assortativity, core connectivity, and betweenness centrality confirm that the system optimally structures its knowledge representation over iterations, reinforcing the hypothesis that self-organized reasoning processes naturally form efficient and resilient knowledge networks. <details> <summary>x6.png Details</summary>  ### Visual Description \n ## Multi-Panel Network Metric Evolution Chart ### Overview The image is a composite figure containing six distinct line/scatter plots, labeled (a) through (f), arranged in a 2x3 grid. Each plot tracks a different network topology metric over a series of iterations, from iteration 0 to approximately 1000. The plots collectively illustrate the evolution of a network's structural properties during some iterative process. ### Components/Axes * **Layout:** Six subplots in two rows and three columns. * **Common X-Axis:** All six plots share the same x-axis label: "Iteration". The scale runs from 0 to 1000, with major tick marks at 0, 200, 400, 600, 800, and 1000. * **Individual Y-Axes:** Each plot has a unique y-axis label and scale corresponding to its metric. * **Data Series:** Each plot contains a single data series represented by colored markers connected by lines. The colors are distinct for each plot: blue, green, red, purple, orange, and teal. * **Titles:** Each subplot has a descriptive title at the top. ### Detailed Analysis **Panel (a): Degree Assortativity vs. Iteration** * **Y-Axis:** "Assortativity". Scale from -0.25 to 0.00. * **Data Series (Blue):** The plot begins with a sharp, volatile drop from near 0.00 to a minimum of approximately -0.27 within the first ~50 iterations. It then recovers sharply to around -0.10, followed by a period of fluctuation with a general upward trend. From iteration ~400 onward, the assortativity stabilizes, oscillating slightly around a value of approximately -0.05. * **Trend:** Initial sharp negative spike, followed by recovery and stabilization at a slightly negative value. **Panel (b): Global Transitivity vs. Iteration** * **Y-Axis:** "Transitivity". Scale from 0.10 to 0.35. * **Data Series (Green):** The metric starts at its peak of approximately 0.37 at iteration 0. It undergoes a rapid, steep decline until around iteration 100, reaching ~0.15. The rate of decrease slows, forming a convex curve that asymptotically approaches a value just below 0.10 by iteration 1000. * **Trend:** Monotonic, rapid decay that slows over time, approaching a low asymptote. **Panel (c): Max k-Core Index vs. Iteration** * **Y-Axis:** "Max k". Scale from 5 to 11. * **Data Series (Red):** This is a step plot. The maximum k-core index starts at 5. It increases in discrete steps: to 7 at ~iteration 20, to 8 at ~iteration 80, to 9 at ~iteration 220, to 10 at ~iteration 240, and finally to 11 at ~iteration 700. It remains at 11 until iteration 1000. * **Trend:** Stepwise, non-decreasing function, indicating the emergence of increasingly dense core structures. **Panel (d): Size of Largest k-Core vs. Iteration** * **Y-Axis:** "#Nodes in max k-core". Scale from 10 to 70. * **Data Series (Purple):** Also a step plot. The size starts around 5 nodes. It increases in steps, with notable jumps at iterations ~200 (to ~22 nodes), ~350 (to ~42 nodes), ~450 (to ~49 nodes), and a large jump at ~600 (to ~75 nodes). After a brief plateau, there is a sharp drop at ~iteration 700 to ~30 nodes, where it stabilizes until iteration 1000. * **Trend:** General stepwise increase, followed by a significant structural drop/collapse around iteration 700. **Panel (e): Avg Betweenness vs. Iteration** * **Y-Axis:** "Betweenness". Scale from 0.00 to 0.14. * **Data Series (Orange):** The average betweenness centrality starts at its maximum of ~0.15. It plummets dramatically within the first ~50 iterations to below 0.02. The decline continues at a much slower rate, approaching near-zero values (≈0.002) by iteration 1000. * **Trend:** Extremely rapid initial decay, followed by a long tail approaching zero. **Panel (f): #Articulation Points vs. Iteration** * **Y-Axis:** "Count". Scale from 0 to 800. * **Data Series (Teal):** The number of articulation points (cut vertices) shows a remarkably steady, near-linear increase throughout the entire process. It starts near 0 and rises to approximately 850 by iteration 1000. The line is thick, indicating small, consistent fluctuations around the linear trend. * **Trend:** Strong, positive linear correlation with iteration. ### Key Observations 1. **Correlated Events:** A major event occurs around iteration 700. The Max k-Core Index (c) reaches its final value of 11, while simultaneously, the Size of the Largest k-Core (d) experiences a dramatic drop from ~75 to ~30 nodes. This suggests a significant reorganization of the network's core. 2. **Divergent Trends:** While transitivity (b) and betweenness (e) decay rapidly and then stabilize at low values, the number of articulation points (f) grows linearly. This indicates a shift from a clustered, locally interconnected structure to a more tree-like, globally fragile structure with many critical nodes. 3. **Stabilization:** Most metrics (a, b, e) show clear stabilization after iteration ~400-600, suggesting the network reaches a quasi-steady state in terms of assortativity, transitivity, and betweenness, even as its core structure (c, d) and vulnerability (f) continue to change. 4. **Initial Volatility:** The first 100-200 iterations are characterized by the most dramatic changes in almost all metrics, indicating a rapid initial transformation phase. ### Interpretation The data depicts the evolution of a network under an iterative process that fundamentally reshapes its topology. The process appears to: 1. **Degrade Local Clustering:** The sharp drop in transitivity (b) and betweenness (e) indicates the dissolution of triangles and the reduction of nodes acting as bridges, respectively. The network loses its "small-world" properties. 2. **Increase Centralization & Fragility:** The linear rise in articulation points (f) is a key finding. It means the network is becoming increasingly reliant on specific, critical nodes whose removal would disconnect the graph. This, combined with the drop in betweenness, suggests a shift towards a more centralized, hub-and-spoke or tree-like architecture. 3. **Reorganize the Core:** The stepwise increase in the max k-core index (c) shows the emergence of denser and denser core structures. However, the dramatic drop in the size of that core (d) at iteration 700, concurrent with the final step in k-core index, is critical. It implies that while a very dense core (k=11) forms, it does so by shedding many nodes, possibly consolidating into a smaller, tighter, and more exclusive central group. The network's "rich club" becomes both denser and smaller. 4. **Establish Negative Assortativity:** The stabilization of degree assortativity (a) at a negative value (-0.05) indicates a final state where high-degree nodes (hubs) are slightly more likely to connect to low-degree nodes than to other hubs. This is consistent with the emerging centralized, non-clustered structure. **In summary,** the iterative process transforms the network from a more clustered, interconnected state into a centralized, fragile, and hierarchical structure with a small, dense core and many peripheral nodes dependent on a few critical articulation points. The event at iteration 700 marks a pivotal reorganization where the core consolidates its density at the expense of its size. </details> Figure 6: Evolution of advanced structural properties in the recursively generated knowledge graph $G_1$ : (a) degree assortativity, (b) global transitivity, (c) maximum k-core index, (d) size of the largest k-core, (e) average betweenness centrality, and (f) number of articulation points. These metrics reveal the emergence of hierarchical organization, hub formation, and increased navigability over recursive iterations. ### 2.3 Evolution of Newly Connected Pairs Figure 7 presents the evolution of newly connected node pairs as a function of iteration, illustrating how the recursive reasoning process expands the knowledge graph over time. This metric captures the rate at which new relationships are established between nodes, providing insights into the self-organizing nature of the network. In the early iterations (0–100), the number of newly connected pairs exhibits high variance, fluctuating between 0 and 400 connections per iteration. This suggests that the initial phase of recursive reasoning leads to significant structural reorganization, where large bursts of new edges are formed as the network establishes its fundamental connectivity patterns. The high variability in this region indicates an exploratory phase, where the graph undergoes rapid adjustments to define its core structure. Beyond approximately 200 iterations, the number of newly connected pairs stabilizes around 500–600 per iteration, with only minor fluctuations. This plateau suggests that the knowledge graph has transitioned into a steady-state expansion phase, where new nodes and edges are integrated into an increasingly structured and predictable manner. Unlike random growth, this behavior indicates that the system follows a self-organized expansion process, reinforcing existing structures rather than disrupting them. The stabilization at a high connection rate suggests the emergence of hierarchical organization, where newly introduced nodes preferentially attach to well-established structures. This pattern aligns with the scale-free properties observed in other experimentally acquired knowledge networks, where central concepts continuously accumulate new links, strengthening core reasoning pathways. The overall trend highlights how recursive self-organization leads to sustained, structured knowledge expansion, rather than arbitrary or saturation-driven growth. <details> <summary>x7.png Details</summary>  ### Visual Description ## Scatter Plot: Newly Connected Pairs (sampled) vs. Iteration ### Overview The image is a scatter plot with connected lines, displaying the relationship between the number of iterations (x-axis) and the count of newly connected pairs (y-axis). The data shows a rapid initial increase followed by a plateau with fluctuations. ### Components/Axes * **Chart Title:** "Newly Connected Pairs (sampled) vs. Iteration" * **X-Axis:** * **Label:** "Iteration" * **Scale:** Linear, ranging from 0 to 1000. * **Major Tick Marks:** 0, 200, 400, 600, 800, 1000. * **Y-Axis:** * **Label:** "Count of newly connected pairs" * **Scale:** Linear, ranging from 0 to 600. * **Major Tick Marks:** 0, 100, 200, 300, 400, 500, 600. * **Data Series:** A single series represented by blue circular markers connected by a thin blue line. There is no legend, as only one data series is present. ### Detailed Analysis The data exhibits two distinct phases: 1. **Initial Rapid Growth (Iterations 0-100):** * The series begins at approximately (0, 0). * It experiences a very sharp, near-vertical increase, reaching a local peak of approximately 450-470 pairs within the first 50 iterations. * This is followed by a sharp decline, dropping to a local minimum of approximately 120-150 pairs around iteration 75-100. 2. **Plateau with Fluctuations (Iterations 100-1000):** * After iteration 100, the count rises steeply again, crossing 500 pairs by approximately iteration 150. * From iteration 200 onward, the data enters a plateau phase. The count fluctuates primarily within the band of 500 to 600 newly connected pairs. * The trend within this plateau shows a very slight, gradual upward slope from ~500 at iteration 200 to ~550-600 by iteration 1000. * **Notable Fluctuations:** * A significant dip occurs between iterations 300 and 400, where the count falls to approximately 460-480. * Another noticeable dip occurs around iteration 850, dropping to approximately 500. * The highest density of points and the apparent maximum values (approaching 600) are clustered in the later iterations (800-1000). ### Key Observations * **High Volatility Early On:** The process is highly unstable in the first 100 iterations, with dramatic swings in the count of new connections. * **Stabilization:** The system reaches a quasi-stable state after iteration 200, where the rate of new connections remains high but relatively consistent. * **Persistent Noise:** Even in the stable phase, the data is noisy, indicating continuous small-scale variation in the process being measured. * **Slight Positive Drift:** There is a subtle but discernible upward trend across the entire plateau phase, suggesting a very slow increase in the baseline rate of new connections over time. ### Interpretation This plot likely visualizes the output of a dynamic network simulation, a machine learning training process, or an optimization algorithm where "newly connected pairs" is a key metric. * **The initial spike and crash** suggest a "discovery" or "exploration" phase where many new connections are made rapidly, followed by a consolidation or pruning phase where some are lost. * **The sustained high plateau** indicates the process has entered a "steady state" of growth or learning, continuously generating new connections at a high rate. The slight upward drift could imply the system is becoming more efficient or expansive over time. * **The persistent fluctuations and specific dips** (e.g., at iteration ~350) are anomalies that would warrant investigation in a technical context. They could correspond to specific events in the process, such as a change in parameters, the introduction of new data, or a periodic reset mechanism. * **Overall Trend:** The data demonstrates a classic pattern of rapid initial adaptation followed by sustained, noisy, but stable operation with a hint of long-term improvement. The process does not appear to converge to a fixed value but rather maintains a dynamic equilibrium. </details> Figure 7: Evolution of newly connected node pairs over recursive iterations, $G_1$ . Early iterations exhibit high variability, reflecting an exploratory phase of rapid structural reorganization. Beyond 200 iterations, the process stabilizes, suggesting a steady-state expansion phase with sustained connectivity formation. The observed transition from high-variance, exploratory graph expansion to a stable, structured growth phase suggests that recursive self-organization follows a process similar to human cognitive learning and scientific discovery. We believe that this indicates that in early iterations, the system explores diverse reasoning pathways, mirroring how scientific fields establish foundational concepts through broad exploration before refining them into structured disciplines [1]. The stabilization of connectivity beyond 200 iterations reflects preferential attachment dynamics, a hallmark of scale-free networks where highly connected nodes continue to accumulate new links, much like citation networks in academia [42]. This mechanism ensures that core concepts serve as attractors for further knowledge integration, reinforcing structured reasoning while maintaining adaptability. Importantly, the system does not exhibit saturation or stagnation, suggesting that open-ended knowledge discovery is possible through recursive reasoning alone, without requiring predefined ontologies or externally imposed constraints. This aligns with findings in AI-driven scientific hypothesis generation, where graph-based models dynamically infer new connections by iterating over expanding knowledge structures [39, 41]. The ability of the system to self-organize, expand, and refine its knowledge base autonomously underscores its potential as a scalable framework for automated scientific discovery and epistemic reasoning. ### 2.4 Analysis of Node Centrality Distributions at Final Stage of Reasoning Next, Figure 8 presents histograms for three key centrality measures—betweenness centrality, closeness centrality, and eigenvector centrality—computed for the recursively generated knowledge graph, at the final iteration. These metrics provide insights into the role of different nodes in maintaining connectivity, network efficiency, and global influence. Figure 8 (a) shows the distribution of betweenness centrality. We find the distribution of betweenness centrality to be highly skewed, with the majority of nodes exhibiting values close to zero. Only a small fraction of nodes attain significantly higher centrality values, indicating that very few nodes serve as critical intermediaries for shortest paths. This pattern is characteristic of hierarchical or scale-free networks, where a small number of hub nodes facilitate global connectivity, while most nodes remain peripheral. The presence of a few high-betweenness outliers suggests that key nodes emerge as crucial mediators of information flow, reinforcing the hypothesis that self-organizing structures lead to the formation of highly connected bridging nodes. Figure 8 (b) depicts the closeness centrality distribution. It follows an approximately normal distribution centered around 0.20, suggesting that most nodes remain well-connected within the network. This result implies that the network maintains a compact structure, allowing for efficient navigation between nodes despite continuous expansion. The relatively low spread indicates that the recursive reasoning process prevents excessive distance growth, ensuring that newly introduced nodes do not become isolated. This reinforces the observation that the graph remains navigable as it evolves, an essential property for maintaining coherent reasoning pathways. Next, Figure 8 (c) shows the eigenvector centrality distribution, identified to be also highly skewed, with most nodes having values close to zero. However, a few nodes attain substantially higher eigenvector centrality scores, indicating that only a select few nodes dominate the network in terms of global influence. This suggests that the network naturally organizes into a hierarchical structure, where dominant hubs accumulate influence over time, while the majority of nodes play a more peripheral role. The emergence of high-eigenvector hubs aligns with scale-free network behavior, further supporting the idea that reasoning-driven recursive self-organization leads to structured knowledge representation. These findings indicate that the recursive knowledge graph balances global connectivity and local modularity, self-organizing into a structured yet efficient system. The few high-betweenness nodes act as key mediators, while the closeness centrality distribution suggests that the network remains efficiently connected. The eigenvector centrality pattern highlights the formation of dominant conceptual hubs, reinforcing the presence of hierarchical knowledge organization within the evolving reasoning framework. <details> <summary>x8.png Details</summary>  ### Visual Description \n ## Histograms: Network Centrality Distributions ### Overview The image displays three horizontally arranged histograms, labeled (a), (b), and (c), each showing the frequency distribution of a different network centrality metric. The plots share a common y-axis label ("Count") and x-axis label ("Value"), but have different x-axis scales and data distributions. The histograms are colored distinctly: blue for (a), red for (b), and green for (c). ### Components/Axes * **Overall Layout:** Three subplots arranged in a single row. * **Subplot (a) - Left:** * **Title:** "Betweenness Centrality" * **Y-axis:** Label "Count". Scale from 0 to 2000, with major ticks at 0, 250, 500, 750, 1000, 1250, 1500, 1750, 2000. * **X-axis:** Label "Value". Scale from 0.00 to 0.25, with major ticks at 0.00, 0.05, 0.10, 0.15, 0.20, 0.25. * **Data Color:** Blue. * **Subplot (b) - Center:** * **Title:** "Closeness Centrality" * **Y-axis:** Label "Count". Scale from 0 to 200, with major ticks at 0, 25, 50, 75, 100, 125, 150, 175, 200. * **X-axis:** Label "Value". Scale from 0.10 to 0.30, with major ticks at 0.10, 0.15, 0.20, 0.25, 0.30. * **Data Color:** Red. * **Subplot (c) - Right:** * **Title:** "Eigenvector Centrality" * **Y-axis:** Label "Count". Scale from 0 to 1400, with major ticks at 0, 200, 400, 600, 800, 1000, 1200, 1400. * **X-axis:** Label "Value". Scale from 0.00 to 0.30, with major ticks at 0.00, 0.05, 0.10, 0.15, 0.20, 0.25, 0.30. * **Data Color:** Green. ### Detailed Analysis * **Subplot (a) - Betweenness Centrality (Blue):** * **Trend:** The distribution is extremely right-skewed. A single, very tall bar dominates the leftmost bin (value ≈ 0.00), with a count of approximately 2050. The counts drop precipitously for the next bin (value ≈ 0.01-0.02) to below 100, and become negligible (near zero) for all values greater than approximately 0.03. * **Subplot (b) - Closeness Centrality (Red):** * **Trend:** The distribution is roughly symmetric and unimodal, resembling a normal distribution. It spans from approximately 0.10 to 0.30. The peak (mode) occurs in the bin centered near 0.19, with a count of approximately 210. The distribution tapers off smoothly on both sides. * **Subplot (c) - Eigenvector Centrality (Green):** * **Trend:** The distribution is strongly right-skewed. The tallest bar is in the leftmost bin (value ≈ 0.00), with a count of approximately 1480. The counts decrease rapidly: the next bin (≈0.01) has a count of ~350, the following (≈0.02) ~150, and so on, approaching zero by a value of approximately 0.10. ### Key Observations 1. **Extreme Skew in (a) and (c):** Both Betweenness and Eigenvector Centrality distributions are dominated by a vast majority of nodes with values very close to zero. This indicates a highly heterogeneous network structure for these metrics. 2. **Contrasting Distribution Shape:** Closeness Centrality (b) shows a much more homogeneous, bell-shaped distribution compared to the other two metrics. This suggests that the property measured by closeness is more evenly distributed among the nodes in the network. 3. **Scale Differences:** The y-axis scales differ significantly. Betweenness Centrality has the highest maximum count (~2050), followed by Eigenvector (~1480), and then Closeness (~210). This reflects the different binning and the concentration of data points. 4. **Value Ranges:** The effective range of values differs. Betweenness values are concentrated below 0.03, Closeness values are spread between 0.10-0.30, and Eigenvector values are concentrated below 0.10. ### Interpretation These histograms provide a comparative snapshot of node importance within a network, as measured by three distinct mathematical concepts. * **Betweenness Centrality (a)** measures how often a node lies on the shortest path between other nodes. The extreme skew indicates that only a tiny handful of nodes (the tall bar near zero) act as critical bridges or brokers in the network. The vast majority of nodes have negligible betweenness, meaning they are not positioned on important communication or connection pathways. * **Closeness Centrality (b)** measures the average distance from a node to all other nodes. The symmetric, normal-like distribution suggests that "closeness" is a more democratically distributed property. Nodes have a typical, average closeness value, with fewer nodes being exceptionally close or exceptionally far from the network's center. This implies a relatively integrated network without extreme centralization in terms of path lengths. * **Eigenvector Centrality (c)** measures a node's influence based on the influence of its neighbors. The strong skew, similar to betweenness but with a different scale, reveals that a very small number of nodes are connected to other highly influential nodes, creating a core of elite, influential actors. Most nodes have low eigenvector centrality, meaning they are not well-connected to this influential core. **Synthesis:** The network analyzed here exhibits a classic "core-periphery" structure for influence and brokerage (highly skewed Betweenness and Eigenvector), but a more uniform structure for accessibility (symmetric Closeness). This pattern is common in many real-world networks (e.g., social, biological, technological), where a small, tightly-knit core of nodes controls information flow and influence, while the overall network remains relatively cohesive in terms of average path lengths. The stark contrast between the distributions highlights the importance of using multiple centrality metrics to understand different facets of node importance. </details> Figure 8: Distribution of node centrality measures in the recursively generated knowledge graph, for $G_1$ : (a) Betweenness centrality, showing that only a few nodes serve as major intermediaries; (b) Closeness centrality, indicating that the majority of nodes remain well-connected; (c) Eigenvector centrality, revealing the emergence of dominant hub nodes. These distributions highlight the hierarchical and scale-free nature of the evolving knowledge graph. Figure 9 presents the distribution of sampled shortest path lengths. This distribution provides insights into the overall compactness, navigability, and structural efficiency of the network. The histogram reveals that the most frequent shortest path length is centered around 5–6 steps, indicating that the majority of node pairs are relatively close in the network. The distribution follows a bell-shaped pattern, suggesting a typical range of distances between nodes, with a slight right skew where some paths extend beyond 10 steps. The presence of longer paths implies that certain nodes remain in the periphery or are indirectly connected to the core reasoning structure. The relatively narrow range of shortest path lengths affirms that the network remains well-integrated, ensuring efficient knowledge propagation and retrieval. The absence of extreme outliers suggests that the recursive expansion process does not lead to fragmented or sparsely connected regions. This structure contrasts with purely random graphs, where shortest path lengths typically exhibit a narrower peak at lower values. The broader peak observed here suggests that the model does not generate arbitrary connections but instead organizes knowledge in a structured manner, balancing global integration with local modularity. The observed path length distribution supports the hypothesis that recursive graph reasoning constructs an efficiently connected knowledge framework, where most concepts can be accessed within a small number of steps. The presence of some longer paths further suggests that the network exhibits hierarchical expansion, with certain areas developing as specialized subdomains that extend outward from the core structure. <details> <summary>x9.png Details</summary>  ### Visual Description ## Histograms: Distribution of Shortest Path Lengths (Sampled) ### Overview The image displays two side-by-side histograms, labeled (a) and (b), both titled "Distribution of Shortest Path Lengths (sampled)". They visualize the frequency distribution of shortest path lengths within two different sampled datasets or networks. The charts are presented in a clean, scientific style with purple bars against a white background. ### Components/Axes * **Chart (a) - Left Histogram:** * **Title:** "Distribution of Shortest Path Lengths (sampled)" * **X-axis Label:** "Shortest Path Length" * **X-axis Scale:** Linear scale with major tick marks at 2, 4, 6, 8, 10, 12. The data appears to span from approximately 1 to 13. * **Y-axis Label:** "Frequency" * **Y-axis Scale:** Linear scale with major tick marks at 0, 100, 200, 300, 400, 500. * **Chart (b) - Right Histogram:** * **Title:** "Distribution of Shortest Path Lengths (sampled)" * **X-axis Label:** "Shortest Path Length" * **X-axis Scale:** Linear scale with major tick marks at 2, 4, 6, 8, 10. The data appears to span from approximately 1 to 11. * **Y-axis Label:** "Frequency" * **Y-axis Scale:** Linear scale with major tick marks at 0, 100, 200, 300, 400, 500. * **General:** Both charts use the same purple color for all bars. There is no legend, as each chart contains only one data series. The labels "(a)" and "(b)" are positioned in the top-left corner above their respective charts. ### Detailed Analysis **Chart (a) Data Approximation (Frequency vs. Shortest Path Length):** * **Trend Verification:** The distribution is unimodal and roughly symmetric, peaking in the center and tapering off on both sides. It resembles a normal or Poisson distribution. * **Data Points (Approximate):** * Path Length ~1: Frequency ~5 * Path Length ~2: Frequency ~50 * Path Length ~3: Frequency ~200 * Path Length ~4: Frequency ~410 * Path Length ~5: Frequency ~560 (Peak) * Path Length ~6: Frequency ~430 * Path Length ~7: Frequency ~210 * Path Length ~8: Frequency ~90 * Path Length ~9: Frequency ~30 * Path Length ~10: Frequency ~20 * Path Length ~11: Frequency ~10 * Path Length ~12: Frequency ~5 * Path Length ~13: Frequency ~1 **Chart (b) Data Approximation (Frequency vs. Shortest Path Length):** * **Trend Verification:** The distribution is also unimodal and roughly symmetric, peaking in the center. It appears slightly more concentrated (narrower spread) than chart (a). * **Data Points (Approximate):** * Path Length ~1: Frequency ~5 * Path Length ~2: Frequency ~75 * Path Length ~3: Frequency ~250 * Path Length ~4: Frequency ~495 * Path Length ~5: Frequency ~525 (Peak) * Path Length ~6: Frequency ~360 * Path Length ~7: Frequency ~215 * Path Length ~8: Frequency ~60 * Path Length ~9: Frequency ~15 * Path Length ~10: Frequency ~5 ### Key Observations 1. **Central Tendency:** Both distributions have their mode (peak frequency) at a shortest path length of approximately 5 or 6. 2. **Spread/Variance:** Chart (a) has a wider spread, with non-zero frequencies extending to a path length of ~13. Chart (b) has a narrower spread, with data effectively ending at a path length of ~10. 3. **Peak Frequency:** The peak frequency in chart (a) (~560) is slightly higher than the peak in chart (b) (~525). 4. **Shape:** Both distributions are unimodal and exhibit a bell-shaped curve, suggesting the underlying networks may have "small-world" properties where most nodes are connected by relatively short paths. 5. **Sampled Data:** The title specifies "(sampled)", indicating these are empirical distributions from a sample, not the complete population of all shortest paths. ### Interpretation These histograms provide a quantitative snapshot of network connectivity. The "shortest path length" between two nodes is a fundamental measure of efficiency in a network (e.g., social, communication, biological). * **What the data suggests:** The concentration of path lengths around 5-6 indicates that, for the sampled networks, most pairs of nodes are separated by a moderate number of steps. This is characteristic of many real-world networks that are not completely random but also not highly ordered grids. * **Relationship between elements:** The x-axis (path length) is the independent variable, and the y-axis (frequency) shows how common each path length is. The shape of the histogram directly reveals the network's structural efficiency. A peak at a low value would indicate a very tightly connected network, while a peak at a high value would indicate a more sparse or elongated network. * **Comparison of (a) and (b):** While both networks share a similar central tendency, network (a) has a "longer tail" to the right. This means network (a) contains a small but notable number of node pairs that are very far apart (path lengths 10-13), which are absent in network (b). This could imply that network (a) is slightly less efficient overall or has a more heterogeneous structure, possibly containing peripheral nodes or clusters that are loosely connected to the main network core. Network (b) appears more uniformly connected within a tighter range of distances. * **Notable Anomaly:** There are no extreme outliers or irregular spikes; the distributions are smooth, which is expected for sampled data from a sufficiently large network. The primary point of interest is the difference in the right-side tails of the two distributions. </details> Figure 9: Distribution of sampled shortest path lengths in the recursively generated knowledge graphs (panel (a), for graph $G_2$ , panel (b), graph $G_2$ ). The peak around 5–6 steps suggests that the network remains compact and navigable, while the slight right skew especially in panel (a) indicates the presence of peripheral nodes or specialized subdomains. ### 2.5 Knowledge Graph Evolution and Conceptual Breakthroughs The evolution of the knowledge graph over iterative expansions discussed so far reveals distinct patterns in knowledge accumulation, conceptual breakthroughs, and interdisciplinary integration. To analyze these processes, we now examine (i) the growth trajectories of major conceptual hubs, (ii) the emergence of new highly connected nodes, and (iii) overall network connectivity trends across iterations. The results of these analyses are presented in Figure 11, which consists of three sub-components. <details> <summary>x10.png Details</summary>  ### Visual Description \n ## [Multi-Panel Chart]: Network Evolution Analysis ### Overview The image contains three distinct charts labeled (a), (b), and (c), which collectively analyze the evolution of a network over a series of iterations. The charts track the growth of specific nodes (hubs), the emergence of new hubs, and the overall network connectivity. The data suggests a simulation or model of a growing network, likely demonstrating principles of preferential attachment or scale-free network formation. ### Components/Axes **Chart (a): Growth of Top Hubs Over Iterations** * **Type:** Line Chart * **X-Axis:** Label: "Iteration". Scale: 0 to 1000, with major ticks every 200 units. * **Y-Axis:** Label: "Absolute Degree". Scale: 0 to 200, with major ticks every 25 units. * **Legend:** Located in the top-right corner of the plot area. Contains 10 entries, each associating a color with a specific node label. * Blue: Node Artificial Intelligence (AI) * Orange: Node Knowledge Graph * Green: Node Urban Ecosystems * Red: Node Bioluminescent Technology * Purple: Node Learning Outcomes * Brown: Node Climate Change * Pink: Node Resilience * Gray: Node Human Well-being * Olive: Node Bioluminescent Organisms * Cyan: Node Symbiotic Relationships **Chart (b): Emergence of New Hubs Over Iterations** * **Type:** Bar Chart (Histogram-like) * **X-Axis:** Label: "Iteration Number". Scale: 0 to 200, with major ticks every 50 units. * **Y-Axis:** Label: "Number of New Hubs". Scale: 0.00 to 2.00, with major ticks every 0.25 units. **Chart (c): Overall Network Connectivity Over Time** * **Type:** Line Chart * **X-Axis:** Label: "Iteration". Scale: 0 to 1000, with major ticks every 200 units. * **Y-Axis:** Label: "Average Node Degree". Scale: 0 to 4.5, with major ticks every 1 unit. ### Detailed Analysis **Chart (a): Growth of Top Hubs Over Iterations** This chart tracks the "Absolute Degree" (number of connections) for 10 specific nodes across 1000 iterations. All lines show a non-decreasing, step-like growth pattern, indicating that connections are added in discrete events. * **Node Artificial Intelligence (AI) [Blue Line]:** Shows the most dominant and consistent growth. Starts near 0, experiences a sharp increase around iteration 50-100, and continues a strong upward trend, ending as the highest node with an approximate degree of **195** at iteration 1000. * **Node Knowledge Graph [Orange Line]:** The second-highest performer. Begins growing later than the AI node, with significant jumps around iterations 400 and 700. Ends with an approximate degree of **135**. * **Node Urban Ecosystems [Green Line]:** Shows moderate growth, ending with an approximate degree of **110**. * **Node Bioluminescent Technology [Red Line]:** Follows a similar trajectory to Urban Ecosystems, ending with an approximate degree of **105**. * **Node Learning Outcomes [Purple Line]:** Grows steadily in the middle of the pack, ending with an approximate degree of **100**. * **Node Climate Change [Brown Line]:** Grows early but plateaus somewhat in the later iterations, ending with an approximate degree of **80**. * **Node Resilience [Pink Line]:** Shows a late surge after iteration 600, ending with an approximate degree of **80**. * **Node Human Well-being [Gray Line]:** Grows slowly and steadily, ending with an approximate degree of **75**. * **Node Bioluminescent Organisms [Olive Line]:** Remains relatively low until a sharp increase after iteration 900, ending with an approximate degree of **65**. * **Node Symbiotic Relationships [Cyan Line]:** The lowest-performing node in this set, with most growth occurring after iteration 600, ending with an approximate degree of **65**. **Chart (b): Emergence of New Hubs Over Iterations** This chart shows discrete events where new nodes achieve "hub" status (likely defined by a degree threshold). The x-axis is zoomed into the first ~230 iterations. * **Cluster 1 (Iterations 0-40):** A series of bars, each with a height of **1.0**, indicating one new hub emerged per iteration in this early phase. * **Cluster 2 (Iterations 80-90):** A prominent bar at approximately iteration 85 with a height of **2.0**, indicating two new hubs emerged simultaneously. This is followed by single-hub bars at iterations ~90 and ~110. * **Isolated Event (Iteration ~225):** A single bar with a height of **1.0**. * **Interpretation:** New hub formation is not continuous but occurs in bursts, with a notable peak of activity around iteration 85. **Chart (c): Overall Network Connectivity Over Time** This chart shows a single, thick blue line representing the average node degree across the entire network. * **Trend:** The line shows a remarkably steady, near-linear increase from an average degree of **~0.1** at iteration 0 to **~4.6** at iteration 1000. * **Implication:** The overall network is becoming denser and more connected at a constant rate over time, despite the uneven growth of individual hubs seen in chart (a). ### Key Observations 1. **Dominant Hub:** The "Artificial Intelligence (AI)" node is the clear outlier in growth, consistently outpacing all other tracked nodes. 2. **Growth Phases:** Hub growth is not smooth but occurs in steps or bursts, suggesting connection events are discrete and possibly triggered by specific model conditions. 3. **Hub Emergence Timing:** The formation of new hubs (chart b) is concentrated in the early phase of the network's evolution (first 120 iterations), with very few new hubs appearing later. 4. **Steady Macro Trend:** Despite the chaotic and unequal growth at the node level (chart a), the network's overall connectivity (chart c) increases with striking regularity. ### Interpretation The three charts together tell a story of **network evolution under a preferential attachment mechanism** (like the Barabási–Albert model). The data suggests: * **"The Rich Get Richer":** The early and rapid growth of the AI node (chart a) indicates it likely gained an early advantage, attracting new connections at an accelerating rate simply because it was already large. This is a hallmark of scale-free networks. * **Network Maturation:** The burst of new hub creation early on (chart b) followed by a long period with few new hubs suggests the network's core structure is established early. Later growth primarily reinforces existing hubs rather than creating new ones. * **Predictable System-Level Behavior:** The perfectly linear growth in average degree (chart c) is a powerful finding. It indicates that while individual node fates are highly variable and path-dependent, the system as a whole evolves with predictable, steady densification. This could be a designed property of the simulation or an emergent property of the attachment rules. * **Domain Context:** The node labels (AI, Knowledge Graph, Urban Ecosystems, etc.) imply this network model might be simulating the growth of a **knowledge graph, a technological ecosystem, or a conceptual map** where ideas or technologies build upon each other. The dominance of the "AI" node could reflect a hypothesis about its central, integrative role in such a system. **Conclusion:** The visualization effectively demonstrates how simple local rules (e.g., preferential attachment) can lead to complex global outcomes: the emergence of dominant hubs, sporadic structural changes, and yet, remarkably stable and predictable system-wide metrics. </details> Figure 10: Evolution of knowledge graph structure across iterations, for $G_1$ . (a) Degree growth of the top conceptual hubs, showing both steady accumulation and sudden breakthroughs. (b) Histogram of newly emerging high-degree nodes across iterations, indicating phases of conceptual expansion. (c) Plot of the mean node degree over time, illustrating the system’s progressive integration of new knowledge. The trajectory of hub development (Figure 10 (a)) suggests two primary modes of knowledge accumulation: steady growth and conceptual breakthroughs. Certain concepts, such as Artificial Intelligence (AI) and Knowledge Graphs, exhibit continuous incremental expansion, reflecting their persistent relevance in structuring knowledge. In contrast, hubs like Bioluminescent Technology and Urban Ecosystems experience extended periods of low connectivity followed by sudden increases in node degree, suggesting moments when these concepts became structurally significant in the knowledge graph. These results indicate that the system does not expand knowledge in a purely linear fashion but undergoes phases of conceptual restructuring, akin to punctuated equilibrium in scientific development. The emergence of new hubs (Figure 10 (b)) further supports this interpretation. Instead of a continuous influx of new central concepts, we observe discrete bursts of hub formation occurring at specific iteration milestones. These bursts likely correspond to the accumulation of contextual knowledge reaching a critical threshold, after which the system autonomously generates new organizing principles to structure its expanding knowledge base. This finding suggests that the system’s reasoning process undergoes alternating cycles of consolidation and discovery, where previously formed knowledge stabilizes before new abstract concepts emerge. The overall network connectivity trends (Figure 10 (c)) demonstrate a steady increase in average node degree, indicating that the graph maintains a structurally stable expansion while integrating additional knowledge. The absence of abrupt drops in connectivity suggests that previously introduced concepts remain relevant and continue to influence reasoning rather than become obsolete. This trend supports the hypothesis that the system exhibits self-organizing knowledge structures, continuously refining its conceptual hierarchy as it expands. These observations lead to several overarching conclusions. First, the results indicate that the system follows a hybrid knowledge expansion model, combining gradual accumulation with disruptive conceptual breakthroughs. This behavior closely mirrors the dynamics of human knowledge formation, where foundational ideas develop progressively, but major paradigm shifts occur when conceptual thresholds are crossed. Second, the persistence of high-degree hubs suggests that knowledge graphs generated in this manner do not suffer from catastrophic forgetting; instead, they maintain and reinforce previously established structures while integrating new insights. Third, the formation of new hubs in discrete bursts implies that knowledge expansion is not driven by uniform growth but by self-reinforcing epistemic structures, where accumulated reasoning reaches a tipping point that necessitates new abstract representations. Additionally, the system demonstrates a structured directionality in knowledge formation, as evidenced by the smooth increase in average node degree without fragmentation. This suggests that new concepts do not disrupt existing structures but are incrementally woven into the broader network. Such behavior is characteristic of self-organizing knowledge systems, where conceptual evolution follows a dynamic yet cohesive trajectory. The model also exhibits potential for cross-domain knowledge synthesis, as indicated by the presence of nodes that transition into highly connected hubs later in the process. These nodes likely act as bridges between previously distinct knowledge clusters, fostering interdisciplinary connections. These analyses provide strong evidence that the recursive graph expansion model is capable of simulating key characteristics of scientific knowledge formation. The presence of alternating stability and breakthrough phases, the hierarchical organization of concepts, and the increasing connectivity across knowledge domains all highlight the potential for autonomous reasoning systems to construct, refine, and reorganize knowledge representations dynamically. Future research could potentially focus on exploring the role of interdisciplinary bridge nodes, analyzing the hierarchical depth of reasoning paths, and examining whether the system can autonomously infer meta-theoretical insights from its evolving knowledge graph. ### 2.6 Structural Evolution of the Knowledge Graph The expansion of the knowledge graph over iterative refinements reveals emergent structural patterns that highlight how knowledge communities form, how interdisciplinary connections evolve, and how reasoning complexity changes over time. These dynamics provide insight into how autonomous knowledge expansion follows systematic self-organization rather than random accumulation. Figure 11 presents three key trends: (a) the formation and growth of knowledge sub-networks, (b) the number of bridge nodes that connect different knowledge domains, and (c) the depth of multi-hop reasoning over iterations. <details> <summary>x11.png Details</summary>  ### Visual Description ## Scatter Plot Series: Evolution of a Knowledge Network ### Overview The image contains three distinct scatter plots, labeled (a), (b), and (c), arranged in a 2x2 grid with the bottom-right quadrant empty. Each plot tracks a different metric of a system's evolution over "Iteration" (x-axis). The plots use different colors for their data points: purple for (a), red for (b), and blue for (c). There is no overarching legend; each plot's color is intrinsically tied to its specific metric. ### Components/Axes **Common Elements:** * **X-Axis (All Plots):** Labeled "Iteration". The scale runs from 0 to approximately 1000 or 1050. * **Grid:** All plots feature a light gray grid for easier value estimation. **Plot (a) - Top Left:** * **Title:** "Evolution of Knowledge Communities Over Time" * **Y-Axis Label:** "Number of Sub-Networks" * **Y-Axis Scale:** Linear, from 0 to 30, with major ticks every 5 units. * **Data Color:** Purple. **Plot (b) - Top Right:** * **Title:** "Number of Concepts Connecting Different Domains Over Time" * **Y-Axis Label:** "Number of Bridge Nodes" * **Y-Axis Scale:** Linear, from 0 to 1200, with major ticks every 200 units. * **Data Color:** Red. **Plot (c) - Bottom Left:** * **Title:** "Depth of Multi-Hop Reasoning Over Time" * **Y-Axis Label:** "Avg Shortest Path Length" * **Y-Axis Scale:** Linear, from 2 to 7, with major ticks every 1 unit. * **Data Color:** Blue. ### Detailed Analysis **Plot (a): Evolution of Knowledge Communities** * **Trend Verification:** The purple data points show a rapid, near-vertical increase from ~4 to ~14 sub-networks within the first ~50 iterations. The growth then decelerates, forming a noisy, upward-sloping plateau. From iteration ~200 onward, the number of sub-networks fluctuates heavily between approximately 18 and 28, with a central tendency that slowly rises from ~20 to ~24 by iteration 1000. * **Key Data Points (Approximate):** * Iteration 0: ~4 sub-networks * Iteration 50: ~14 sub-networks * Iteration 200: ~20 sub-networks (with high variance) * Iteration 1000: ~24 sub-networks (range: ~18-28) **Plot (b): Number of Connecting Concepts** * **Trend Verification:** The red data points exhibit a remarkably consistent, near-linear upward trend with very low variance. The line of points has a constant positive slope, indicating steady growth. * **Key Data Points (Approximate):** * Iteration 0: ~0 bridge nodes * Iteration 150: ~200 bridge nodes * Iteration 450: ~600 bridge nodes * Iteration 750: ~900 bridge nodes * Iteration 1050: ~1200 bridge nodes **Plot (c): Depth of Multi-Hop Reasoning** * **Trend Verification:** The blue data points show a dramatic, sharp spike at the very beginning, reaching a peak. This is followed by a rapid decline and then a long, stable plateau with minimal fluctuation. * **Key Data Points (Approximate):** * Iteration 0: ~2.5 avg shortest path length * Peak (Iteration ~20): ~7.0 * Iteration 100: ~5.5 * Iteration 200: ~5.2 * Iteration 400 to 1000: Stable at ~4.9 to 5.0 ### Key Observations 1. **Divergent Growth Patterns:** The three metrics evolve in fundamentally different ways. "Bridge Nodes" (b) grow linearly and predictably. "Sub-Networks" (a) grow logistically with high noise. "Avg Shortest Path Length" (c) exhibits a transient spike before stabilizing. 2. **Phase Change in Reasoning Depth:** Plot (c) clearly shows two distinct phases: an initial exploration phase where reasoning paths become very deep (high avg shortest path length), followed by an optimization phase where the network reorganizes to maintain shorter, more efficient paths. 3. **Noise vs. Signal:** Plot (a) is characterized by high-frequency noise (large vertical scatter), suggesting the number of sub-networks is a volatile metric. In contrast, plots (b) and (c) show much tighter data point clustering, indicating more stable, deterministic growth in those metrics. 4. **Temporal Correlation:** The initial spike in reasoning depth (c, iterations 0-100) coincides with the period of fastest growth in sub-networks (a) and the beginning of bridge node accumulation (b). The stabilization of reasoning depth (c, after iteration ~200) occurs as the growth of sub-networks (a) enters its noisy plateau phase. ### Interpretation This data collectively narrates the evolution of a growing knowledge or concept network. The process appears to follow a logical sequence: 1. **Initial Fragmentation & Exploration (Iterations 0-100):** The system rapidly generates many distinct sub-networks (a) and simultaneously explores deep, complex connections between concepts, leading to a spike in average path length (c). This is the "brainstorming" or "specialization" phase. 2. **Integration & Optimization (Iterations 100-400):** The rate of new sub-network creation slows. The system focuses on building bridges between existing domains (b continues its steady climb). Crucially, it optimizes its internal structure, drastically reducing the average reasoning path length (c) from its peak. This suggests the formation of more direct, efficient links between previously distant concepts. 3. **Steady-State Growth (Iterations 400+):** The network reaches a dynamic equilibrium. The number of communities (a) fluctuates around a slowly increasing mean, indicating ongoing reorganization. The number of interdisciplinary bridges (b) continues its relentless linear growth, showing constant integration. The reasoning depth (c) remains stable and low, indicating the network has achieved an efficient "small-world" property where most concepts are connected via short paths. **In essence, the system evolves from a fragmented, deep, and inefficient state into an integrated, optimized, and scalable network.** The linear growth of bridge nodes is the most robust indicator of ongoing interdisciplinary synthesis, while the stabilization of path length confirms the network's maturation into an efficient knowledge structure. The noise in sub-network count may reflect the dynamic competition and merging of ideas within the system. </details> Figure 11: Structural evolution of the knowledge graph across iterations. (a) The number of distinct knowledge communities over time, showing an increasing trend with some fluctuations, for graph $G_1$ . (b) The growth of bridge nodes that connect multiple knowledge domains, following a steady linear increase. (c) The average shortest path length over iterations, indicating shifts in reasoning complexity as the graph expands. Figure 11 (a) illustrates the formation of knowledge sub-networks over time. The number of distinct communities increases as iterations progress, reflecting the system’s ability to differentiate between specialized fields of knowledge. The trend suggests two key observations: (i) an early rapid formation of new communities as novel knowledge domains emerge and (ii) a later stage where the number of communities stabilizes with occasional fluctuations. The latter behavior indicates that rather than indefinitely forming new disconnected knowledge clusters, the system reaches a regime where previously distinct domains remain relatively stable while undergoing minor structural reorganizations. The fluctuations in the later stages may correspond to moments where knowledge clusters merge or when new abstractions cause domain shifts. Figure 11 (b) tracks the number of bridge nodes (concepts that serve as interdisciplinary connectors) over iterative expansions. The steady, almost linear increase in bridge nodes suggests that as knowledge expands, more concepts naturally emerge as crucial links between different domains. This behavior reflects the self-reinforcing nature of knowledge integration, where new ideas not only expand within their respective fields but also introduce new ways to connect previously unrelated disciplines. Interestingly, there is no evidence of saturation in the number of bridge nodes, implying that the graph remains highly adaptive, continuously uncovering interdisciplinary relationships without premature convergence. This property is reminiscent of human knowledge structures, where interdisciplinary connections become more prevalent as scientific inquiry deepens. Figure 11 (c) examines the depth of multi-hop reasoning over iterations by measuring the average shortest path length in the graph. Initially, reasoning depth fluctuates significantly, which corresponds to the early phase of knowledge graph formation when structural organization is still emergent. As iterations progress, the average path length stabilizes, indicating that the system achieves a balance between hierarchical depth and accessibility of information. The early fluctuations may be attributed to the rapid reorganization of knowledge, where some paths temporarily become longer as new concepts emerge before stabilizing into more efficient reasoning structures. The eventual stabilization suggests that the graph reaches an equilibrium in how information propagates through interconnected domains, maintaining reasoning efficiency while still allowing for complex inferential pathways. Taken together, these findings suggest that the autonomous knowledge expansion model exhibits structured self-organization, balancing specialization and integration. The interplay between distinct community formation, interdisciplinary connectivity, and reasoning depth highlights the emergence of a dynamically evolving but structurally coherent knowledge network. The continuous increase in bridge nodes reinforces the idea that interdisciplinary reasoning remains a central feature throughout the system’s expansion, which may have significant implications for autonomous discovery processes. Future analyses will explore whether certain bridge nodes exhibit long-term persistence as central knowledge connectors or if interdisciplinary pathways evolve dynamically based on newly introduced concepts. ### 2.7 Persistence of Bridge Nodes in Knowledge Evolution To understand the structural stability of interdisciplinary connections, we further analyze the persistence of bridge nodes—concepts that act as connectors between distinct knowledge domains, over multiple iterations. Figure 12 presents a histogram of bridge node lifespans, showing how long each node remained an active bridge in the knowledge graph. <details> <summary>x12.png Details</summary>  ### Visual Description ## Histogram with Trend Line: Bridge Node Persistence Over Time ### Overview The image displays a histogram titled "Bridge Node Persistence Over Time," illustrating the distribution of how long nodes in a network maintain their role as "bridge nodes." The chart includes a histogram (light blue bars with black outlines) and an overlaid trend line (darker blue). The data is right-skewed, indicating that most bridge nodes persist for a short duration, while a smaller number persist for much longer periods. ### Components/Axes * **Title:** "Bridge Node Persistence Over Time" (centered at the top). * **X-Axis:** Labeled "Number of Iterations as a Bridge Node." It is a linear scale ranging from 0 to 800, with major tick marks and grid lines every 100 units (0, 100, 200, ..., 800). * **Y-Axis:** Labeled "Number of Nodes." It is a linear scale ranging from 0 to 350, with major tick marks and grid lines every 50 units (0, 50, 100, ..., 350). * **Legend:** There is no explicit legend. The histogram bars and the trend line are the only data series. * **Grid:** A light gray grid is present, aligned with the major ticks on both axes. ### Detailed Analysis **Histogram Data (Approximate Values):** The histogram bins appear to have a width of approximately 25 iterations. The height of each bar represents the count of nodes that persisted for that number of iterations. * **Bin 0-25:** ~350 nodes (the tallest bar, located at the far left). * **Bin 25-50:** ~135 nodes. * **Bin 50-75:** ~110 nodes. * **Bin 75-100:** ~90 nodes. * **Bin 100-125:** ~90 nodes. * **Bin 125-150:** ~70 nodes. * **Bin 150-175:** ~90 nodes. * **Bin 175-200:** ~60 nodes. * **Bin 200-225:** ~80 nodes. * **Bin 225-250:** ~70 nodes. * **Bin 250-275:** ~70 nodes. * **Bin 275-300:** ~60 nodes. * **Bin 300-325:** ~45 nodes. * **Bin 325-350:** ~65 nodes. * **Bin 350-375:** ~70 nodes. * **Bin 375-400:** ~40 nodes. * **Bin 400-425:** ~35 nodes. * **Bin 425-450:** ~40 nodes. * **Bin 450-475:** ~45 nodes. * **Bin 475-500:** ~50 nodes. * **Bin 500-525:** ~25 nodes. * **Bin 525-550:** ~25 nodes. * **Bin 550-575:** ~20 nodes. * **Bin 575-600:** ~35 nodes. * **Bin 600-625:** ~25 nodes. * **Bin 625-650:** ~25 nodes. * **Bin 650-675:** ~20 nodes. * **Bin 675-700:** ~20 nodes. * **Bin 700-725:** ~15 nodes. * **Bin 725-750:** ~15 nodes. * **Bin 750-775:** ~25 nodes. * **Bin 775-800:** ~25 nodes. **Trend Line Analysis:** The smooth, darker blue trend line represents a fitted curve to the histogram data. * **Starting Point:** Begins at approximately y=110 when x=0. * **Peak:** Rises to a peak of approximately y=130 near x=50. * **Trend:** After the peak, it follows a steady, gradual downward slope across the remainder of the chart. * **Ending Point:** Ends at approximately y=10 when x=800. ### Key Observations * **Extreme Right Skew:** The distribution is heavily right-skewed. The single highest frequency is in the first bin (0-25 iterations), containing nearly twice as many nodes as the next bin. * **Rapid Initial Drop-off:** There is a sharp decline in node count after the first bin, with the count dropping by more than half by the third bin (50-75 iterations). * **Long Tail:** Despite the rapid initial drop, the histogram has a long tail extending to 800 iterations, showing that a non-trivial number of nodes maintain their bridge role for a very long time. * **Local Fluctuations:** While the overall trend is downward, there are minor local peaks and valleys in the histogram (e.g., around 150-175, 325-375, and 475-500 iterations), suggesting some variability in persistence durations. * **Trend Line Confirmation:** The overlaid trend line visually confirms the overall pattern: a brief initial increase followed by a monotonic decrease in the number of nodes as persistence duration increases. ### Interpretation This chart provides a quantitative view of node role stability within a dynamic network. The data suggests that the "bridge node" role is highly transient for the vast majority of nodes. Most nodes assume this role for only a few dozen iterations before losing it. This could indicate a network with high churn, where connectivity paths are frequently reconfigured, or where the bridge role is competitively or randomly assigned. The presence of the long tail, however, is significant. It demonstrates that a small subset of nodes are exceptionally stable, persisting as bridges for hundreds of iterations. These nodes likely form the persistent backbone of the network's connectivity. The minor fluctuations in the histogram might correspond to specific network events, protocols, or structural properties that favor certain persistence durations over others. From a systems perspective, this distribution implies that analyses or optimizations relying on bridge nodes should not assume long-term stability for most nodes. Instead, they must be designed for high turnover, while potentially identifying and leveraging the small set of highly persistent nodes for more stable functions. The trend line provides a simplified model for predicting the expected number of nodes at a given persistence duration, which could be useful for capacity planning or reliability modeling. </details> Figure 12: Histogram of bridge node persistence over iterations, for $G_1$ . The distribution follows a long-tail pattern, indicating that while most bridge nodes exist only briefly, a subset remains active across hundreds of iterations. The distribution in Figure 12 suggests that knowledge graph connectivity follows a hybrid model of structural evolution. The majority of bridge nodes appear only for a limited number of iterations, reinforcing the hypothesis that interdisciplinary pathways frequently evolve as new concepts emerge and replace older ones. This aligns with earlier observations that the knowledge system exhibits a high degree of conceptual dynamism. However, a subset of bridge nodes remains persistent for hundreds of iterations. These nodes likely correspond to fundamental concepts that sustain long-term interdisciplinary connectivity. Their extended presence suggests that the system does not solely undergo continuous restructuring; rather, it maintains a set of core concepts that act as stable anchors in the evolving knowledge landscape. These results refine our earlier observations by distinguishing between transient interdisciplinary connections and long-term structural stability. While knowledge graph expansion is dynamic, certain foundational concepts maintain their bridging role, structuring the broader knowledge network over extended periods. This hybrid model suggests that autonomous knowledge expansion does not operate under complete conceptual turnover but instead converges toward the emergence of stable, high-impact concepts that persist across iterations. Related questions that could be explored in future research is whether these persistent bridge nodes correspond to widely used theoretical frameworks, methodological paradigms, or cross-domain knowledge principles. Additionally, further analysis is needed to examine whether long-term bridge nodes exhibit distinct topological properties, such as higher degree centrality or clustering coefficients, compared to short-lived connectors. ### 2.8 Early Evolution of Bridge Nodes in Knowledge Expansion To examine the mechanics of the formation of interdisciplinary connections in the early stages of knowledge graph evolution, we pay close attention to the process. In the analysis discussed here, we identify the first occurrences of bridge nodes over the initial 200 iterations. Figure 13 presents a binary heatmap, where each row represents a bridge node, and each column corresponds to an iteration. The bridge nodes are sorted by the iteration in which they first appeared, providing a clearer view of how interdisciplinary connectors emerge over time. <details> <summary>x13.png Details</summary>  ### Visual Description ## Heatmap Chart: Bridge Node Appearance Over Early Iterations (Sorted by First Appearance) ### Overview This image is a binary presence/absence heatmap (or "rug plot") visualizing the appearance of 100 specific "bridge nodes" across the first 200 iterations of a process. The chart is sorted by the first iteration in which each node appears, creating a diagonal cascade pattern from the top-left to the bottom-right. Dark blue indicates the node is present in that iteration; white indicates absence. ### Components/Axes * **Title:** "Bridge Node Appearance Over Early Iterations (Sorted by First Appearance)" * **Y-Axis (Vertical):** Labeled "Top 100 Earliest Appearing Bridge Nodes". It lists 100 distinct conceptual nodes, likely from a knowledge graph or conceptual model. The nodes are sorted in descending order of their first appearance iteration. * **X-Axis (Horizontal):** Labeled "Iteration (First 200)". It represents a sequence of iterations or time steps. The axis markers are numerical, starting at 2 and ending at 199, with labeled ticks at irregular intervals (e.g., 2, 5, 8, 11, 17, 23, 29, 35, 40, 44, 50, 53, 56, 60, 63, 66, 69, 73, 76, 82, 87, 90, 94, 100, 105, 108, 112, 116, 120, 125, 130, 133, 137, 142, 146, 149, 152, 156, 159, 164, 169, 176, 179, 184, 188, 192, 195, 199). * **Legend/Color Key:** Implicit. A solid dark blue rectangle represents "presence" in an iteration. White represents "absence". There is no separate legend box; the color meaning is inferred from the chart's structure. ### Detailed Analysis **List of Bridge Nodes (Y-Axis, from top to bottom):** 1. Closed-Loop Life Cycle Design 2. Environmental Sustainability 3. Human Well-being 4. Material Utilization 5. Material Waste 6. Recycling 7. Bio-inspired Materials 8. Bio-inspired Materials Science 9. Closed-loop Life Cycle Design 10. Design Approach 11. Development of Novel, Adaptive Urban Ecosystems 12. Materials 13. Materials Science 14. Nature 15. Novel, Adaptive Urban Ecosystems 16. Social Impact 17. Sustainable Materials Development 18. Self-healing Infrastructure 19. Environmental Impact 20. More Resilient Urban Systems 21. Urban Planning and Development 22. Adaptability of cities to climate change 23. Enhancement of Adaptability and Resilience in cities 24. Integration 25. Key Design Considerations 26. Sustainability 27. Adaptability and Resilience of Cities 28. Climate Change 29. Smart Systems 30. Biological and Bio-Inspired Materials 31. Materials 32. Urban Infrastructure Design 33. Environmental Protection 34. Flood Resilience 35. Infrastructure 36. Adaptive 37. Advanced Materials 38. Economic Impact 39. Economic Outcome 40. Floodwall System 41. Smart Materials 42. Urban Flood Defenses 43. Urban Infrastructure 44. Adaptive, Modular Design 45. Economic Growth of Affected Communities 46. Self-healing Concrete 47. Artificial Intelligence (AI) 48. Feedback Mechanism 49. Inclusive Learning Ecosystem (ILE) 50. Personalized Learning Experience 51. Personalized Learning Environment 52. Adaptive Learning 53. Learning Effectiveness 54. Learning Pathways 55. Personalized Learning 56. Adaptive Learning Systems 57. Cognitive Profiling 58. Learning Environment 59. Learning Motivation 60. Learning Outcomes 61. AI-driven Knowledge Graph (KG) 62. Adaptive Assessments 63. Knowledge Graph-based Adaptation (KG-bA) 64. Personalized Learning Path 65. Personalized Learning Pathways (PLP) 66. Adaptive Learning System (ALS) 67. Flow 68. Individual Differences 69. Knowledge Graph 70. Knowledge Graph Construction 71. Knowledge Representation 72. Learning Analytics 73. Learning Preferences 74. Neuroplasticity 75. Neuroplasticity-Based Learning 76. Personalized Education Strategies 77. Learning Approach 78. Learning Outcome 79. Learning Process 80. Student Success 81. VR 82. AI-Driven Narrative Generation 83. Personalized Adaptive Narratives 84. Anxiety Disorders 85. Immersive Storytelling 86. Virtual Reality (VR) Therapy 87. BCIs 88. Long-term Outcomes 89. Personalized VR Therapy 90. Therapeutic Approach 91. User Engagement 92. Treatment Plans 93. Brain-Computer Interfaces (BCIs) 94. Neurological Disorders 95. Outcome 96. Recovery 97. Technology 98. Treatment Longevity 99. Personalization and Adaptivity 100. Therapy **Appearance Pattern Analysis:** * **Trend:** The chart exhibits a strong diagonal trend. Nodes at the top of the list (e.g., "Closed-Loop Life Cycle Design", "Environmental Sustainability") have their first dark blue block at the far left (low iteration numbers, starting at iteration 2). Nodes at the bottom (e.g., "Therapy", "Personalization and Adaptivity") have their first dark blue block much further to the right (higher iteration numbers, appearing after iteration 100). * **Persistence:** After their first appearance, many nodes show intermittent or continuous presence (solid or broken dark blue lines extending to the right). Some nodes, like "Materials" (#12 and #31) and "Sustainability" (#26), show very high persistence, appearing as nearly solid blue lines across most iterations. Others, like "Anxiety Disorders" (#84) or "VR" (#81), appear only sporadically after their first appearance. * **Clustering:** There are visible clusters of nodes that first appear around similar iteration ranges, suggesting phases or waves of concept introduction. For example, a large cluster of learning-related nodes (e.g., "Adaptive Learning", "Personalized Learning") appears between iterations ~50-80. Another cluster related to VR and therapy appears after iteration ~100. ### Key Observations 1. **Foundational Concepts:** The earliest-appearing nodes (top of the list) are broad, foundational concepts related to sustainability, materials science, and urban systems (e.g., "Closed-Loop Life Cycle Design", "Environmental Sustainability", "Human Well-being"). 2. **Domain Shift:** The list transitions from physical systems (materials, urban infrastructure) to digital and cognitive systems (AI, Knowledge Graphs, Adaptive Learning) and finally to therapeutic applications (VR Therapy, BCIs, Neurological Disorders). 3. **Variable Persistence:** There is no uniform pattern of persistence. Some foundational concepts remain consistently present, while more specialized or applied concepts appear and disappear. 4. **Data Density:** The heatmap is dense, indicating that most of the 100 tracked nodes are active in a significant portion of the first 200 iterations. The white spaces (absences) become more common for nodes lower on the list, particularly in the early iterations before they first appear. ### Interpretation This chart likely visualizes the evolution of a complex knowledge graph or conceptual model during an iterative generative or learning process (e.g., an AI system building a knowledge base, a simulation evolving, or a research field developing). * **What it demonstrates:** It shows the **temporal emergence and consolidation of concepts**. Foundational, high-level ideas are established first and tend to persist. More specific, derivative, or application-oriented concepts emerge later as the system or field matures. The intermittent appearance of some nodes suggests they are context-dependent or activated only under certain conditions within the process. * **Relationships:** The sorting by first appearance implicitly maps a **hierarchy of conceptual dependency or generality**. The diagonal pattern is a direct visual representation of this temporal hierarchy. The clustering of similar nodes (e.g., all the "Adaptive Learning" variants) indicates the development of coherent sub-domains within the broader model. * **Notable Anomalies/Patterns:** * The duplicate entry for "Closed-loop Life Cycle Design" (items #1 and #9) and "Materials" (#12 and #31) may indicate a data artifact or the existence of conceptually similar but distinct nodes in the underlying graph. * The very late and sparse appearance of highly specific terms like "Anxiety Disorders" (#84) suggests they are niche applications that only become relevant after a substantial foundational framework (VR, Therapy, Personalization) is in place. * The chart's structure allows one to infer the **"conceptual distance"** between nodes. Nodes that appear close together vertically and have similar persistence patterns are likely more closely related in the model's ontology than nodes far apart vertically. </details> Figure 13: Emergence of bridge nodes over the first 200 iterations, sorted by first appearance, for $G_1$ . White regions indicate the absence of a node as a bridge, while dark blue regions denote its presence. Nodes that appear earlier in the graph evolution are positioned at the top. The structured emergence pattern suggests phases of knowledge expansion and stabilization. The heatmap in Figure 13 reveals several key trends in the evolution of bridge nodes. Notably, the earliest iterations feature a rapid influx of bridge nodes, reflecting the initial structuring phase of the knowledge graph. Many nodes appear and remain active for extended periods, suggesting that certain concepts establish themselves as core interdisciplinary connectors early in the process. These nodes likely play a foundational role in structuring knowledge integration across domains. A second notable pattern is the episodic emergence of new bridge nodes, rather than a continuous accumulation. The visualization shows distinct clusters of newly appearing bridge nodes, interspersed with periods of relative stability. These bursts suggest that knowledge integration occurs in structured phases rather than through gradual accumulation. Such phases may represent moments when the system reaches a threshold where newly integrated concepts allow for the creation of previously infeasible interdisciplinary links. In contrast to the early-established bridge nodes, a subset of nodes appears only in later iterations. These late-emerging bridge nodes indicate that interdisciplinary roles are notably not static; rather, the system continuously restructures itself, incorporating new ideas as they gain relevance. This supports the hypothesis that certain bridge nodes emerge not from initial structuring but from later stages of conceptual refinement, possibly as higher-order abstractions connecting previously developed knowledge clusters. The distribution of bridge node activity also suggests a mix of persistent and transient connectors. While some nodes appear briefly and disappear, others remain active over long stretches. This behavior reinforces the idea that knowledge expansion is both dynamic and structured, balancing exploration (where new connections are tested) and stabilization (where key interdisciplinary links persist). We note that the structured emergence of bridge nodes may indicate that interdisciplinary pathways do not form randomly but are shaped by systematic phases of knowledge integration and refinement. Future analyses could explore the long-term impact of early bridge nodes, assessing whether they remain influential throughout the knowledge graph’s evolution, and whether the structure of interdisciplinary connectivity stabilizes or continues to reorganize over extended iterations. ### 2.9 Evolution of Key Bridge Nodes Over Iterations To investigate how interdisciplinary pathways evolve in the knowledge graph, we analyzed the betweenness centrality of the most influential bridge nodes across 1,000 iterations. Figure 14 presents the trajectory of the top 10 bridge nodes, highlighting their shifting roles in facilitating interdisciplinary connections. <details> <summary>x14.png Details</summary>  ### Visual Description \n ## Line Chart: Evolution of Top 10 Bridge Nodes Over Iterations ### Overview The image is a line chart titled "Evolution of Top 10 Bridge Nodes Over Iterations." It plots the "Betweenness Centrality" of ten distinct conceptual nodes against the number of "Iterations," showing how their relative importance within a network changes over time. The chart displays significant initial volatility, with most nodes experiencing a rapid decline in centrality, followed by a long tail where values stabilize at lower levels. ### Components/Axes * **Chart Title:** "Evolution of Top 10 Bridge Nodes Over Iterations" (centered at the top). * **Y-Axis:** Labeled "Betweenness Centrality." The scale runs from 0.0 to 0.7, with major gridlines at intervals of 0.1. * **X-Axis:** Labeled "Iteration." The scale runs from 0 to 1000, with major gridlines and labels at intervals of 200 (0, 200, 400, 600, 800, 1000). * **Legend:** Positioned in the top-right corner, outside the main plot area. It lists 10 data series with corresponding colored markers and lines: 1. **Closed-Loop Life Cycle Design** (Blue line, circle marker) 2. **Human Well-being** (Orange line, circle marker) 3. **Feedback Mechanism** (Green line, circle marker) 4. **Adaptive** (Red line, circle marker) 5. **Adaptability and Resilience of Cities** (Purple line, circle marker) 6. **Artificial Intelligence (AI)** (Brown line, circle marker) 7. **Environmental Sustainability** (Pink line, circle marker) 8. **Outcome** (Gray line, circle marker) 9. **Closed-loop Life Cycle Design** (Yellow-green line, circle marker) *[Note: This appears to be a duplicate or variant of item 1, with slightly different capitalization]* 10. **Bio-inspired Materials** (Cyan line, circle marker) ### Detailed Analysis **Trend Verification & Data Points (Approximate Values):** * **Closed-Loop Life Cycle Design (Blue):** Starts at the highest point on the chart (~0.70 at Iteration 0). Experiences an extremely sharp, near-vertical drop within the first ~50 iterations, falling below 0.1. Continues a gradual decline, converging with the cluster of low-centrality lines near 0.0 by iteration 200 and remaining there. * **Human Well-being (Orange):** Starts very high (~0.56 at Iteration 0). Drops sharply but less vertically than the blue line, showing some volatility between iterations 0-100. It has a secondary peak around iteration 150 (~0.45) before entering a steady, gradual decline. It remains the second-highest line for most of the chart after iteration 200, ending at approximately 0.05 at iteration 1000. * **Feedback Mechanism (Green):** Starts moderately high (~0.45 at Iteration 0). Peaks early at approximately iteration 50 (~0.52). Then declines sharply, joining the low-centrality cluster below 0.1 by iteration 200. * **Adaptive (Red):** Starts high (~0.49 at Iteration 0). Shows a volatile decline in the first 100 iterations, with a notable dip and recovery. It falls below 0.1 by iteration 200 and remains near zero. * **Adaptability and Resilience of Cities (Purple):** Starts at a moderate level (~0.38 at Iteration 0). Declines rapidly and smoothly, reaching near-zero values by iteration 100 and staying there. * **Artificial Intelligence (AI) (Brown):** Exhibits a unique trend. Starts moderately (~0.35 at Iteration 0). Instead of an immediate drop, it rises to become the dominant line, peaking broadly between iterations 150-300 at approximately 0.43. After iteration 300, it begins a long, steady, and relatively smooth decline, but maintains a significantly higher centrality than all other nodes except "Human Well-being" for the entire duration. It ends at approximately 0.24 at iteration 1000. * **Environmental Sustainability (Pink):** Starts moderately (~0.44 at Iteration 0). Declines very rapidly, reaching near-zero by iteration 100 and remaining flat. * **Outcome (Gray):** Starts moderately (~0.39 at Iteration 0). Shows a volatile decline similar to "Adaptive," with a distinct dip around iteration 200 (~0.18). It stabilizes at a low level (~0.02-0.03) after iteration 300. * **Closed-loop Life Cycle Design (Yellow-green):** Starts moderately (~0.36 at Iteration 0). Declines rapidly, joining the near-zero cluster by iteration 200. * **Bio-inspired Materials (Cyan):** Starts moderately (~0.37 at Iteration 0). Declines rapidly, joining the near-zero cluster by iteration 200. **Spatial Grounding & Component Isolation:** * **Header Region (Title):** Clear and descriptive. * **Main Chart Region:** The plot area is dominated by two distinct visual groups after iteration 200: 1. **High-Centrality Group:** The brown line ("AI") and, to a lesser extent, the orange line ("Human Well-being") occupy the upper portion of the chart (centrality > 0.05). 2. **Low-Centrality Cluster:** The remaining eight lines converge into a dense, overlapping band very close to the x-axis (centrality ≈ 0.0 to 0.05). Individual lines in this cluster are difficult to distinguish after iteration 400. * **Footer Region (Axes):** Labels are clear. The x-axis extends slightly beyond the last data point at iteration 1000. ### Key Observations 1. **Initial Dominance and Collapse:** Several nodes ("Closed-Loop Life Cycle Design," "Human Well-being," "Feedback Mechanism") start with very high betweenness centrality (>0.5) but collapse within the first 10-20% of the iterations. 2. **The Anomaly of AI:** "Artificial Intelligence (AI)" is the clear outlier. It not only avoids the immediate collapse but gains centrality early on, sustaining a position of high importance throughout the entire process. Its decline is much more gradual. 3. **Convergence to Low Importance:** By iteration 400, 8 out of the 10 tracked nodes have betweenness centrality values at or very near zero, indicating they have ceased to act as significant bridges in the network. 4. **Two-Tiered Outcome:** The final state (iteration 1000) shows a clear hierarchy: "AI" is the most central bridge node (~0.24), "Human Well-being" is a distant second (~0.05), and all others are negligible. ### Interpretation This chart likely visualizes the results of a network analysis simulation, possibly in the context of systems design, innovation research, or conceptual modeling. "Betweenness Centrality" measures how often a node lies on the shortest path between other nodes, making it a key indicator of a node's role as a connector or broker of information/flow. The data suggests a dynamic process where the network structure rapidly reorganizes. Initially, many concepts act as critical bridges, but this structure is unstable. The network quickly evolves to rely on a much smaller set of concepts for connectivity. The sustained high centrality of **"Artificial Intelligence (AI)"** implies that, within the modeled system, AI consistently serves as a fundamental connector between other ideas or components throughout its evolution. Its role is not only persistent but becomes increasingly dominant as other potential bridges fade. The early collapse of nodes like **"Closed-Loop Life Cycle Design"** and **"Feedback Mechanism"** suggests these concepts, while initially important for connecting parts of the system, become either integrated into other processes (losing their distinct bridging role) or marginalized as the network optimizes. The **"Human Well-being"** node's trajectory is notable—it remains relevant as a secondary bridge, indicating it retains a consistent, though not primary, connecting function in the mature system. **Overall, the chart tells a story of network simplification and the emergence of a dominant, resilient connector (AI) from an initially complex and distributed bridging structure.** This could reflect a design process converging on a core technology, a knowledge network solidifying around a key paradigm, or a system finding its most efficient architecture. </details> Figure 14: Evolution of the top 10 bridge nodes over iterations, for $G_1$ . Each curve represents the betweenness centrality of a bridge node, indicating its role in facilitating knowledge integration. Nodes that initially had high centrality later declined, while some concepts maintained their influence throughout the graph’s evolution. The trends in Figure 14 reveal distinct patterns in how bridge nodes emerge, peak in influence, and decline over time. Notably, nodes such as Closed-Loop Life Cycle Design and Human Well-being exhibit high betweenness centrality in the early iterations, suggesting that they played a fundamental role in structuring the initial interdisciplinary landscape. However, as the knowledge graph expanded, these nodes saw a gradual decline in their centrality, indicating that their role as primary connectors was replaced by alternative pathways. A second class of bridge nodes, including Adaptability and Resilience of Cities and Artificial Intelligence (AI), maintained high centrality values for a longer duration, suggesting that certain concepts remain essential to interdisciplinary knowledge integration even as the graph evolves. These nodes acted as long-term knowledge stabilizers, facilitating interactions between different research domains throughout a significant portion of the knowledge expansion process. Interestingly, a subset of nodes, such as Feedback Mechanism and Outcome, gradually gained importance over time. Unlike early bridge nodes that peaked and declined, these nodes started with lower centrality but increased in influence in later iterations. This suggests that some interdisciplinary pathways only become critical after sufficient knowledge accumulation, reinforcing the idea that interdisciplinary roles are not static but continuously reorganize as the knowledge graph matures. Furthermore, we observe that by approximately iteration 400-600, most bridge nodes’ betweenness centrality values begin converging toward lower values, indicating that knowledge transfer is no longer reliant on a small set of nodes. This suggests that, as the graph expands, alternative pathways develop, leading to a more distributed and decentralized knowledge structure where connectivity is no longer dominated by a few highly influential nodes. These findings support the hypothesis that interdisciplinary pathways evolve dynamically, with early-stage knowledge formation relying on a few key concepts, followed by a transition to a more robust and distributed network where multiple redundant pathways exist. Future analyses will focus on: - Identifying which nodes replaced early bridge nodes as major interdisciplinary connectors in later iterations. - Comparing early vs. late-stage bridge nodes to assess whether earlier nodes tend to be general concepts, while later bridge nodes represent more specialized interdisciplinary knowledge. - Analyzing the resilience of the knowledge graph by simulating the removal of early bridge nodes to determine their structural significance. These results provide a perspective on how interdisciplinary linkages emerge, stabilize, and reorganize over time, offering insights into the self-organizing properties of large-scale knowledge systems. ### 2.10 Evolution of Betweenness Centrality Distribution To analyze the structural evolution of the knowledge graph, we next examine the distribution of betweenness centrality at different iterations. Betweenness centrality is a measure of a node’s importance in facilitating knowledge transfer between different parts of the network. Formally, the betweenness centrality of a node $v$ is given by: $$ C_B(v)=∑_s≠ v≠ t\frac{σ_st(v)}{σ_st}, \tag{1} $$ where $σ_st$ is the total number of shortest paths between nodes $s$ and $t$ , and $σ_st(v)$ is the number of those paths that pass through $v$ . A higher betweenness centrality indicates that a node serves as a critical intermediary in connecting disparate knowledge domains. Figure S3 presents histograms of betweenness centrality distribution at four key iterations (2, 100, 510, and 1024), illustrating the shifting role of bridge nodes over time. Initially, at Iteration 2, the network is highly centralized, with a small number of nodes exhibiting extremely high betweenness centrality (above 0.6), while the majority of nodes have near-zero values. This indicates that only a few nodes act as critical interdisciplinary connectors, facilitating nearly all knowledge transfer. By Iteration 100, the distribution has broadened, meaning that more nodes participate in knowledge transfer. The highest betweenness values have decreased compared to Iteration 2, and more nodes exhibit low but nonzero centrality, suggesting an increase in redundant pathways and reduced dependency on a few dominant bridge nodes. At Iteration 510, the distribution becomes more skewed again, with fewer nodes having high betweenness centrality and a stronger concentration at low values. This suggests that the network has undergone a phase of structural consolidation, where interdisciplinary pathways reorganize around fewer, more stable bridges. Finally, at Iteration 1024, the histogram shows that most nodes have low betweenness centrality, and only a few retain moderate values. This suggests that the network has matured into a more distributed structure, where no single node dominates knowledge transfer. The observed trend indicates that as the knowledge graph expands, the burden of interdisciplinary connectivity is increasingly shared among many nodes rather than concentrated in a few. These results suggest that the system undergoes a dynamic reorganization process, shifting from an initial hub-dominated structure to a more distributed and resilient network. Future work could potentially explore whether these trends continue as the graph scales further and whether the eventual network state remains stable or undergoes additional restructuring. To examine the overall structural properties of the knowledge graph, we analyzed the distribution of betweenness centrality across all iterations. Figure 15 presents a histogram of betweenness centrality values collected from all iterations of the knowledge graph. The distribution was generated by computing betweenness centrality for each iteration and aggregating all node values overall iterations. <details> <summary>x15.png Details</summary>  ### Visual Description ## Histogram: Distribution of Betweenness Centrality Across All Iterations ### Overview The image displays a histogram titled "Distribution of Betweenness Centrality Across All Iterations." It visualizes the frequency distribution of a network metric called "betweenness centrality" for a large set of nodes, aggregated across multiple iterations of a process or simulation. The data is presented on a semi-logarithmic scale, with the y-axis (frequency) using a base-10 logarithmic scale to accommodate the vast range in node counts. ### Components/Axes * **Chart Title:** "Distribution of Betweenness Centrality Across All Iterations" (centered at the top). * **X-Axis:** * **Label:** "Betweenness Centrality" * **Scale:** Linear scale from 0.0 to 0.7. * **Major Tick Marks:** 0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7. * **Y-Axis:** * **Label:** "Number of Nodes (Log Scale)" * **Scale:** Logarithmic scale (base 10). * **Major Tick Marks (Powers of 10):** 10⁰ (1), 10¹ (10), 10² (100), 10³ (1,000), 10⁴ (10,000), 10⁵ (100,000), 10⁶ (1,000,000). * **Data Series:** A single series represented by vertical blue bars. There is no legend, as the chart represents one dataset. * **Grid:** Horizontal dashed grid lines are present at each major y-axis tick (10⁰, 10¹, etc.). ### Detailed Analysis The histogram shows a highly right-skewed, heavy-tailed distribution. The vast majority of nodes have very low betweenness centrality, with the frequency dropping dramatically as centrality increases. **Approximate Data Points (Bar Heights):** | Centrality (Approx.) | Number of Nodes (Approx.) | | :--- | :--- | | ~0.0 | 1,500,000 | | ~0.02 | 20,000 | | ~0.04 | 7,000 | | ~0.06 | 4,000 | | ~0.08 | 2,000 | | ~0.10 | 800 | | ~0.12 | 600 | | ~0.14 | 400 | | ~0.16 | 150 | | ~0.18 | 100 | | ~0.20 | 100 | | ~0.22 | 50 | | ~0.24 | 60 | | ~0.26 | 180 | | ~0.28 | 160 | | ~0.30 | 90 | | ~0.32 | 50 | | ~0.34 | 40 | | ~0.36 | 60 | | ~0.38 | 90 | | ~0.40 | 50 | | ~0.42 | 90 | | ~0.44 | 30 | | ~0.46 | 10 | | ~0.48 | 8 | | ~0.50 | 10 | | ~0.52 | 10 | | ~0.56 | 1 | | ~0.58 | 1 | | ~0.70 | 1 | **Trend Verification:** The visual trend is a steep, near-exponential decay from the leftmost bin. The line of bar tops slopes sharply downward from left to right, with a minor, localized increase (a "bump") in the 0.24-0.28 range. The distribution becomes sparse and discontinuous beyond a centrality of 0.5. ### Key Observations 1. **Extreme Skew:** Over 99% of the nodes appear to have a betweenness centrality below 0.1. The single most frequent category is the lowest bin (0.0). 2. **Heavy Tail:** Despite the skew, there is a long tail extending to a centrality of 0.7, indicating the presence of a very small number of extremely central nodes. 3. **Logarithmic Scale Necessity:** The use of a log scale on the y-axis is essential. On a linear scale, all bars except the first would be visually indistinguishable from zero. 4. **Data Sparsity:** The rightmost portion of the chart (centrality > 0.5) shows significant gaps and isolated single-node bins, highlighting the rarity of high-centrality nodes. 5. **Local Peak:** A small but noticeable cluster of nodes exists in the 0.24-0.28 centrality range, suggesting a minor subgroup with moderately high importance. ### Interpretation This histogram characterizes the structural importance of nodes within a large network (or across iterations of a dynamic network). Betweenness centrality measures how often a node lies on the shortest path between other nodes. * **Network Structure:** The distribution suggests a **scale-free or hub-and-spoke-like network topology**. The overwhelming majority of nodes are peripheral, serving as endpoints rather than bridges. A tiny fraction of nodes (the "hubs" in the far-right tail) are critical connectors, controlling the flow of information or resources across the network. * **Robustness and Vulnerability:** Such a network is typically robust to random failures (removing a random node is unlikely to affect overall connectivity) but highly vulnerable to targeted attacks on the high-centrality hubs. * **Process Implications:** If this data comes from an iterative process (e.g., a simulation, optimization, or learning algorithm), it indicates that the process consistently identifies or creates a very small set of highly influential nodes. The local peak around 0.26 might represent a stable, secondary tier of important nodes that emerge under certain conditions. * **Data Quality Note:** The values are approximate, read from a visual chart. The exact counts, especially for the tallest bar and the sparse tail, should be verified from the source data for precise analysis. The log scale can sometimes mask the true magnitude of differences; the difference between 10⁶ and 10⁵ nodes is 900,000 nodes, not just one order of magnitude. </details> Figure 15: Distribution of betweenness centrality across all iterations, $G_1$ . The y-axis is log-scaled, showing the frequency of nodes with different centrality values. A small number of nodes dominate knowledge transfer, while most nodes exhibit near-zero centrality. The histogram in Figure 15 reveals a highly skewed distribution, where the majority of nodes exhibit near-zero betweenness centrality, while a small subset maintains significantly higher values. This pattern suggests that knowledge transfer within the network is primarily governed by a few dominant bridge nodes, which facilitate interdisciplinary connections. The presence of a long tail in the distribution indicates that these high-betweenness nodes persist throughout multiple iterations. Interestingly, the distribution also exhibits multiple peaks, suggesting that the network consists of different classes of bridge nodes. Some nodes act as long-term stable interdisciplinary connectors, while others emerge as transient bridges that facilitate knowledge transfer only for limited iterations. The log scale on the $y$ -axis reveals that while most nodes contribute little to betweenness centrality, a significant number of nodes still exhibit low but nonzero values indicating that knowledge flow is distributed across many minor pathways. Over multiple iterations, it is expected that betweenness centrality values redistribute, reducing dependency on early dominant nodes and leading to a more decentralized knowledge structure. These findings highlight that the knowledge graph maintains a core-periphery structure, where a few key nodes play a disproportionate role in bridging knowledge across disciplines. Future work will explore how the distribution evolves over time, identifying whether the network transitions toward a more evenly distributed structure or remains reliant on a small number of high-centrality nodes. ### 2.11 Evolution of Betweenness Centrality in the Knowledge Graph To analyze the structural evolution of the knowledge graph, we tracked the changes in betweenness centrality over 1,000 iterations. Betweenness centrality quantifies the extent to which a node serves as a bridge between other nodes by appearing on shortest paths. A node with high betweenness centrality facilitates interdisciplinary knowledge transfer by linking otherwise disconnected regions of the network. Figures 16 (a) and 16 (b) illustrate how mean and maximum betweenness centrality evolve over time. The first plot captures the average importance of nodes in knowledge transfer, while the second identifies the most dominant bridge nodes at each iteration. <details> <summary>x16.png Details</summary>  ### Visual Description ## Line Charts: Betweenness Centrality Metrics Over Iterations ### Overview The image displays two side-by-side line charts, labeled (a) and (b), which plot network centrality metrics against the number of iterations of an unspecified process. Both charts share the same x-axis ("Iteration") but measure different aspects of betweenness centrality on their respective y-axes. The charts use distinct colors (blue and red) and markers to differentiate the data series. ### Components/Axes **Chart (a) - Left Panel:** * **Title:** "Mean Betweenness Centrality Over Time" * **X-axis:** Label: "Iteration". Scale: Linear, from 0 to 1000, with major ticks at 0, 200, 400, 600, 800, 1000. * **Y-axis:** Label: "Mean Betweenness Centrality". Scale: Linear, from 0.00 to 0.12, with major ticks at 0.00, 0.02, 0.04, 0.06, 0.08, 0.10, 0.12. * **Legend:** Positioned in the top-right corner. Contains a blue line with a circular marker labeled "Mean Betweenness". * **Data Series:** A single blue line with circular markers. **Chart (b) - Right Panel:** * **Title:** "Maximum Betweenness Centrality Per Iteration" * **X-axis:** Label: "Iteration". Scale: Linear, from 0 to 1000, with major ticks at 0, 200, 400, 600, 800, 1000. * **Y-axis:** Label: "Max Betweenness Centrality". Scale: Linear, from 0.2 to 0.7, with major ticks at 0.2, 0.3, 0.4, 0.5, 0.6, 0.7. * **Legend:** Positioned in the top-right corner. Contains a red line with a circular marker labeled "Max Betweenness". * **Data Series:** A single red line with circular markers. ### Detailed Analysis **Chart (a) - Mean Betweenness Centrality:** * **Trend Verification:** The blue line exhibits a very sharp, near-vertical decline at the beginning, followed by a rapid deceleration in the rate of decrease, eventually approaching and stabilizing near zero. * **Data Points (Approximate):** * Iteration 0: ~0.118 (highest point). * Iteration ~10: ~0.082. * Iteration ~20: ~0.070. * Iteration ~50: ~0.035. * Iteration ~100: ~0.015. * Iteration ~200: ~0.008. * Iteration ~400: ~0.003. * Iteration ~600 to 1000: The value asymptotically approaches 0.000, appearing to be below 0.001 by iteration 1000. **Chart (b) - Maximum Betweenness Centrality:** * **Trend Verification:** The red line shows high initial volatility with a sharp spike, followed by a period of significant fluctuation, and then a more gradual, noisy decline over the remaining iterations. * **Data Points (Approximate):** * Iteration 0: ~0.70 (highest point, sharp spike). * Iteration ~5: ~0.15 (sharp drop to a local minimum). * Iteration ~10: ~0.56 (rebound). * Iteration ~50: ~0.52. * Iteration ~100: ~0.42. * Iteration ~200: ~0.40. * Iteration ~300: ~0.41. * Iteration ~400: ~0.38. * Iteration ~600: ~0.30. * Iteration ~800: ~0.26. * Iteration ~1000: ~0.24. ### Key Observations 1. **Contrasting Scales:** The mean centrality (chart a) operates on a much smaller scale (0.00-0.12) compared to the maximum centrality (chart b, 0.2-0.7), indicating that the average node's importance is low, but the most important node is significantly more central. 2. **Initial Transient Phase:** Both metrics show dramatic changes in the first ~50-100 iterations, suggesting a rapid reorganization of the network's structure early in the process. 3. **Convergence vs. Persistence:** The mean betweenness converges smoothly and quickly to near-zero. In contrast, the maximum betweenness, while trending downward, remains substantially above zero and exhibits persistent fluctuations, indicating that a few key nodes retain relatively high centrality throughout. 4. **Volatility:** Chart (b) is far more volatile than chart (a). The maximum centrality can change dramatically between consecutive iterations (e.g., the drop from ~0.70 to ~0.15), while the mean changes smoothly. ### Interpretation The data suggests a dynamic network process where the overall structure becomes increasingly decentralized over time. The rapid drop in **mean betweenness centrality** indicates that, on average, nodes become less critical for connecting other nodes in the network; shortest paths are likely being distributed more evenly or the network is fragmenting. However, the **maximum betweenness centrality** tells a more nuanced story. Its initial spike and subsequent high values imply that at least one node (or a small set of nodes) acts as a major hub or bridge early on. The gradual decline of this maximum value suggests these hubs slowly lose their dominant position, but the persistent fluctuations indicate the network's "backbone" or most critical pathways are unstable and shift between different nodes as the iterations progress. The process appears to move from a centralized, hub-dominated structure toward a more distributed one, but the presence of a persistently high maximum centrality shows the transition is incomplete, and key structural nodes remain important. This pattern is common in network optimization, resilience testing, or adaptive network models where connections are rewired or weighted over time. </details> Figure 16: Evolution of betweenness centrality in the knowledge graph, $G_1$ . Panel (a): Mean betweenness centrality over time, showing a transition from early high centralization to a more distributed state. Panel (b): Maximum betweenness centrality per iteration, highlighting how the most dominant bridge nodes shift and decline in influence. Figure 16 (a) tracks the mean betweenness centrality, providing insight into how the overall distribution of knowledge transfer roles evolves. In the earliest iterations, the mean betweenness is extremely high, indicating that only a few nodes dominate knowledge exchange. However, as the graph expands and alternative pathways form, the mean betweenness declines rapidly within the first 100 iterations. Between iterations 100 and 500, we observe a continued decline, but at a slower rate. This suggests that knowledge transfer is being shared across more nodes, reducing reliance on a small set of dominant bridges. After iteration 500, the values stabilize near zero, indicating that the network has reached a decentralized state, where multiple nodes contribute to knowledge integration instead of a few key intermediaries. These trends suggest a self-organizing process, where the knowledge graph transitions from a highly centralized system into a more distributed and resilient network. The final structure is more robust, with many small bridges collectively supporting interdisciplinary connectivity instead of a few dominant hubs. Figure 16 (b) examines the highest betweenness centrality recorded in each iteration, tracking the most dominant knowledge bridge at each stage. In the earliest iterations, a single node reaches an extreme betweenness value of around 0.7, indicating that knowledge transfer is highly bottlenecked through one or very few key nodes. Between iterations 50 and 300, the maximum betweenness remains high, fluctuating between 0.3 and 0.5. This suggests that while the network becomes less dependent on a single node, a small number of highly central nodes still dominate knowledge flow. This phase represents a transition period, where the network starts distributing knowledge transfer across multiple nodes. After iteration 500, the maximum betweenness exhibits a gradual decline, eventually stabilizing around 0.2. This suggests that the network has successfully decentralized, and knowledge transfer is no longer dominated by a single key node. The presence of multiple lower-betweenness bridge nodes implies that redundant pathways have developed, making the system more resilient to disruptions. This is in general agreement with earlier observations. The combined results from Figures 16 (a) and 16 (b) suggest that the knowledge graph undergoes a fundamental structural transformation over time: - Initially, a few dominant nodes control knowledge flow, leading to high mean and maximum betweenness centrality. - As the graph expands, new pathways emerge, and betweenness is distributed across more nodes. - By the later iterations, no single node dominates, and knowledge transfer occurs through a decentralized structure. This evolution suggests that the knowledge graph self-organizes into a more distributed state, where interdisciplinary connectivity is no longer constrained by a few central hubs. Future studies can explore whether this trend continues at larger scales and analyze which specific nodes maintained high betweenness longest and which replaced them in later iterations. ### 2.12 Analysis of longest shortest path in $G_2$ and analysis using agentic reasoning While the primary focus of this study is targeting a detailed analysis of graph dynamic experiments during reasoning, we also explore how graph reasoning based on the in-situ generated graph can be used to improve responses through in-context learning [11] (here, we use meta-llama/Llama-3.2-3B-Instruct). The methodology employs a graph-based reasoning framework to enhance LLM responses through structured knowledge extraction obtained through the method described above. Figure 17 (b) depicts additional analysis, showing a correlation heatmap of path-level metrics, computed for the first 30 longest shortest paths. <details> <summary>x17.png Details</summary>  ### Visual Description ## [Combined Figure]: Knowledge Graph and Correlation Heatmap ### Overview The image is a composite figure containing two distinct technical visualizations labeled (a) and (b). Part (a) is a knowledge graph or concept map illustrating relationships between concepts in materials science, sustainability, and data analysis. Part (b) is a correlation heatmap displaying the statistical relationships between seven different network path metrics. The overall purpose appears to be demonstrating conceptual connections and quantitative relationships within a research domain, likely related to network analysis of materials or sustainability systems. ### Components/Axes **Part (a) - Knowledge Graph:** * **Central Node:** "Impact-Resistant Materials" (large, purple-outlined circle, positioned right-of-center). * **Connected Nodes (with relationship labels):** * "Self-healing Materials" (connected via "RELATES-TO") * "Environmental Sustainability" (connected via "INFLUENCES") * "Machine Learning (ML) Algorithms" (connected via "RELATES-TO") * **Secondary Nodes & Relationships (forming two main branches):** * **Top-Left Branch (Materials/Sustainability):** * "Self-healing Materials in Infrastructure Design" (connected to "Self-healing Materials" via "RELATES-TO") * "Development of novel materials for infrastructure design" (connected to "Self-healing Materials in Infrastructure Design" via "INFLUENCES") * "Pollution Mitigation" (connected to "Development of novel materials..." via "INFLUENCES" and to "Environmental Sustainability" via "RELATES-TO") * "Materials for infrastructure design" (connected to "Biodegradable Microplastic Materials" via "IS-A") * "Biodegradable Microplastic Materials" (connected to "Pollution mitigation" via "RELATES-TO") * **Bottom-Left Branch (Data/AI):** * "Predictive Modelling" (connected to "Machine Learning (ML) Algorithms" via "RELATES-TO") * "AI Techniques" (connected to "Predictive Modelling" via "RELATES-TO") * "Data Analysis" (connected to "AI Techniques" via "RELATES-TO" and to "Knowledge Discovery" via "IS-A") * "Knowledge Discovery" (connected to "Personalized Medicine" via "INFLUENCES") * "Personalized Medicine" (connected to "Rare Genetic Disorders" via "RELATES-TO") **Part (b) - Correlation Heatmap:** * **Title:** "Correlation Between Path Metrics" * **Axes (Identical for rows and columns):** 1. Avg Degree 2. Avg Betweenness 3. Avg Closeness 4. Avg Eigenvector 5. Avg PageRank 6. Avg Clustering 7. Path Density * **Legend/Color Scale:** A vertical bar on the right side. The scale runs from **1.0 (bright yellow)** at the top, through green and teal, to **0.0 (dark purple)**, and down to **-0.17 (very dark purple/black)** at the bottom. The scale is labeled at 0.0, 0.2, 0.4, 0.6, 0.8, and 1.0. * **Data Matrix:** A 7x7 grid of colored cells, each containing a numerical correlation coefficient. ### Detailed Analysis **Part (a) - Knowledge Graph Content Details:** The graph maps a network of interdisciplinary concepts. The central hub is "Impact-Resistant Materials." One major branch connects this to themes of sustainable infrastructure (self-healing materials, pollution mitigation, biodegradable materials). Another major branch connects it to data-driven methodologies (machine learning, predictive modeling, AI, data analysis, knowledge discovery), which further links to applications in personalized medicine. The relationships are explicitly labeled as "RELATES-TO," "INFLUENCES," or "IS-A." **Part (b) - Correlation Heatmap Data Points:** The following correlation coefficients are extracted from the matrix. Values are read directly from the cells. The color of each cell corresponds to the value according to the legend (yellow = high positive, purple = low/negative). | Metric 1 (Row) | Metric 2 (Column) | Correlation Value | Visual Trend (Color) | | :--- | :--- | :--- | :--- | | **Avg Degree** | Avg Betweenness | 0.99 | Bright Yellow | | **Avg Degree** | Avg Closeness | 0.47 | Green-Teal | | **Avg Degree** | Avg Eigenvector | 0.88 | Yellow-Green | | **Avg Degree** | Avg PageRank | 0.95 | Bright Yellow | | **Avg Degree** | Avg Clustering | 0.25 | Teal | | **Avg Degree** | Path Density | 0.05 | Dark Purple | | **Avg Betweenness** | Avg Closeness | 0.41 | Green | | **Avg Betweenness** | Avg Eigenvector | 0.93 | Bright Yellow | | **Avg Betweenness** | Avg PageRank | 0.97 | Bright Yellow | | **Avg Betweenness** | Avg Clustering | 0.17 | Dark Teal | | **Avg Betweenness** | Path Density | -0.03 | Very Dark Purple | | **Avg Closeness** | Avg Eigenvector | 0.14 | Dark Teal | | **Avg Closeness** | Avg PageRank | 0.32 | Teal | | **Avg Closeness** | Avg Clustering | 0.65 | Light Green | | **Avg Closeness** | Path Density | 0.42 | Green | | **Avg Eigenvector** | Avg PageRank | 0.96 | Bright Yellow | | **Avg Eigenvector** | Avg Clustering | -0.02 | Very Dark Purple | | **Avg Eigenvector** | Path Density | -0.17 | Very Dark Purple (lowest) | | **Avg PageRank** | Avg Clustering | 0.05 | Dark Purple | | **Avg PageRank** | Path Density | -0.11 | Very Dark Purple | | **Avg Clustering** | Path Density | 0.52 | Green | *Note: The matrix is symmetric, so only the upper triangle is listed. The diagonal (a metric correlated with itself) is always 1.00 (bright yellow).* ### Key Observations **Knowledge Graph (a):** * The graph has a clear hub-and-spoke structure with "Impact-Resistant Materials" as the primary hub. * Two distinct thematic clusters emerge: one focused on **materials and environmental sustainability**, and another on **data science and AI techniques**. * "Environmental Sustainability" and "Machine Learning (ML) Algorithms" act as secondary hubs, connecting the central concept to broader fields. **Correlation Heatmap (b):** * **Strong Positive Correlations (>0.85):** There is a very strong cluster of high positive correlations between **Avg Degree, Avg Betweenness, Avg Eigenvector, and Avg PageRank**. These four metrics are highly interrelated (all pairwise correlations ≥ 0.88). * **Moderate Positive Correlations:** **Avg Closeness** shows moderate positive correlation with **Avg Clustering (0.65)** and **Path Density (0.42)**. * **Weak or Negative Correlations:** **Path Density** and **Avg Clustering** show very weak or negative correlations with the core group of four metrics (Degree, Betweenness, Eigenvector, PageRank). The strongest negative correlation in the table is between **Avg Eigenvector and Path Density (-0.17)**. * **Avg Clustering** is somewhat isolated, showing its strongest link with **Avg Closeness (0.65)** and weak links to most other metrics. ### Interpretation **What the data suggests:** This composite figure likely comes from a study analyzing a network (e.g., a citation network, a material property network, or a sustainability project network). Part (a) provides the conceptual framework, showing that the research sits at the intersection of advanced materials, sustainability, and data-driven methods. Part (b) provides quantitative analysis of the network's structure. The heatmap reveals that traditional centrality measures (Degree, Betweenness, Eigenvector, PageRank) are largely redundant for this specific network—they tell a very similar story about node importance. A researcher could likely use just one of these four without losing much information. In contrast, **Avg Closeness**, **Avg Clustering**, and **Path Density** capture different, complementary aspects of the network structure. The negative correlation between Eigenvector centrality and Path Density is particularly interesting; it suggests that nodes which are important based on their connections to other important nodes (high Eigenvector) tend to exist in regions of the network that are less densely connected overall (low Path Density). **How elements relate:** The knowledge graph (a) defines the *what*—the conceptual entities and their hypothesized relationships. The correlation matrix (b) analyzes the *how*—the statistical properties of the underlying network formed by these or similar concepts. The strong correlations in (b) validate that certain structural properties of the network co-occur, which might reflect the real-world interdependencies suggested by the links in (a). For example, the cluster of highly correlated centralities might correspond to the well-connected "hub" concepts visible in the graph. **Notable Anomalies:** The most notable anomaly is the stark divide between the tightly correlated group of four centrality metrics and the other three metrics. This is not always the case in network analysis and is a key finding for this specific dataset. It indicates that the network has a particular structure where global importance (PageRank, Eigenvector) is tightly coupled with local connectivity (Degree) and brokerage potential (Betweenness). </details> Figure 17: Longest shortest path analysis. Panel (a): Visualization of the longest shortest path (diameter path) in $G_2$ , presenting a fascinating chain of interdisciplinary relationships across medicine, data science and AI, materials science, sustainability, and infrastructure. Panel (b): Correlation heatmap of path-level metrics, computed for the first 30 longest shortest paths. Degree and betweenness centrality are highly correlated, indicating that high-degree nodes frequently serve as key connectors. Eigenvector centrality and PageRank also show strong correlation, highlighting their shared role in capturing node influence. Path density exhibits a weak or negative correlation with centrality measures, suggesting that highly connected nodes often form less dense structures. The metrics were computed for each path by extracting node-level properties (degree, betweenness, closeness, eigenvector centrality, PageRank, clustering coefficient) from the original graph and averaging them over all nodes in the path. Path density was calculated as the ratio of actual edges to possible edges within the path subgraph. Correlations were then derived from these aggregated values across multiple paths. The extracted longest shortest path depicted in Figure 17 (a) presents a compelling sequence of relationships spanning biotechnology, artificial intelligence, materials science, and sustainability, illustrating how advancements in one domain influence others. The overall logical flow is well-structured, with clear and expected progressions, such as Rare Genetic Disorders leading to Personalized Medicine and Knowledge Discovery, reflecting that the model captures the increasing role of AI in medical research. The sequence from AI Techniques to Predictive Modeling and Machine Learning (ML) Algorithms is similarly intuitive, as computational models underpin predictive simulations across disciplines (details on methods, see Section 4.5). However, some unexpected connections emerge, suggesting areas for further exploration. The link from Machine Learning (ML) Algorithms to Impact-Resistant Materials stands out – not as a weak connection, but as an intriguing suggestion of AI-driven materials design rather than mere discovery. Computational techniques, such as reinforcement learning and generative modeling, could optimize material structures for durability, opening new pathways in materials engineering. Another unconventional relationship is the transition from Biodegradable Microplastic Materials to Infrastructure Design. These two areas typically operate separately, yet this link may hint at the emergence of biodegradable composites for construction or sustainable materials engineering. Further investigation into the practical applications of biodegradable materials in structural design could strengthen this connection. A notable redundancy appears in the presence of Pollution Mitigation twice, spelled differently, which results from a lack of node merging rather than a distinct conceptual relationship. This duplication suggests that similar concepts are being represented as separate nodes, potentially affecting graph-based reasoning. Similarly, Self-Healing Materials in Infrastructure Design loops back to Pollution Mitigation, reinforcing an already established sustainability link. While valid, this repetition could be streamlined for clarity. We find that the logical progression effectively captures key interdisciplinary relationships while revealing areas for refinement. The structure underscores the increasing role of AI in materials science, the integration of sustainability into materials design, and the interplay between predictive modeling and physical sciences. Addressing node duplication and refining transitions between traditionally separate fields—such as biodegradable materials in construction—would enhance the clarity and coherence of the path, making it an even more insightful representation of scientific knowledge. Agentic Reasoning over the Path We apply an agentic model to analyze the longest shortest path. For this analysis, an agentic system first analyzes each node in the subgraph, then each of the relationships, and then synthesizes them into a “Final Synthesized Discovery” (in blue font for clarity). The analysis identifies key concepts such as biodegradable microplastics, self-healing materials, pollution mitigation, and AI-driven predictive modeling, ultimately synthesizing the Bio-Inspired, Adaptive Materials for Resilient Ecosystems (BAMES) paradigm. The resulting document, Supporting Text 1, presents the results. The proposed discovery proposes self-healing, bio-inspired materials that integrate microbial, plant, and animal-derived mechanisms with AI-driven optimization to create adaptive, environmentally responsive materials. By embedding microorganisms for pollutant degradation and leveraging machine learning for real-time optimization, the model suggests that BAMES extends conventional self-healing materials beyond infrastructure applications into active environmental remediation [43]. The concept of temporal memory, where materials learn from past environmental conditions and adjust accordingly, introduces a novel paradigm in smart materials [44]. Additionally, the hypothesis that interconnected materials could develop emergent, collective behavior akin to biological ecosystems presents an interesting perspective on material intelligence and sustainability [45, 46]. Agentic Compositional Reasoning We can formalize this approach further and induce agentic strategy to develop compositional reasoning (see, Section 4.5.1 for details). In this experiment, implement a systematic development of hierarchical reasoning over concepts, pairs of concepts, and so on. The resulting document is shown in Supporting Text 2, and Figure 18 shows a flowchart of the reasoning process. <details> <summary>x18.png Details</summary>  ### Visual Description ## Diagram: Interdisciplinary Research Pathway to "EcoCycle: A Sustainable Infrastructure Framework" ### Overview The image is a complex flowchart or concept map illustrating a research and development pathway. It shows how foundational scientific and engineering concepts ("Atomic Components") are combined into more applied research areas ("Pairwise Compositional Fusions"), which then synergize into broader interdisciplinary themes ("Bridge Synergies"), ultimately converging into a single, comprehensive framework called "EcoCycle." The diagram flows from left to right, with arrows indicating the direction of influence or composition. ### Components/Axes The diagram is organized into four vertical columns or regions, each with a distinct title and bordered by a colored rectangle. 1. **Region 1 (Leftmost): Atomic Components** * **Border Color:** Blue. * **Content:** 16 individual boxes, each representing a foundational research area or technology. All boxes have blue borders. * **List of Components (Top to Bottom):** * Materials for Infrastructure Design * Biodegradable Microplastic Materials * Pollution Mitigation * Self-healing Materials in Infrastructure Design * Development of Novel Infrastructure Materials * Self-healing Materials * Environmental Sustainability * Impact-Resistant Materials * Machine Learning (ML) Algorithms * Predictive Modeling * AI Techniques * Data Analysis * Knowledge Discovery * Personalized Medicine * Rare Genetic Disorders 2. **Region 2 (Center-Left): Pairwise Compositional Fusions** * **Border Color:** Red. * **Content:** 16 boxes, each representing a more applied research topic formed by combining one or two "Atomic Components." All boxes have red borders. * **List of Fusions (Top to Bottom):** * Eco-Resilient Infrastructure Design * Sustainable Pollution Mitigation * Smart Infrastructure for Sustainable Ecosystems * Autonomous Repairable Infrastructure * Sustainable Infrastructure Development * Environmental Self-Healing Systems * Eco-Repair Systems * Eco-Toughened Materials * Damage Forecasting Systems * Explainable Predictive Models * AI-Driven Predictive Systems * Explainable Machine Learning (XML) * Explainable Insights * Precision Medicine Informatics * Precision Medicine for Rare Genetic Disorders 3. **Region 3 (Center-Right): Bridge Synergies** * **Border Color:** Blue. * **Content:** 3 boxes representing high-level, interdisciplinary synthesis themes. Boxes have blue borders. * **List of Synergies (Top to Bottom):** * Environmental Sustainability + Tech Innovation * Holistic Understanding of Complex Systems * Convergence of Diverse Disciplines 4. **Region 4 (Rightmost): Final Expanded Discovery** * **Border Color:** Red. * **Content:** A single, culminating box with a red border. * **Final Output:** EcoCycle: A Sustainable Infrastructure Framework ### Detailed Analysis: Connection Flow The core information is in the directed arrows connecting the boxes. Below is a precise mapping of these connections. * **From Atomic Components to Pairwise Fusions:** * "Materials for Infrastructure Design" → "Eco-Resilient Infrastructure Design" * "Biodegradable Microplastic Materials" → "Sustainable Pollution Mitigation" * "Pollution Mitigation" → "Sustainable Pollution Mitigation" AND "Smart Infrastructure for Sustainable Ecosystems" * "Self-healing Materials in Infrastructure Design" → "Autonomous Repairable Infrastructure" * "Development of Novel Infrastructure Materials" → "Sustainable Infrastructure Development" * "Self-healing Materials" → "Environmental Self-Healing Systems" * "Environmental Sustainability" → "Environmental Self-Healing Systems" AND "Eco-Repair Systems" * "Impact-Resistant Materials" → "Eco-Toughened Materials" * "Machine Learning (ML) Algorithms" → "Damage Forecasting Systems" * "Predictive Modeling" → "Damage Forecasting Systems" AND "Explainable Predictive Models" * "AI Techniques" → "AI-Driven Predictive Systems" * "Data Analysis" → "AI-Driven Predictive Systems" AND "Explainable Machine Learning (XML)" * "Knowledge Discovery" → "Explainable Insights" * "Personalized Medicine" → "Precision Medicine Informatics" * "Rare Genetic Disorders" → "Precision Medicine for Rare Genetic Disorders" * **From Pairwise Fusions to Bridge Synergies:** * "Eco-Resilient Infrastructure Design" → "Environmental Sustainability + Tech Innovation" * "Sustainable Pollution Mitigation" → "Environmental Sustainability + Tech Innovation" * "Smart Infrastructure for Sustainable Ecosystems" → "Environmental Sustainability + Tech Innovation" * "Autonomous Repairable Infrastructure" → "Holistic Understanding of Complex Systems" * "Sustainable Infrastructure Development" → "Holistic Understanding of Complex Systems" * "Environmental Self-Healing Systems" → "Holistic Understanding of Complex Systems" * "Eco-Repair Systems" → "Convergence of Diverse Disciplines" * "Eco-Toughened Materials" → "Convergence of Diverse Disciplines" * "Damage Forecasting Systems" → "Convergence of Diverse Disciplines" * "Explainable Predictive Models" → "Convergence of Diverse Disciplines" * "AI-Driven Predictive Systems" → "Convergence of Diverse Disciplines" * "Explainable Machine Learning (XML)" → "Convergence of Diverse Disciplines" * "Explainable Insights" → "Convergence of Diverse Disciplines" * "Precision Medicine Informatics" → "Convergence of Diverse Disciplines" * "Precision Medicine for Rare Genetic Disorders" → "Convergence of Diverse Disciplines" * **From Bridge Synergies to Final Discovery:** * "Environmental Sustainability + Tech Innovation" → "EcoCycle: A Sustainable Infrastructure Framework" * "Holistic Understanding of Complex Systems" → "EcoCycle: A Sustainable Infrastructure Framework" * "Convergence of Diverse Disciplines" → "EcoCycle: A Sustainable Infrastructure Framework" ### Key Observations 1. **Asymmetric Input Density:** The "Convergence of Diverse Disciplines" Bridge Synergy receives the highest number of inputs (9 arrows), primarily from the AI, data science, and medicine-related Pairwise Fusions. In contrast, "Environmental Sustainability + Tech Innovation" receives only 3 inputs, all from infrastructure and environment-focused fusions. 2. **Interdisciplinary Leap:** The diagram explicitly connects traditionally separate fields. For example, "Personalized Medicine" and "Rare Genetic Disorders" (medical fields) are shown as foundational components that, through a series of fusions, contribute to a sustainable infrastructure framework. This suggests a model where insights from precision medicine (e.g., complex systems analysis, personalized solutions) are metaphorically or directly applied to infrastructure challenges. 3. **Hierarchical Synthesis:** The structure is a clear funnel. It starts with 16 atomic ideas, combines them into 16 more focused applications, synthesizes those into 3 broad interdisciplinary themes, and finally converges on 1 unified framework. This represents a systematic approach to innovation. 4. **Color-Coded Semantics:** The alternating blue/red borders between columns (Blue -> Red -> Blue -> Red) may be a purely visual design choice to distinguish stages, or it could imply a cyclical or complementary relationship between the stages. ### Interpretation This diagram is a conceptual model for creating "EcoCycle," presented as a novel, sustainable infrastructure framework. Its primary argument is that such a framework cannot emerge from civil engineering or environmental science alone. Instead, it requires the deliberate fusion of: * **Materials Science** (self-healing, biodegradable, impact-resistant materials). * **Environmental Science** (pollution mitigation, sustainability). * **Artificial Intelligence & Data Science** (ML, predictive modeling, explainable AI). * **Systems Theory** (holistic understanding of complex systems). * **Biomedical Informatics** (precision medicine, knowledge discovery). The inclusion of medical disciplines is the most striking and non-obvious connection. It implies that the methodology for handling rare genetic disorders—characterized by complex data, personalized interventions, and systems-level understanding—provides a valuable template for managing the complex, interconnected systems of sustainable infrastructure. The "Convergence of Diverse Disciplines" acts as the critical hub where these disparate data-driven and analytical approaches merge. Ultimately, the diagram posits that "EcoCycle" is not just a set of technologies, but a new *framework* born from a structured, interdisciplinary research pipeline. It visualizes innovation as a process of compositional synthesis, where foundational blocks are combined and recombined across traditional field boundaries to solve complex, modern challenges. </details> Figure 18: Compositional framework applied to the longest shortest path. The flowchart illustrates the hierarchical process of compositional reasoning, beginning with atomic components (fundamental scientific concepts, left, as identified in the longest shortest path (Figure 17 (a))) and progressing through pairwise fusions, bridge synergies, and a final expanded discovery. Each stage (Steps A, B, C and D) integrates concepts systematically, ensuring interoperability, generativity, and hierarchical refinement, culminating in the EcoCycle framework for sustainable infrastructure development. The example ultimately presents a structured approach to compositional scientific discovery, integrating principles from infrastructure materials science, environmental sustainability, and artificial intelligence to develop a novel framework for sustainable infrastructure, termed EcoCycle. As can be seen in Supporting Text 2 and in Figure 18, the compositional reasoning process proceeded through multiple hierarchical steps, ensuring the systematic combination of concepts with well-defined relationships. At the foundational level, atomic components were identified, each representing an independent domain concept, such as biodegradable microplastic materials, self-healing materials, predictive modeling, and knowledge discovery. These fundamental elements were then combined into pairwise fusions, leveraging shared properties to generate novel synergies. For instance, the fusion of self-healing materials with pollution mitigation led to environmental self-healing systems, integrating autonomous repair mechanisms with pollution reduction strategies. Similarly, combining impact-resistant materials with machine learning algorithms enabled damage forecasting systems, enhancing predictive maintenance in infrastructure. The validity of this compositional reasoning was established by ensuring that each fusion preserved the integrity of its constituent concepts while generating emergent functionalities. The process adhered to key compositionality principles: (1) Interoperability, ensuring that combined components interacted meaningfully rather than arbitrarily; (2) Generativity, whereby new properties emerged that were not present in the individual components; and (3) Hierarchical Refinement, wherein smaller-scale synergies were recursively integrated into higher-order bridge synergies. This led to overarching themes such as the intersection of environmental sustainability and technological innovation and the holistic understanding of complex systems, demonstrating the robustness of the approach. Ultimately, these synergies converged into the EcoCycle framework, encapsulating self-healing, eco-responsive, and AI-optimized infrastructure solutions. The structured composition ensured that emergent discoveries were not mere aggregations but cohesive, context-aware innovations, validating the methodological rigor of the compositional approach. Using a strategy of adhering to systematic composition principles, the method used here demonstrates how interdisciplinary insights can be synthesized into scientific concepts. For comparison, Supporting Text 3 shows the same experiment but where we use o1-pro in the final step of synthesis. Putting this into context, earlier work [47, 48, 49, 50] have highlighted significant limitations in large language models (LLMs) concerning their ability to perform systematic compositional reasoning, particularly in domains requiring logical integration and generalization. Our approach directly addresses these deficiencies by structuring reasoning processes in a progressive and interpretable manner. Despite possessing individual components of knowledge, LLMs often struggle to integrate these dynamically to detect inconsistencies or solve problems requiring novel reasoning paths. We mitigate this by explicitly encoding relationships between concepts within a graph structure. Unlike conventional LLMs that rely on associative pattern recognition or statistical co-occurrence [47], our structured approach mitigates the concerns of mere connectionist representations by enforcing rule-based, interpretable generalization mechanisms that allow for dynamic recombination of learned knowledge in novel contexts. Further, our approach ensures that each reasoning step builds upon prior knowledge in a structured hierarchy. Steps A-D in our framework progressively construct solutions by leveraging explicit connections between concepts, enforcing compositionality rather than assuming it. For example, our approach connects biodegradable microplastic materials with self-healing materials, not merely through surface-level similarities but through defined mechanisms such as thermoreversible gelation and environmental interactions. Instead of expecting an LLM to infer relationships in a single step, our agentic model progressively traverses reasoning graphs, ensuring that the final outcome emerges through logically justified intermediary steps. This not only reduces reliance on pattern memorization but also enhances interpretability and robustness in novel scenarios. Our model further enhances compositional reasoning through three key mechanisms: 1. Explicit Pathway Construction: By mapping dependencies between concepts in a structured graph, our model ensures that each step in the reasoning process is explicitly defined and logically connected. 1. Adaptive Contextual Integration: Instead of treating reasoning steps as isolated tasks, the model dynamically integrates intermediate results to refine its conclusions, ensuring that errors or inconsistencies in earlier stages are corrected before final predictions. 1. Hierarchical Synergy Identification: Our model analyzes multi-domain interactions through graph traversal and thereby identify emergent patterns that standard LLMs would overlook, enabling more robust and flexible reasoning. These mechanisms collectively establish a reasoning framework that mitigates compositional deficiencies and facilitates the structured synthesis of knowledge. Table 2 summarizes how our approach directly addresses key LLM limitations identified in earlier work. | Fails to compose multiple reasoning steps into a coherent process | Uses hierarchical reasoning with Steps A-D, ensuring progressive knowledge integration through structured dependencies. | | --- | --- | | Struggles to generalize beyond memorized patterns | Uses explicit graph structures to enforce systematic knowledge composition, allowing for novel reasoning paths. | | Overfits to reasoning templates, failing on unseen reformulations | Introduces pairwise and bridge synergies to enable dynamic recombination of knowledge through structured traversal and adaptive reasoning. | | Does not simulate "slow thinking" or iterative reasoning well | Implements an agentic model that explicitly traverses a reasoning graph rather than relying on a single forward pass, ensuring each step refines and validates prior knowledge. | Table 2: Comparison of limitations of conventional LLMs, and our approach addresses these. By explicitly structuring relationships between concepts, breaking down reasoning into progressive steps, and incorporating dynamic knowledge recombination, our approach achieves a higher level of structured compositionality that conventional LLMs struggle with. Future work could further refine this approach by introducing adaptive feedback loops, reinforcing causal reasoning, and incorporating quantitative constraints to strengthen knowledge synergies. Further analysis of these is left to future work, as they would exceed the scope of the present paper. The experiments show that principled approaches to expand knowledge can indeed be implemented using the methodologies described above, complementing other recent work that has explored related topics [29, 49, 23, 50, 47]. ### 2.13 Utilization of Graph Reasoning over Key Hubs and Influencer Nodes in Response Generation In this example, we analyze the knowledge graph $G_2$ using NetworkX to compute node centralities (betweenness and eigenvector centrality), identifying key hubs and influencers. Community detection via the Louvain method partitions the graph into conceptual clusters, extracting representative nodes per community. Key relationships are identified by examining high-centrality nodes and their strongest edges. These insights are formatted into a structured context and integrated into a task-specific prompt for LLM reasoning on impact-resistant materials, the same prompt that was used to construct the original graph. The model’s response is generated both with and without graph data, followed by a comparative evaluation based on graph utilization, depth of reasoning, scientific rigor, and innovativeness. Raw responses for both models are shown in Text Boxes Supplementary Information and Supplementary Information. Table S1 provides a detailed comparison, and Figure 19 compares responses based on four key evaluation metrics (Graph Utilization, Depth of Reasoning, Scientific Rigor, and Innovativeness, along with the overall score). <details> <summary>x19.png Details</summary>  ### Visual Description ## Grouped Bar Chart: Comparison of Responses on Impact-Resistant Material Design ### Overview This is a grouped bar chart comparing the performance scores of two different responses ("Response 1" and "Response 2") across five evaluation categories related to impact-resistant material design. The chart visually demonstrates that Response 1, which incorporates graph data, consistently scores equal to or higher than Response 2, which does not use graph data. ### Components/Axes * **Chart Title:** "Comparison of Responses on Impact-Resistant Material Design" (centered at the top). * **Y-Axis:** * **Label:** "Score" (rotated vertically on the left side). * **Scale:** Linear scale from 0 to 17.5, with major tick marks at intervals of 2.5 (0, 2.5, 5.0, 7.5, 10.0, 12.5, 15.0, 17.5). * **X-Axis:** * **Categories (from left to right):** "Graph Utilization", "Depth of Reasoning", "Scientific Rigor", "Innovativeness", "Overall Score". * The category labels are rotated approximately 30 degrees for readability. * **Legend:** Located in the top-left corner of the plot area. * **Red Square:** "Response 1 (With Graph Data)" * **Yellow Square:** "Response 2 (Without Graph Data)" * **Data Series:** Two series of vertical bars, one for each response, grouped by category. * **Response 1 (Red Bars):** Positioned as the left bar in each category group. * **Response 2 (Yellow Bars):** Positioned as the right bar in each category group. * **Data Labels:** Numerical values are displayed directly above each bar. ### Detailed Analysis The following table reconstructs the data presented in the chart. All values are exact as labeled. | Category | Response 1 (With Graph Data) Score | Response 2 (Without Graph Data) Score | Difference (R1 - R2) | | :--- | :---: | :---: | :---: | | **Graph Utilization** | 5 | 0 | +5 | | **Depth of Reasoning** | 4 | 3 | +1 | | **Scientific Rigor** | 4 | 4 | 0 | | **Innovativeness** | 5 | 3 | +2 | | **Overall Score** | 18 | 10 | +8 | **Trend Verification per Category:** 1. **Graph Utilization:** The red bar (R1) is significantly taller than the yellow bar (R2), which is at the baseline (0). 2. **Depth of Reasoning:** The red bar (R1) is slightly taller than the yellow bar (R2). 3. **Scientific Rigor:** The red (R1) and yellow (R2) bars are of equal height. 4. **Innovativeness:** The red bar (R1) is moderately taller than the yellow bar (R2). 5. **Overall Score:** The red bar (R1) is dramatically taller than the yellow bar (R2), representing the largest absolute difference on the chart. ### Key Observations * **Dominant Performance:** Response 1 outperforms or matches Response 2 in every single category. * **Maximum Disparity:** The greatest performance gap is in "Graph Utilization" (5 vs. 0), which is the defining characteristic separating the two responses. * **Parity Point:** The only category where the responses are equal is "Scientific Rigor" (both score 4). * **Aggregate Score:** The "Overall Score" (18 vs. 10) shows that the cumulative advantage of Response 1 is substantial, nearly double that of Response 2. * **Visual Hierarchy:** The "Overall Score" bars are the tallest and most visually prominent element, drawing immediate attention to the final comparison. ### Interpretation The data strongly suggests that the inclusion of graph data ("Response 1") has a positive and measurable impact on the evaluation of a response concerning impact-resistant material design. The advantage is not uniform but is most pronounced in the category directly related to the differentiating factor ("Graph Utilization"). The parity in "Scientific Rigor" indicates that both responses may be grounded in similar foundational knowledge or methodology. However, the superior scores for Response 1 in "Depth of Reasoning" and "Innovativeness" imply that the graph data does more than just fulfill a requirement; it likely enables deeper analysis and facilitates more creative or novel solutions. The "Overall Score" confirms that these incremental advantages across multiple dimensions compound into a significantly stronger final product. From a Peircean perspective, the chart itself is an icon of the performance gap, and the numerical labels are indices pointing to specific magnitudes. The interpretation is that visual data representation (graphs) is not merely an add-on but a critical tool for enhancing reasoning, innovation, and overall output quality in technical design contexts. The zero score for Response 2 in "Graph Utilization" is a stark outlier that fundamentally defines the comparison. </details> Figure 19: Comparison of Responses on Impact-Resistant Material Design. This plot compares two responses based on four key evaluation metrics: Graph Utilization, Depth of Reasoning, Scientific Rigor, and Innovativeness, along with the overall score. Response 1, which incorporates graph-based insights, AI/ML techniques, and interdisciplinary approaches, outperforms Response 2 in all categories. Response 2 follows a more conventional materials science approach without leveraging computational methods. The higher overall score of Response 1 highlights the benefits of integrating advanced data-driven methodologies in material design. ### 2.14 Use of an Agentic Deep Reasoning Model to Generate new Hypotheses and Anticipated Material Behavior Next, we use the SciAgents model [51] with the o3-mini reasoning model [52] as the back-end, and graph $G_2$ to answer this question: Create a research idea around impact resistant materials and resilience. Rate the novelty and feasibility in the end. The path-finding algorithm that integrates node embeddings and a degree of randomness to enhance exploration sampling strategy [51] extracts this sub-graph from the larger graph: Iterative Reasoning $i<N$ ⬇ Impact Resistant Materials -- IS - A -- Materials -- IS - A -- Impact - Resistant Materials -- INFLUENCES -- Modular Infrastructure Systems -- RELATES - TO -- Self - Healing Materials -- RELATES - TO -- Long - term Sustainability and Environmental Footprint of Infrastructure -- RELATES - TO -- Self - Healing Materials -- RELATES - TO -- Infrastructure -- IS - A -- Infrastructure Resilience -- RELATES - TO -- Smart Infrastructure -- RELATES - TO -- Impact - Resistant Materials -- RELATES - TO -- Machine Learning Algorithms -- RELATES - TO -- Impact - Resistant Materials -- RELATES - TO -- Resilience As described in [51] paths are sampled using a path-finding algorithm that utilizes both node embeddings and a degree of randomness to enhance exploration as a path is identified between distinct concepts. Critically, instead of simply identifying the shortest path, the algorithm introduces stochastic elements by selecting waypoints and modifying priority queues in a modified version of Dijkstra’s algorithm. This allows for the discovery of richer and more diverse paths in a knowledge graph. The resulting paths serve as the foundation for graph-based reasoning specifically geared towards research hypothesis generation, ensuring a more extensive and insightful exploration of scientific concepts. Visualizations of the subgraph are shown in Figure 20, depicting the subgraph alone (Figure 20 (a)) and the subgraph with second hops (Figure 20 (b), showing the deep interconnectness that can be extracted). <details> <summary>x20.png Details</summary>  ### Visual Description ## Network Diagrams: Sparse vs. Dense Connectivity ### Overview The image displays two distinct network diagrams, labeled (a) and (b), presented side-by-side on a white background. These are visual representations of nodes (circles) connected by edges (lines), illustrating relational structures. Diagram (a) shows a sparse, clustered network, while diagram (b) depicts a highly dense, complex network. No numerical data, axis titles, or legends are present. The only embedded text consists of the labels "(a)" and "(b)". ### Components/Axes * **Labels:** The text "(a)" is positioned in the top-left corner above the left diagram. The text "(b)" is positioned in the top-left corner above the right diagram. * **Nodes:** Represented as circles of varying sizes and colors. * **Edges:** Represented as curved lines connecting the nodes. * **Color Schemes:** * **Diagram (a):** Uses a monochromatic red/pink palette. Node colors range from dark red to light pink. Edge colors are shades of red. * **Diagram (b):** Uses a dual-color scheme. Nodes are primarily teal/dark cyan, with several prominent nodes in orange. Edges are a mix of teal and a brownish-gold color. ### Detailed Analysis #### Diagram (a): Sparse Network * **Structure:** A relatively simple, hierarchical-looking network with clear clusters. * **Node Analysis:** * One very large, dark red node is positioned on the left side, acting as a major hub. * A second large, dark red node is positioned towards the bottom-center. * Several medium-sized nodes (in medium red/orange) are connected to these hubs. * Numerous small nodes (in light pink) are connected to the medium nodes or directly to the large hubs. * **Edge Analysis:** Connections are clearly visible and not overly tangled. The edges form distinct pathways between the major hubs and the peripheral nodes. The network appears to have a core-periphery structure. #### Diagram (b): Dense Network * **Structure:** An extremely complex and densely interconnected network, resembling a "hairball" graph common in large-scale network visualization. * **Node Analysis:** * Hundreds of small teal nodes form the vast majority of the network. * Approximately 8-12 larger orange nodes are scattered throughout the structure, acting as significant hubs. One particularly large orange node is located in the lower-left quadrant. * **Edge Analysis:** The connections are so numerous and overlapping that they create a dense, textured web. The teal and gold edges are interwoven, making it difficult to trace individual connections. The overall shape is roughly spherical or globular. ### Key Observations 1. **Contrast in Scale and Complexity:** The primary observation is the stark contrast between the two networks. Diagram (a) is simple and interpretable, while diagram (b) is complex and opaque at first glance. 2. **Hub Identification:** Both networks feature hub nodes (large circles), but their prominence and number differ. Diagram (a) has 2-3 dominant hubs, while diagram (b) has multiple significant hubs (orange nodes) embedded within a sea of smaller nodes. 3. **Color Function:** In diagram (a), color (shade of red) appears to correlate with node size/importance. In diagram (b), color (orange vs. teal) is used to categorically distinguish hub nodes from peripheral nodes. 4. **Spatial Layout:** Diagram (a) has an open layout with visible white space. Diagram (b) is compact and fills its allotted space, indicating a much higher node and edge count. ### Interpretation These diagrams are likely used to visually communicate fundamental concepts in network science, such as scale-free networks, small-world properties, or the difference between simple and complex systems. * **Diagram (a)** could represent a small social group, a simple organizational chart, or a basic food web. Its structure suggests clear lines of influence or communication flowing through central hubs. * **Diagram (b)** is characteristic of large, real-world networks like the internet, a protein-protein interaction network, a large social media platform, or a citation network. The presence of multiple hubs (orange nodes) suggests a "scale-free" property, where a few nodes have very high connectivity. The dense interconnectivity implies robustness (the network can withstand many random failures) but also potential for rapid spread of information or contagion. The side-by-side comparison is a powerful visual tool to demonstrate how network properties change with size and complexity, moving from a system that is easily understood to one that requires computational analysis to decipher its patterns. The absence of specific labels or data indicates the image's purpose is conceptual illustration rather than presenting specific empirical findings. </details> Figure 20: Visualization of subgraphs extracted from $G_2$ by SciAgents, for use in graph reasoning. The left panel (a) represents the primary subgraph containing only nodes from the specified reasoning path. Node size is proportional to the original degree in the full network, highlighting key entities with high connectivity. The structure is sparse, with key nodes acting as central hubs in the reasoning framework. The right panel (b) represents an expanded subgraph that includes second-hop neighbors. Nodes from the original subgraph are colored orange, while newly introduced second-hop nodes are green. The increased connectivity and density indicate the broader network relationships captured through second-hop expansion. Larger orange nodes remain dominant in connectivity, while green nodes form supporting structures, emphasizing peripheral interactions and their contribution to knowledge propagation. This visualization highlights how expanding reasoning pathways in a graph framework integrates additional contextual information, enriching the overall structure.. The resulting document Supporting Text 4 presents the results of applying SciAgents to $G_2$ in the context of impact-resistant materials and infrastructure resilience. The graph representation serves as a structured framework for reasoning about the relationships between key concepts—impact-resistant materials, self-healing mechanisms, machine learning optimization, and modular infrastructure—by encoding dependencies and influences between them. Graph 2 specifically captures these interconnected domains as nodes, with edges representing logical or causal links, enabling a systematic exploration of pathways that lead to optimal material design strategies. The path traversal within the graph identifies key dependencies, such as how impact-resistant materials influence infrastructure resilience or how machine learning refines self-healing efficiency. This structured pathway-based reasoning allows SciAgents to generate research hypotheses that maximize cross-domain synergies, ensuring that material properties are not optimized in isolation but rather in concert with their broader applications in engineering and sustainability. Furthermore, graph traversal reveals emergent relationships—such as how integrating real-time sensor feedback into modular infrastructure could create self-improving materials—that might not be immediately evident through conventional linear analysis. Thus, the use of graph-based reasoning is pivotal in formulating a research framework that is not only interdisciplinary but also systematically optimized for long-term infrastructure resilience and material adaptability. In terms of specific content, the proposed research explores an advanced composite material that integrates carbon nanotube (CNT)-reinforced polymer matrices with self-healing microcapsules, embedded sensor networks, and closed-loop ML optimization. The goal is to create a dynamically self-improving material system that enhances impact resistance and longevity in modular infrastructure. The material design is structured around several key components: (1) CNT reinforcement (1–2 wt%) to improve tensile strength and fracture toughness, (2) self-healing microcapsules (50–200 $μ$ m) filled with polymerizable agents, (3) embedded graphene-based or PVDF strain sensors for real-time monitoring, and (4) adaptive ML algorithms that regulate stress distributions and healing responses. The proposal establishes interconnections between several domains, highlighting the interdisciplinary nature of the research: impact-resistant materials are a subset of general materials with enhanced energy dissipation properties, modular infrastructure benefits from these materials due to increased durability, self-healing materials reduce maintenance cycles, and machine learning optimizes real-time responses to structural stress. This holistic framework aims to advance infrastructure resilience and sustainability. The research hypothesizes that embedding self-healing microcapsules within a CNT-reinforced polymer matrix will yield a composite with superior impact resistance and adaptive repair capabilities. Expected performance gains include a 50% increase in impact energy absorption (surpassing 200 J/m²), up to 80% recovery of mechanical properties after micro-damage, an estimated 30% improvement in yield strain, a 50% extension in structural lifetime, and a 30% reduction in required maintenance interventions. The composite operates via a multi-scale integration strategy where nanoscale CNTs form a stress-bridging network, microscale healing agents autonomously restore structural integrity, and macroscale sensors collect real-time strain data to inform machine learning-based optimizations. The closed-loop ML system refines material responses dynamically, preemptively addressing stress concentrations before catastrophic failure occurs. This iterative self-optimization process is represented in the flowchart shown in Figure 21. Iterative Reasoning $i<N$ Impact Event (Material undergoes structural stress or damage) Sensor Detection (Real-time strain monitoring via embedded graphene/PVDF sensors) Machine Learning Analysis (Prediction of stress distribution, micro-damage evolution) Healing Response Adjustment (ML-optimized activation of microcapsules based on sensor data) Microcapsule Rupture and Repair (Self-healing agent polymerization to restore mechanical integrity) Material Performance Feedback (Updated data informs next optimization cycle) Adaptive Learning Cycle: Sensors collect new data, ML refines healing response Figure 21: Flowchart of the Self-Optimizing Composite System proposed by SciAgents after reasoning over $G_2$ . Upon an impact event, embedded sensors (cyan) detect strain changes and transmit real-time data to a machine learning system (violet). This system predicts stress evolution and dynamically adjusts healing response thresholds (light violet). Microcapsules containing polymerizable agents (green) rupture at critical points, autonomously restoring material integrity. A feedback mechanism (yellow) continuously refines the process, ensuring adaptive optimization over multiple impact cycles. The dashed feedback loop signifies that each iteration improves the material’s ability to predict and mitigate future stress events, making the system progressively more efficient. Compared to conventional high-performance composites such as ultra-high molecular weight polyethylene (UHMWPE) and standard carbon fiber-reinforced polymers, the proposed material demonstrates superior mechanical performance and autonomous damage remediation. Traditional impact-resistant materials typically absorb 120–150 J/m² of energy, whereas this system is designed to exceed 200 J/m². Additionally, existing self-healing materials recover only 50–60% of their mechanical properties, while this composite targets an 80% restoration rate. The modular design ensures seamless integration into existing infrastructure, supporting scalability and standardization. Beyond its core functions, the composite exhibits several emergent properties: (1) localized reinforcement zones where healing chemistry alters stress distributions, (2) increased energy dissipation efficiency over repeated impact cycles, (3) long-term self-improving feedback where ML-driven adjustments refine material performance, and (4) potential microstructural evolution, such as crystalline phase formation, that enhances impact resistance. These unexpected yet beneficial attributes highlight the adaptive nature of the material system. The broader implications of this research include significant economic and environmental benefits. By reducing maintenance frequency by 30%, the composite lowers infrastructure downtime and lifecycle costs. The extended service life translates to a 25–30% reduction in resource consumption and associated carbon emissions. While the upfront processing cost is higher due to advanced material fabrication and sensor integration, the long-term cost per operational year is projected to be competitive with, or superior to, existing alternatives. This interdisciplinary fusion of nanomaterials, self-healing chemistry, real-time sensor feedback, and machine learning-based control represents a fundamental shift from passive materials to smart, self-optimizing systems. The proposed research not only addresses impact resistance and self-repair but also pioneers an adaptable, continuously improving infrastructure material. The combination of rigorous experimental validation (e.g., ASTM mechanical testing, finite element modeling, and real-world simulations) ensures that the material’s theoretical advantages translate into practical performance gains. This research positions itself as a transformative solution for infrastructure resilience, bridging the gap between static engineering materials and dynamically intelligent, self-regulating composites. ## 3 Conclusion This work introduced a framework for recursive graph expansion, demonstrating that self-organizing intelligence-like behavior can emerge through iterative reasoning without predefined ontologies, external supervision, or centralized control. Unlike conventional knowledge graph expansion techniques that rely on static extractions, probabilistic link predictions, or reinforcement learning-based traversal, extensive test-time compute Graph-PReFLexOR graph reasoning actively restructures its own knowledge representation as it evolves, allowing for dynamic adaptation and autonomous knowledge synthesis. These findings are generally in line with other recent results that elucidated the importance of inference scaling methods [25, 52, 53, 26]. Through extensive graph-theoretic analysis, we found that the recursively generated knowledge structures exhibit scale-free properties, hierarchical modularity, and sustained interdisciplinary connectivity, aligning with patterns observed in human knowledge systems. The formation of conceptual hubs (Figures 4 - 5) and the emergence of bridge nodes (Figures 12) demonstrate that the system autonomously organizes information into a structured yet flexible network, facilitating both local coherence and global knowledge integration. Importantly, the model does not appear to saturate or stagnate; instead, it continuously reorganizes relationships between concepts by reinforcing key conceptual linkages while allowing new hypotheses to emerge through iterative reasoning (Figures 11 and 14). One of the most striking findings is the self-regulation of knowledge propagation pathways. The early stages of graph expansion relied heavily on a few dominant nodes (high betweenness centrality), but over successive iterations, knowledge transfer became increasingly distributed and decentralized (Figure S3). This structural transformation suggests that recursive self-organization naturally reduces bottlenecks, enabling a more resilient and scalable knowledge framework. Additionally, we observed alternating phases of conceptual stability and breakthrough, indicating that knowledge formation follows a punctuated equilibrium model, rather than purely incremental accumulation. More broadly, the recursive self-organization process produces emergent, fractal-like knowledge structures, suggesting that similar principles may underlie both human cognition and the design of intelligent systems [42]. Moreover, the potential role of bridge nodes—as connectors and as natural intervention points—is underscored by their persistent yet shifting influence, implying they could be strategically targeted for system updates or error correction in a self-organizing network. Additionally, the observed alternating phases of stable community formation punctuated by sudden breakthroughs appear to mirror the concept of punctuated equilibrium in scientific discovery [1], offering a promising framework for understanding the natural emergence of innovation. These insights extend the implications of our work beyond scientific discovery, hinting at broader applications in autonomous reasoning, such as adaptive natural language understanding and real-time decision-making in complex environments. We demonstrated a few initial use cases where we used graph structures in attempts towards compositional reasoning, as shown in Figure 18. ### 3.1 Graph Evolution Dynamics: Interplay of Network Measures The evolution of the knowledge graph reveals a complex interplay between growth, connectivity, centralization, and structural reorganization, with different network-theoretic measures exhibiting distinct yet interdependent behaviors over iterations. Initially, the system undergoes rapid expansion, as seen in the near-linear increase in the number of nodes and edges (Figure 4). However, despite this outward growth, the clustering coefficient stabilizes early (around 0.16), suggesting that the graph maintains a balance between connectivity and modularity rather than devolving into isolated clusters. This stabilization indicates that the system does not expand chaotically but instead integrates new knowledge in a structured and preferentially attached manner, reinforcing key concepts while allowing for exploration. One of the most informative trends is the evolution of betweenness centrality (Figure 16), which starts highly concentrated in a few key nodes but then redistributes over time, reflecting a transition from hub-dominated information flow to a more decentralized and resilient network. This shift aligns with the gradual stabilization of average shortest path length (around 4.5, see Figure 9) and the graph diameter (around 16–18 steps, see Figure 5), implying that while knowledge expands, it remains navigable and does not suffer from excessive fragmentation. Meanwhile, the maximum $k$ -core index (Figure 6) exhibits a stepwise increase, reflecting structured phases of densification where core knowledge regions consolidate before expanding further. This suggests that the system undergoes punctuated reorganization, where newly introduced concepts occasionally necessitate internal restructuring before further outward growth. Interestingly, the degree assortativity starts strongly negative (around -0.25) and trends toward neutrality (-0.05), indicating that high-degree nodes initially dominate connections but later distribute their influence, allowing mid-degree nodes to contribute to network connectivity. This effect is reinforced by the persistence of bridge nodes (Figures 6 - 16), where we see a long-tail distribution of interdisciplinary connectors—some nodes serve as transient links that appear briefly, while others persist across hundreds of iterations, indicating stable, high-impact conceptual connectors. Taken together, these experimentally observed trends suggest that the system self-regulates its expansion, dynamically shifting between growth, consolidation, and reorganization phases. The absence of saturation in key structural properties (such as new edge formation and bridge node emergence) indicates that the model supports continuous knowledge discovery, rather than converging to a fixed-state representation. This emergent behavior, where network-wide connectivity stabilizes while conceptual expansion remains open-ended, suggests that recursive graph reasoning could serve as a scalable foundation for autonomous scientific exploration, adaptive learning, and self-organizing knowledge systems. ### 3.2 Relevance in the Context of Materials Science The framework introduced in this work offers a novel paradigm for accelerating discovery in materials science by systematically structuring and expanding knowledge networks. Unlike traditional approaches that rely on static databases or predefined ontologies [54, 55, 56, 57, 58], our self-organizing method enables dynamic hypothesis generation, uncovering hidden relationships between material properties, synthesis pathways, and functional behaviors. The emergent scale-free networks observed in our experiments reflect the underlying modularity and hierarchical organization often seen in biological and engineered materials, suggesting that recursive graph-based reasoning could serve as a computational analogue to self-assembling and adaptive materials. Applied to materials design, the approach developed in this paper could reveal unexpected synergies between molecular architectures and macroscale performance, leading to new pathways for bioinspired, multifunctional, and self-healing materials. Future work can integrate experimental data directly into these reasoning loops, allowing AI-driven materials discovery to move beyond retrieval-focused recognition toward novel inference and innovation. We believe it is essential to bridge the gap between autonomous reasoning and materials informatics to ultimately create self-improving knowledge systems that can adaptively guide materials engineering efforts in real-time [59]. ### 3.3 Broader Implications The observations put forth in this paper have potential implications for AI-driven scientific reasoning, autonomous hypothesis generation, and scientific inquiry. As our results demonstrate, complex knowledge structures can self-organize without explicit goal-setting. This work challenges a prevailing assumption that intelligence requires externally imposed constraints or supervision. Instead, it suggests that intelligent reasoning may emerge as a fundamental property of recursive, feedback-driven information processing, mirroring cognitive processes observed in scientific discovery and human learning. Our experiments that directed the evolution of the thinking mechanisms towards a certain goal were provided with relational modeling that incorporated these concepts in a more pronounced manner, as expected, provisioning a powerful substrate for deeper reasoning. Future work could potentially explore extending this framework to multi-agent reasoning environments, cross-domain knowledge synthesis, and real-world applications in AI-driven research discovery. Additionally, refining interpretability mechanisms will be crucial for ensuring that autonomously generated insights align with human epistemic standards, minimizing risks related to misinformation propagation and reasoning biases. Bridging graph-theoretic modeling, AI reasoning, and self-organizing knowledge dynamics, allowed us to provide a step toward building AI systems capable of autonomous, scalable, and transparent knowledge formation on their own. We note that wile our agentic deep graph reasoning framework demonstrates promise in achieving self-organizing knowledge formation, several challenges remain. In particular, the computational scalability of recursive graph expansions and the sensitivity of emergent structures to parameter choices warrant further investigation. Future work should explore robust error-correction strategies, enhanced interpretability of evolving networks, and ethical guidelines to ensure transparency in autonomous reasoning systems, especially if deployed in commercial or public settings beyond academic research. Addressing these issues will not only refine the current model but also paves the way for its application in real-world autonomous decision-making and adaptive learning environments. ## 4 Materials and Methods We describe key materials and methods developed and used in the course of this study in this section. ### 4.1 Graph-PReFLexOR model development A detailed account of the Graph-PReFLexOR is provided in [27]. Graph-PReFLexOR (Graph-based Preference-based Recursive Language Modeling for Exploratory Optimization of Reasoning) is an AI model integrating in-situ graph reasoning, symbolic abstraction, and recursive reflection into generative modeling. The model was trained on a set of around 1,000 scientific papers in the biological materials and bio-inspired materials domain, as discussed in [27]. We refer readers to the original paper for implementation details, but provide a high-level summary here. The method defines reasoning as a structured mapping: $$ M:T→(G,P,A), \tag{2} $$ where a given task $T$ generates a knowledge graph $G=(V,E)$ with nodes $V$ representing key concepts and edges $E$ denoting relationships, abstract patterns $P$ capturing structural dependencies, and final answers $A$ . Inspired by category theory, the approach encodes knowledge through hierarchical inference, leveraging isomorphisms to generalize across domains. The model autonomously constructs symbolic representations via a reasoning phase marked by <|thinking|> … <|/thinking|> tokens, refining understanding before generating outputs. Recursive optimization can further improve logical coherence, aligning responses with generalizable principles, a particular feature that will be expanded on in this paper. To enhance the adaptability of structured reasoning, Graph-PReFLexOR employs an iterative feedback mechanism: $$ R_i+1=f_eval(R_i,F_i), \tag{3} $$ where $R_i$ denotes the intermediate reasoning at step $i$ , $F_i$ is the feedback applied to improve logical structure, and $f_eval$ evaluates alignment with domain principles. The final answer $A$ is derived after $N$ refinements as: $$ A=g(R_N). \tag{4} $$ Through the idea to explicitly model knowledge graphs and symbolic representations, this method attempts to bridge connectionist and symbolic paradigms, facilitating multi-step reasoning, hypothesis generation, and interdisciplinary knowledge expansion. Empirical evaluations in [27] demonstrated its capability to generalize beyond training data. In this study, we take advantage of the capability of Graph-PReFLexOR to generate graph representations on the fly over a great number of iterations during which the model continues to expand its reasoning tokens. ### 4.2 Iterative Unconstrained Graph Reasoning on General Topic We develop an iterative knowledge extraction pipeline to construct a structured knowledge graph using a LLM, following the flowchart shown in Figure 1. The method systematically expands a graph representation of relationships by extracting structured knowledge from model-generated reasoning sequences and generating follow-up queries to refine exploration. We use this method to construct $G_1$ . At the start of each run, the algorithm initializes an initial question or prompt. This can be very general or focus on a particular topic that defines the area of scientific inquiry. In the example, the topic is set as: Iterative Reasoning $i<N$ ⬇ prompt = " Discuss an interesting idea in bio - inspired materials science." The LLM then generates structured reasoning responses within the <|thinking|> … <|/thinking|> tokens. The response is processed to extract structured knowledge by isolating the graph. To convert the extracted knowledge into a structured representation, the model is queried with an additional instruction to transform the resulting raw text that contains the reasoning graph (denoted by {raw graph}) into a Python dictionary formatted for graph representation: Iterative Reasoning $i<N$ ⬇ You are an AI that extracts information from structured text and outputs a graph in Python dictionary format compatible with NetworkX. Given the following structured text: {raw graph} Output the graph as a Python dictionary without any additional text or explanations. Ensure the dictionary is properly formatted for immediate evaluation in Python. The output is parsed and structured using ast.literal_eval() to construct a directed graph $G_local^i$ in NetworkX, where nodes represent entities such as materials, properties, and scientific concepts, while edges encode relationships such as HAS, INFLUENCES, and SIMILAR-TO. At each iteration $i$ , the newly extracted knowledge graph is appended to an evolving global graph: $$ G←G∪G_local^i. \tag{5} $$ The extracted structure is parsed using: graph_code, graph_dict = extract_graph_from_text(graph) The graph is progressively expanded by adding newly introduced nodes and edges, ensuring that redundant relationships are not duplicated. The final knowledge graph is stored in multiple formats, including GraphML for structural analysis and PNG for visualization. To facilitate continued exploration, a follow-up question is generated at each iteration. The LLM is queried to produce a question that introduces a new aspect of the domain, ensuring an iterative, self-refining process that utilizes the previously generated entities and relations: Iterative Reasoning $i<N$ ⬇ Consider this list of topics / keywords. Formulate a creative follow - up question to ask about a totally new concept. Your question should include at least one of the original topics / keywords. Original list of topics / keywords: {latest extracted entities and relations} Reply only with the new question. The new question is: This ensures that subsequent queries remain contextually grounded in the domain while promoting scientific discovery. The generated question is appended to the reasoning token structure and fed back into the LLM, thereby continuing the iterative learning process. The algorithm runs for a total of $N$ iterations, progressively refining the knowledge graph. At each step, we track the growth of the graph by recording the number of nodes and edges over time. The final knowledge graph provides a structured and extensible representation of insights extracted from the LLM, enabling downstream analysis of emerging concepts. The reasoning process (Figure 1) unfolds sequentially over a period of several days (using a consumer GPU, like NVIDIA A6000 Ada). ### 4.3 Iterative Graph Reasoning on a Particular Topic As an alternative to the approach above, we can tailor the reasoning process to focus more strongly on a particular topic. We use this method to construct $G_2$ . For instance, at the beginning of each run, the algorithm is initialized with a user-defined topic: Iterative Reasoning $i<N$ ⬇ topic = " impact resistant materials " This variable defines the area of exploration and is dynamically incorporated into the model prompts. The LLM is then queried with a topic-conditioned instruction to generate structured reasoning tokens: Iterative Reasoning $i<N$ ⬇ Describe a way to design {topic}. The model generates textual responses that include explicit reasoning within the <|thinking|> … <|/thinking|> markers. As before, from this output, we extract structured knowledge by isolating the section labeled graph, to extract entity-relationship pairs. A follow-up question is generated at each iteration to drive the discovery process forward. This prompt ensures that new queries focus on underexplored aspects of the knowledge graph while maintaining the topic-conditioned structure: Iterative Reasoning $i<N$ ⬇ Consider this list of keywords. Considering the broad topic of {topic}, formulate a creative follow - up question to ask about a totally new aspect. Your question should include at least one of the original keywords. Original list of keywords: {latest extracted entities and relations} Reply only with the new question. The new question is: This ensures that each iteration remains contextually grounded in the specified domain while continuously expanding the knowledge graph. The process continues for $N$ steps, progressively refining the knowledge graph. At each iteration, we track the growth of the graph by recording the number of nodes and edges. The resulting knowledge graph serves as a structured repository of insights extracted from the LLM, enabling downstream analysis of materials properties and design principles. Naturally, other variants of these strategies could easily be devised, for instance to create other generalist graphs (akin to $G_1$ ) or specialized graphs (akin to $G_2$ ). Prompt engineering can be human-tailored or developed agentically by other AI systems. ### 4.4 Graph Analysis and Visualization Graph analysis and visualizations are conducted using NetworkX [60], Gephi [61], Cytoscope [62], Mermaid https://mermaid.js.org/, and various plugins within these packages. #### 4.4.1 Basic Analysis of Recursive Graph Growth over Reasoning Iterations To analyze the recursive expansion of the knowledge graph, we computed a set of graph-theoretic properties at each iteration using the NetworkX Python library. Graph data was stored in GraphML format, with filenames encoded to reflect the iteration number, allowing for chronological tracking of structural changes. Each graph was sequentially loaded and processed to extract key metrics that characterize its connectivity, topology, and hierarchical organization. The fundamental properties of the graph, including the number of nodes and edges, were directly retrieved from the graph structure. The degree distribution was computed across all nodes to derive the average degree, representing the mean connectivity per node, and the maximum degree, which highlights the most connected node at each iteration. To assess network cohesion, the largest connected component (LCC) was extracted by identifying the largest strongly connected component in directed graphs and the largest connected subgraph in undirected cases. The clustering coefficient was computed using the standard local clustering metric, which quantifies the likelihood that a node’s neighbors are also connected to each other. The average clustering coefficient was obtained by averaging over all nodes in the graph, providing insight into the tendency of local structures to form tightly connected clusters. To assess global connectivity and efficiency, we computed the average shortest path length (SPL) and the graph diameter within the largest connected component. The SPL was obtained by calculating the mean shortest path distance between all pairs of nodes in the LCC, while the diameter was determined as the longest shortest path observed in the component. Since these calculations are computationally expensive for large graphs, they were conditionally executed only when the LCC was sufficiently small or explicitly enabled in the analysis. For community detection, we applied the Louvain modularity algorithm using the community-louvain package. The graph was treated as undirected for this step, and the modularity score was computed by partitioning the graph into communities that maximize the modularity function. This metric captures the extent to which the graph naturally organizes into distinct clusters over iterations. The entire analysis pipeline iterated over a series of GraphML files, extracting the iteration number from each filename and systematically computing these metrics. The results were stored as time series arrays and visualized through multi-panel plots, capturing trends in network evolution. To optimize performance, computationally intensive operations, such as shortest path calculations and modularity detection, were executed conditionally based on graph size and software availability. To further examine the structural evolution of the recursively generated knowledge graph, we computed a set of advanced graph-theoretic metrics over iterative expansions. As before, the analysis was conducted over a series of iterations, allowing for the study of emergent network behaviors. The degree assortativity coefficient was computed to measure the correlation between node degrees, assessing whether high-degree nodes preferentially connect to similar nodes. This metric provides insight into the network’s structural organization and whether its expansion follows a preferential attachment mechanism. The global transitivity, defined as the fraction of closed triplets among all possible triplets, was calculated to quantify the overall clustering tendency of the graph and detect the emergence of tightly interconnected regions. To assess the hierarchical connectivity structure, we performed $k$ -core decomposition, which identifies the maximal subgraph where all nodes have at least $k$ neighbors. We extracted the maximum $k$ -core index, representing the deepest level of connectivity within the network, and computed the size of the largest $k$ -core, indicating the robustness of highly connected core regions. For understanding the importance of individual nodes in information flow, we computed average betweenness centrality over the largest connected component. Betweenness centrality quantifies the extent to which nodes serve as intermediaries in shortest paths, highlighting critical nodes that facilitate efficient navigation of the knowledge graph. Since exact computation of betweenness centrality can be computationally expensive for large graphs, it was performed only within the largest component to ensure feasibility. Additionally, we identified articulation points, which are nodes whose removal increases the number of connected components in the network. The presence and distribution of articulation points reveal structural vulnerabilities, highlighting nodes that serve as key bridges between different knowledge regions. #### 4.4.2 Prediction of Newly Connected Pairs To track the evolution of connectivity in the recursively expanding knowledge graph, we employed a random sampling approach to estimate the number of newly connected node pairs at each iteration. Given the computational cost of computing all-pairs shortest paths in large graphs, we instead sampled a fixed number of node pairs per iteration and measured changes in their shortest path distances over time. Sampling Strategy. At each iteration, we randomly selected 1,000 node pairs from the current set of nodes in the global knowledge graph. For each sampled pair $(u,v)$ , we computed the shortest path length in the graph using Breadth-First Search (BFS), implemented via nx.single_source_shortest_path_length(G, src). If a path existed, its length was recorded; otherwise, it was marked as unreachable. Tracking Newly Connected Pairs. To detect the formation of new connections, we maintained a record of shortest path distances from the previous iteration and compared them with the current distances. A pair $(u,v)$ was classified as: - Newly connected if it was previously unreachable ( $dist_before=None$ ) but became connected ( $dist_now≠None$ ). - Having a shorter path if its shortest path length decreased between iterations ( $dist_now<dist_before$ ). The number of newly connected pairs and the number of pairs with shortened paths were recorded for each iteration. Graph Integration and Visualization. At each iteration, the newly processed graph was merged into a global knowledge graph, ensuring cumulative analysis over time. The number of newly connected pairs per iteration was plotted as a time series, revealing patterns in connectivity evolution. This method effectively captures structural transitions, particularly the initial burst of connectivity formation followed by a steady-state expansion phase, as observed in the results. By employing this approach, we achieved a computationally efficient yet statistically robust estimate of network connectivity evolution, allowing us to analyze the self-organizing dynamics of the reasoning process over large iterative expansions. #### 4.4.3 Graph Structure and Community Analysis To examine the structural properties of the recursively generated knowledge graph, we performed a comprehensive analysis of node connectivity, degree distribution, clustering behavior, shortest-path efficiency, and community structure. The graph was loaded from a GraphML file using the NetworkX library, and various metrics were computed to assess both local and global network properties. Basic Graph Properties. The fundamental characteristics of the graph, including the number of nodes, edges, and average degree, were extracted. Additionally, the number of self-loops was recorded to identify redundant connections that may influence network dynamics. Graph Component Analysis. To ensure robust connectivity analysis, the largest connected component (LCC) was extracted for undirected graphs, while the largest strongly connected component (SCC) was used for directed graphs. This ensured that further structural computations were performed on a fully connected subgraph, avoiding artifacts from disconnected nodes. Degree Distribution Analysis. The degree distribution was computed and visualized using both a linear-scale histogram and a log-log scatter plot. The latter was used to assess whether the network exhibits a power-law degree distribution, characteristic of scale-free networks. Clustering Coefficient Analysis. The local clustering coefficient, which quantifies the tendency of nodes to form tightly connected triads, was computed for each node. The distribution of clustering coefficients was plotted, and the average clustering coefficient was recorded to evaluate the extent of modular organization within the network. Centrality Measures. Three centrality metrics were computed to identify influential nodes: (i) Betweenness centrality, which measures the extent to which nodes act as intermediaries in shortest paths, highlighting key connectors in the knowledge graph; (ii) Closeness centrality, which quantifies the efficiency of information propagation from a given node; (iii) Eigenvector centrality, which identifies nodes that are highly influential due to their connections to other high-importance nodes. Shortest Path Analysis. The average shortest path length (SPL) and graph diameter were computed to evaluate the network’s navigability. Additionally, a histogram of sampled shortest path lengths was generated to analyze the distribution of distances between randomly selected node pairs (2,000 samples used). Community Detection and Modularity. The Louvain modularity algorithm was applied (if available) to partition the network into communities and assess its hierarchical structure. The modularity score was computed to quantify the strength of the detected community structure, and the resulting partitions were visualized using a force-directed layout. #### 4.4.4 Analysis of Conceptual Breakthroughs The evolution of knowledge graphs is analyzed by processing a sequence of graph snapshots stored in GraphML format. Each graph is indexed by an iteration number, extracted using a regular expression from filenames of the form graph_iteration_#.graphml. The graphs are sequentially loaded and processed to ensure consistency across iterations. If the graph is directed, it is converted to an undirected format using the networkx.to_undirected() function. To ensure structural integrity, we extract the largest connected component using the networkx.connected_components() function, selecting the subgraph with the maximum number of nodes. For each iteration $t$ , we compute the degree distribution of all nodes in the largest connected component. The degree of a node $v$ in graph $G_t=(V_t,E_t)$ is given by: $$ d_t(v)=∑_u∈ V_{t}A_t(v,u) \tag{6} $$ where $A_t$ is the adjacency matrix of $G_t$ . The computed degree distributions are stored in a dictionary and later aggregated into a pandas DataFrame for further analysis. To track the emergence of top hubs, we define a node $v$ as a hub if it attains a high degree at any iteration. The set of top hubs is determined by selecting the nodes with the highest maximum degree across all iterations: $$ H=\{v\mid\max_td_t(v)≥ d_top,10\} $$ where $d_top,10$ is the degree of the 10th highest-ranked node in terms of maximum degree. The degree growth trajectory of each hub is then extracted by recording $d_t(v)$ for all $t$ where $v∈ V_t$ . To quantify the emergence of new hubs, we define an emergence threshold $d_emerge=5$ , considering a node as a hub when its degree first surpasses this threshold. The first significant appearance of a node $v$ is computed as: $$ t_emerge(v)=\min\{t\mid d_t(v)>d_emerge\} $$ for all $v$ where such $t$ exists. The histogram of $t_emerge(v)$ across all nodes provides a temporal distribution of hub emergence. To evaluate global network connectivity, we compute the mean degree at each iteration: $$ \bar{d}_t=\frac{1}{|V_t|}∑_v∈ V_{t}d_t(v) \tag{7} $$ capturing the overall trend in node connectivity as the knowledge graph evolves. Three key visualizations are generated: (1) the degree growth trajectories of top hubs, plotted as $d_t(v)$ over time for $v∈ H$ ; (2) the emergence of new hubs, represented as a histogram of $t_emerge(v)$ ; and (3) the overall network connectivity, visualized as $\bar{d}_t$ over iterations. #### 4.4.5 Structural Evolution of the Graphs: Knowledge Communities, Bridge Nodes and Multi-hop Reasoning We analyze the structural evolution of knowledge graphs by computing three key metrics: (1) the number of distinct knowledge communities over time, (2) the emergence of bridge nodes that connect different knowledge domains, and (3) the depth of multi-hop reasoning based on shortest path lengths. These metrics are computed for each iteration $t$ of the evolving graph and visualized as follows. The evolution of knowledge communities is measured using the Louvain modularity optimization algorithm, implemented via community.best_partition(), which partitions the graph into distinct communities. For each iteration, the number of detected communities $|C_t|$ is computed as: $$ |C_t|=|\{c\mid c=P_t(v),v∈ V_t\}| $$ where $P_t(v)$ maps node $v$ to its assigned community at iteration $t$ . The values of $|C_t|$ are plotted over iterations to track the subdivision and merging of knowledge domains over time. The emergence of bridge nodes, nodes that connect multiple communities, is determined by examining the community affiliations of each node’s neighbors. A node $v$ is classified as a bridge node if: $$ |C(v)|>1, where C(v)=\{P_t(u)\mid u∈ N( v)\} $$ and $N(v)$ represents the set of neighbors of $v$ . The number of bridge nodes is computed per iteration and plotted to analyze how interdisciplinary connections emerge over time. The depth of multi-hop reasoning is quantified by computing the average shortest path length for the largest connected component at each iteration: $$ L_t=\frac{1}{|V_t|(|V_t|-1)}∑_v,u∈ V_{t,v≠ u}d_sp(v,u) $$ where $d_sp(v,u)$ is the shortest path distance between nodes $v$ and $u$ , computed using networkx.average_shortest_path_length(). This metric captures the evolving complexity of conceptual reasoning chains in the knowledge graph. We generate three plots: (1) the evolution of knowledge communities, visualizing $|C_t|$ over time; (2) the emergence of bridge nodes, displaying the number of inter-community connectors per iteration; and (3) the depth of multi-hop reasoning, tracking $L_t$ as a function of iteration number. To analyze the temporal stability of bridge nodes in the evolving knowledge graph, we compute the persistence of bridge nodes, which quantifies how long individual nodes function as bridges across multiple iterations. Given the bridge node set $B_t$ at iteration $t$ , the persistence count for a node $v$ is defined as: $$ P(v)=∑_t1(v∈ B_t) $$ where $1(·)$ is the indicator function that equals 1 if $v$ appears as a bridge node at iteration $t$ , and 0 otherwise. This metric captures the frequency with which each node serves as a conceptual connector between different knowledge domains. To visualize the distribution of bridge node persistence, we construct a histogram of $P(v)$ across all detected bridge nodes, with kernel density estimation (KDE) applied for smoother visualization. The histogram provides insight into whether bridge nodes are transient or persist over multiple iterations. The persistence values are computed and stored in a structured dataset, which is then used to generate a plot of the histogram of bridge node persistence. To analyze the temporal dynamics of bridge node emergence, we construct a binary presence matrix that tracks when individual nodes first appear as bridges. The matrix is used to visualize the earliest bridge nodes over time, capturing the structural formation of key conceptual connectors. The binary presence matrix is defined as follows. Given a set of bridge node lists $B_t$ for each iteration $t$ , we construct a matrix $M$ where each row corresponds to an iteration and each column corresponds to a unique bridge node. The matrix entries are: $$ M_t,v=\begin{cases}1,&v∈ B_t\\ 0,&otherwise\end{cases} $$ where $M_t,v$ indicates whether node $v$ appears as a bridge at iteration $t$ . The full set of unique bridge nodes across all iterations is extracted to define the columns of $M$ . To identify the earliest appearing bridge nodes we compute the first iteration in which each node appears: $$ t_first(v)=\min\{t\mid M_t,v=1\} $$ The top 100 earliest appearing bridge nodes are selected by ranking nodes based on $t_first(v)$ , keeping those with the smallest values. The binary matrix is then restricted to these nodes. To capture early-stage network formation, the analysis is limited to the first 200 iterations, ensuring that the onset of key bridge nodes is clearly visible. The final presence matrix $M^\prime$ is reordered so that nodes are sorted by their first appearance, emphasizing the sequential nature of bridge formation. The matrix is visualized as a heatmap (Figure 13), where rows correspond to the top 100 earliest appearing bridge nodes and columns represent iterations. A blue-scale colormap is used to indicate presence (darker shades for active nodes). To analyze the evolution of key bridge nodes in the knowledge graph, we compute and track the betweenness centrality of all nodes across multiple iterations. Betweenness centrality quantifies the importance of a node as an intermediary in shortest paths and is defined as: $$ C_B(v)=∑_s≠ v≠ t\frac{σ_st(v)}{σ_st} $$ where $σ_st$ is the total number of shortest paths between nodes $s$ and $t$ , and $σ_st(v)$ is the number of those paths that pass through $v$ . This measure is recalculated at each iteration to observe structural changes in the network. The computational procedure is as follows: 1. Graph Loading: Graph snapshots are loaded from GraphML files, indexed by iteration number. If a graph is directed, it is converted to an undirected format using networkx.to_undirected() to ensure consistent betweenness computations. 1. Betweenness Centrality Calculation: For each graph $G_t$ at iteration $t$ , the betweenness centrality for all nodes is computed using networkx.betweenness_centrality(). 1. Time Series Construction: The computed centrality values are stored in a time-series matrix $B$ , where rows correspond to iterations and columns correspond to nodes: $$ B_t,v=C_B(v) ∀ v∈ V_t $$ Missing values (nodes absent in certain iterations) are set to zero to maintain a consistent matrix structure. To identify key bridge nodes, we extract the top ten nodes with the highest peak betweenness at any iteration: $$ H=\{v\mid\max_tB_t,v≥ B_top,10\} $$ where $B_top,10$ represents the 10th highest betweenness value recorded across all iterations. The time-series data is filtered to retain only these nodes. To visualize the dynamic role of key bridge nodes, we generate a line plot of betweenness centrality evolution where each curve represents the changing centrality of a top bridge node over iterations. This graph captures how structural importance fluctuates over time. ### 4.5 Agentic Approach to Reason over Longest Shortest Paths We employ an agentic approach to analyze structured knowledge representations in the form of a graph $G=(V,E)$ , where $V$ represents the set of nodes (concepts) and $E$ represents the set of edges (relationships). The methodology consists of four primary steps: (i) extraction of the longest knowledge path, (ii) decentralized node and relationship reasoning, (iii) multi-agent synthesis, and (iv) structured report generation. Path Extraction. The input knowledge graph $G$ is first converted into an undirected graph $G^\prime=(V,E^\prime)$ where $E^\prime$ contains bidirectional edges to ensure reachability across all nodes. We extract the largest connected component $G_c$ by computing: $$ G_c=\arg\max_S∈C(G^\prime)|S| $$ where $C(G^\prime)$ is the set of all connected components in $G^\prime$ . The longest shortest path, or diameter path, is determined by computing the eccentricity: $$ ε(v)=\max_u∈ Vd(v,u), $$ where $d(v,u)$ is the shortest path length between nodes $v$ and $u$ . The source node is selected as $v^*=\arg\max_v∈ Vε(v)$ , and the farthest reachable node from $v^*$ determines the longest path. Numerically, the longest paths are determined by computing node eccentricities using networkx.eccentricity(), which identifies the most distant node pairs in terms of shortest paths. The five longest shortest paths are extracted with networkx.shortest_path(). For each extracted path, we assign node-level structural metrics computed from the original graph. The node degree is obtained using networkx.degree(), betweenness centrality is computed with networkx.betweenness_centrality(), and closeness centrality is determined via networkx.closeness_centrality(). Each identified path is saved as a GraphML file using networkx.write_graphml() with these computed node attributes for further analysis. Decentralized Node and Relationship Reasoning. Each node $v_i∈ V$ and each relationship $e_ij∈ E$ along the longest path is analyzed separately. A language model $f_θ$ is prompted with: $$ LLM(v_i)=f_θ(``Analyze concept v_i in a novel scientific context.") $$ for nodes, and $$ LLM(e_ij)=f_θ(``Analyze relationship e_ij and hypothesize new implications.") $$ for relationships. This enables independent hypothesis generation at the atomic level. Multi-Agent Synthesis. The set of independent insights $I=\{I_1,I_2,\dots\}$ is aggregated, and a final inference step is performed using: $$ I_final=f_θ(``Synthesize a novel discovery from I.") $$ This allows the model to infer higher-order patterns beyond individual node-relationship reasoning. Structured Report Generation. The final response, along with intermediate insights, is formatted into a structured markdown report containing: - The extracted longest path - Individual insights per node and relationship - The final synthesized discovery This approach leverages multi-step reasoning and recursive inference, allowing for emergent discoveries beyond explicit graph-encoded knowledge. #### 4.5.1 Agent-driven Compositional Reasoning We employ a multi-step agentic approach that couples LLMs with graph-based compositional reasoning. To develop such an approach, we load the graph and locate its largest connected component. We compute eccentricities to identify two far-apart nodes, then extract the longest shortest path between them. Each node in that path becomes a “building block,” for which the LLM provides a concise definition, principles, and a property conducive to synergy (Step A). Next, we prompt the LLM to create pairwise synergies by merging adjacent building blocks, encouraging a short, compositional statement that unifies the nodes’ respective features (Step B). To deepen the layering of ideas, we consolidate multiple synergy statements into bridge synergies that capture cross-cutting themes (Step C). Finally, we issue a more elaborate prompt asking the LLM to integrate all building blocks and synergies into an expanded, coherent “final discovery,” referencing both prior statements and each node’s defining traits (Step D). This process yields a multi-step compositional approach, wherein each synergy can build on earlier results to reveal increasingly sophisticated connections. The initial steps A-C are carried out using meta-llama/Llama-3.2-3B-Instruct, whereas the final integration of the response in Step D is conducted using meta-llama/Llama-3.3-70B-Instruct. We also experimented with other models, such as o1-pro as discussed in the main text. ### 4.6 Scale free analysis To determine whether a given network exhibits scale-free properties, we analyze its degree distribution using the power-law fitting method implemented in the powerlaw Python package. The algorithm extracts the degree sequence from the input graph and fits a power-law distribution, estimating the exponent $α$ and lower bound $x_\min$ . To assess whether the power-law is a preferable fit, we compute the log-likelihood ratio (LR) between the power-law and an exponential distribution, along with the corresponding $p$ -value. A network is classified as scale-free if LR is positive and $p<0.05$ , indicating statistical support for the power-law hypothesis. The method accounts for discrete degree values and excludes zero-degree nodes from the fitting process. ### 4.7 Audio Summary in the Form of a Podcast Supplementary Audio A1 presents an audio summary of this paper in the style of a podcast, created using PDF2Audio (https://huggingface.co/spaces/lamm-mit/PDF2Audio [51]). The audio format in the form a conversation enables reader to gain a broader understanding of the results of this paper, including expanding the broader impact of the work. The transcript was generated using the o3-mini model [52] from the final draft of the paper. ## Code, data and model weights availability Codes, model weights and additional materials are available at https://huggingface.co/lamm-mit and https://github.com/lamm-mit/PRefLexOR. 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Buehler Laboratory for Atomistic and Molecular Mechanics Center for Computational Science and Engineering Schwarzman College of Computing Massachusetts Institute of Technology Cambridge, MA 02139, USA mbuehler@MIT.EDU <details> <summary>x21.png Details</summary>  ### Visual Description ## Network Graph: Complex Multi-Cluster Force-Directed Layout ### Overview The image is a high-density, force-directed network graph visualization. It displays a complex system of interconnected nodes (points) and edges (lines) arranged in a roughly circular, organic layout against a plain white background. The graph exhibits clear community structure, with distinct clusters of nodes connected more densely within themselves and more sparsely to other clusters. There is **no textual information, labels, titles, legends, or axis markers** present in the image. ### Components/Axes * **Nodes:** Represented as small circles. Their size varies, with some nodes appearing significantly larger than others (e.g., a prominent dark blue node in the lower-left quadrant, a bright green node in the upper-right quadrant). Node color varies across a broad spectrum. * **Edges:** Represented as thin, curved lines connecting nodes. The edges are colored, often matching or relating to the color of the nodes they connect. The density of edges is extremely high, creating a tangled, web-like appearance. * **Clusters/Communities:** The graph is organized into several major color-coded clusters: * **Lower-Left:** A dense cluster dominated by cyan and light blue nodes/edges, with a large, dark blue central node. * **Lower-Center:** A diffuse cluster of pink and light red nodes/edges. * **Upper-Right:** A dense cluster featuring bright green, magenta, and orange nodes/edges. * **Upper-Left:** A cluster with yellow and orange tones. * **Periphery:** Scattered nodes and edges in purple, grey, and other colors connect the major clusters or exist on the outskirts. * **Spatial Layout:** The clusters are not perfectly separated; they are interconnected by numerous long-range edges, indicating relationships between different communities. The overall shape is amorphous but contained within a circular boundary. ### Detailed Analysis * **Node Distribution:** Node density is highest within the identified color clusters. The largest nodes (by visual size) appear to be hub nodes within their respective communities (e.g., the dark blue hub in the cyan cluster, the bright green hub in the upper-right cluster). * **Edge Characteristics:** Edges are not straight lines but follow curved paths, typical of force-directed algorithms that minimize edge crossings and energy. The color of an edge often blends between the colors of the two nodes it connects, suggesting a potential gradient or relationship strength. * **Color Palette:** The visualization uses a wide, non-categorical color palette including: cyan, light blue, dark blue, pink, light red, magenta, bright green, yellow, orange, purple, and grey. Without a legend, the semantic meaning of these colors is unknown. They likely represent node attributes, community membership, or another categorical variable. * **Scale and Quantification:** There is no scale, axis, or numerical data provided. Therefore, it is impossible to extract specific data points, counts, or quantitative relationships. The analysis is purely topological and visual. ### Key Observations 1. **Clear Community Structure:** The most salient feature is the organization of the network into distinct, color-coded communities. This suggests the underlying data has strong modular properties. 2. **Presence of Hub Nodes:** Several communities appear to be organized around one or more significantly larger nodes, indicating a potential scale-free or hub-and-spoke topology within those clusters. 3. **High Inter-Connectivity:** Despite the clear clustering, there is a substantial number of edges connecting different communities, indicating the network is not fully segregated. Some clusters (like the cyan and pink ones) appear more interconnected than others. 4. **Global vs. Local Structure:** The graph shows both local cohesion (dense clusters) and global connectivity (long-range edges linking clusters), which is characteristic of many real-world networks like social networks, biological networks, or citation networks. 5. **Absence of Metadata:** The complete lack of labels, a legend, or a title is a critical limitation. It prevents any definitive interpretation of what the nodes, edges, or colors represent. ### Interpretation This visualization demonstrates the **structural properties of a complex network**. The force-directed layout successfully reveals the inherent community structure, which is a primary goal of such visualizations. * **What the data suggests:** The graph suggests the underlying system consists of several tightly-knit groups or modules (the color clusters) that interact with each other to a lesser degree. The presence of hub nodes implies that certain elements within these groups are disproportionately important or connected. * **How elements relate:** Nodes within the same color cluster are more likely to be connected to each other than to nodes in other clusters. The long-range edges represent bridges or weak ties between these communities, which are often crucial for information flow or system resilience in network theory. * **Notable anomalies/limitations:** The primary anomaly is the **complete absence of explanatory text**. For a technical document, this renders the graph an abstract illustration of network topology rather than an informative data visualization. To be actionable, it would require a legend explaining the color coding, labels for key hub nodes, and a title describing the network's context (e.g., "Co-authorship Network of AI Researchers, 2020-2025"). * **Peircean Investigation:** From a semiotic perspective, the image is an **icon** (it resembles a network) and an **index** (it is directly generated from data). However, without a **symbol** layer (text, labels, legend), its specific meaning is indeterminate. It effectively communicates the *existence* of structure and community but not the *identity* of that structure. The viewer can infer patterns but cannot derive factual conclusions about the subject matter. </details> Figure S1: Knowledge graph $G_1$ after around 1,000 iterations, under a flexible self-exploration scheme initiated with the prompt Discuss an interesting idea in bio-inspired materials science.. In this visualization, nodes/edges are colored according to cluster ID. <details> <summary>x22.png Details</summary>  ### Visual Description ## Network Diagram: Complex Multi-Cluster Graph ### Overview The image displays a complex, force-directed network graph or node-link diagram on a plain white background. It consists of numerous nodes (points) connected by curved edges (lines). The graph exhibits a clear community structure, with several dense clusters of nodes interconnected by sparser, longer-range links. There is no textual information, labels, axis titles, legends, or numerical data present in the image. ### Components/Axes * **Nodes:** Represented as small dots. Their size appears relatively uniform, with one notably larger, dark teal node located near the center of the largest cluster. Node color varies and seems to correspond to cluster membership. * **Edges:** Represented as thin, curved lines of varying colors. The color of an edge often matches the color of the nodes it connects, suggesting it may represent the type or strength of connection within a community. * **Clusters/Communities:** The graph is organized into several distinct, densely interconnected groups: 1. A large, central, and very dense cluster dominated by teal, blue, and purple nodes/edges. 2. A prominent cluster in the upper-left quadrant, characterized by bright green nodes and edges. 3. A cluster in the upper-right area, featuring orange and brown tones. 4. A distinct, somewhat isolated cluster in the lower-right quadrant, primarily orange. 5. A smaller, loose cluster in the lower-left, with pink and blue nodes. 6. Several peripheral, less dense groupings and individual nodes scattered around the main structure. * **Spatial Layout:** The overall shape is irregular. The largest cluster forms the core. The green cluster extends to the left, the orange/brown cluster to the upper right, and the isolated orange cluster to the lower right. Long, sweeping edges connect these major clusters across the white space. ### Detailed Analysis * **Trend Verification (Visual):** The diagram does not show trends over time or measured values. Instead, it visualizes relational data. The primary "trend" is the strong tendency for nodes of similar color to be densely connected to each other, forming tight communities. * **Data Points:** No numerical data points, coordinates, or quantitative values are provided. The information is purely topological and relational. * **Color-Coding:** The color palette is diverse and appears categorical. Key observed colors include: teal/dark cyan, bright green, orange, brown, purple, pink, blue, and yellow. The large central node is a distinct dark teal. * **Connectivity Pattern:** Within clusters, connections are extremely dense, creating a tangled, almost solid appearance. Between clusters, connections are fewer and more distinct, acting as bridges. Some nodes on the periphery have only one or two connections. ### Key Observations 1. **Absence of Text:** The image contains zero textual elements—no labels for nodes, no title, no legend explaining the color coding, and no scale or key. 2. **Clear Community Structure:** The most striking feature is the segmentation into color-coded communities. This is the primary information conveyed. 3. **Central Hub:** The single large, dark teal node in the central cluster suggests it may be a hub of high importance or connectivity within that community. 4. **Variable Cluster Density:** The central and green clusters appear most densely interconnected, while the lower-right orange cluster is somewhat more loosely structured. 5. **Long-Range Links:** A few edges span significant distances across the graph, connecting otherwise distant clusters (e.g., from the central cluster to the lower-right orange cluster). ### Interpretation This diagram is a visualization of a complex network, likely representing one of the following: * A **social network**, where nodes are individuals and edges are relationships, with colors representing different social circles or communities. * A **biological network**, such as a protein-protein interaction map or a neural network, where clusters represent functional modules. * A **information or citation network**, where nodes are documents or concepts, and clusters represent specific topics or fields. * A **computer network** topology. **What the data suggests:** The structure strongly indicates a **modular network**. The system is not random; it is composed of tightly-knit subgroups that are themselves interconnected. This is a hallmark of many real-world complex systems. The large central node could be a critical point of failure or a key influencer within its community. **Notable Anomalies/Limitations:** The complete lack of metadata (labels, legend, title) is the critical limitation. Without this context, the specific meaning of the clusters, the identity of the nodes, and the nature of the connections are entirely unknown. The visualization effectively shows *that* there is structure, but not *what* that structure represents. To derive actionable insight, this graph must be paired with its corresponding key and dataset. </details> Figure S2: Knowledge graph $G_2$ after around 500 iterations, under a topic-specific self-exploration scheme initiated with the prompt Describe a way to design impact resistant materials. Nodes/edges are colored according to cluster ID. <details> <summary>x23.png Details</summary>  ### Visual Description ## Histograms: Betweenness Centrality Distribution Across Iterations ### Overview The image displays a 2x2 grid of four histograms, each titled "Betweenness Centrality Distribution" followed by an iteration number in parentheses. The charts visualize how the distribution of betweenness centrality values for nodes in a network evolves over time (iterations). All charts use a logarithmic scale for the vertical axis (Number of Nodes) and a linear scale for the horizontal axis (Betweenness Centrality). ### Components/Axes * **Chart Type:** Four separate histograms (bar charts). * **Titles:** * Top-Left: "Betweenness Centrality Distribution (Iteration 2)" * Top-Right: "Betweenness Centrality Distribution (Iteration 100)" * Bottom-Left: "Betweenness Centrality Distribution (Iteration 510)" * Bottom-Right: "Betweenness Centrality Distribution (Iteration 1024)" * **X-Axis (All Charts):** Label: "Betweenness Centrality". The scale range varies per chart. * **Y-Axis (All Charts):** Label: "Number of Nodes (Log Scale)". The scale is logarithmic (base 10), with major grid lines at powers of 10 (10⁰, 10¹, 10², 10³). * **Visual Elements:** Blue bars with black outlines represent the frequency (node count) for bins of betweenness centrality values. Dashed horizontal grid lines correspond to the logarithmic y-axis ticks. ### Detailed Analysis **1. Iteration 2 (Top-Left)** * **X-Axis Range:** 0.0 to 0.7. * **Distribution:** Extremely sparse. The vast majority of nodes have a betweenness centrality near 0.0. * **Key Data Points (Approximate):** * A dominant bar at ~0.0 centrality reaches just below 10¹ (≈8-9 nodes). * A smaller bar at ~0.06 centrality has a height of ~2-3 nodes. * Isolated, single-node bars (height = 10⁰) appear at approximately 0.23, 0.31, 0.34, and 0.69. * **Trend:** The distribution is highly skewed with a few outlier nodes possessing very high centrality. **2. Iteration 100 (Top-Right)** * **X-Axis Range:** 0.00 to 0.40. * **Distribution:** More nodes are present, forming a clearer, right-skewed distribution. The maximum centrality value has decreased. * **Key Data Points (Approximate):** * The tallest bar at ~0.00 centrality is between 10² and 10³ (≈300-400 nodes). * A rapid decay follows: bars at ~0.01 (≈40 nodes), ~0.02 (≈15 nodes), ~0.03 (≈10 nodes), ~0.04 (≈5 nodes), ~0.05 (≈3 nodes). * A small cluster appears around 0.09 (≈3 nodes). * Isolated single-node bars are at ~0.14, ~0.15, ~0.25, and ~0.39. * **Trend:** The network has grown, and centrality is more distributed, though still heavily concentrated near zero. **3. Iteration 510 (Bottom-Left)** * **X-Axis Range:** 0.00 to 0.35. * **Distribution:** The number of nodes has increased by an order of magnitude. The distribution is smoother but still strongly right-skewed. * **Key Data Points (Approximate):** * The peak at ~0.00 centrality is now above 10³ (≈1500-2000 nodes). * The decay is more gradual: bars at ~0.01 (≈60 nodes), ~0.02 (≈20 nodes), ~0.03 (≈10 nodes), ~0.04 (≈5 nodes), ~0.05 (≈2 nodes). * A small bump appears at ~0.06 (≈2 nodes). * Isolated single-node bars are at ~0.11, ~0.16, and ~0.35. * **Trend:** Continued network growth. The "tail" of the distribution (nodes with moderate centrality) is becoming more populated. **4. Iteration 1024 (Bottom-Right)** * **X-Axis Range:** 0.00 to 0.25. * **Distribution:** Similar in shape to Iteration 510, but the maximum centrality value has further decreased. The total node count appears similar or slightly higher. * **Key Data Points (Approximate):** * The peak at ~0.00 centrality is again above 10³ (≈2000-3000 nodes). * The decay pattern is consistent: bars at ~0.01 (≈80 nodes), ~0.02 (≈25 nodes), ~0.03 (≈15 nodes), ~0.04 (≈3 nodes), ~0.05 (≈4 nodes), ~0.06 (≈2 nodes). * Isolated single-node bars are at ~0.11 and ~0.24. * **Trend:** The distribution appears to be stabilizing. The network is large, and high betweenness centrality (above 0.1) is becoming increasingly rare for individual nodes. ### Key Observations 1. **Network Growth:** The total number of nodes (inferred from the area under the histogram and the y-axis peak) increases dramatically from Iteration 2 to Iteration 1024. 2. **Concentration at Zero:** In all iterations, the mode of the distribution is at or very near a betweenness centrality of 0.0, indicating most nodes lie on very few or no shortest paths between other nodes. 3. **Decreasing Maximum Centrality:** The highest observed betweenness centrality value decreases steadily across iterations: ~0.69 (It. 2) → ~0.39 (It. 100) → ~0.35 (It. 510) → ~0.24 (It. 1024). 4. **Distribution Shape Evolution:** The distribution evolves from a few extreme outliers (It. 2) to a smooth, rapidly decaying right-skewed distribution (It. 100 onwards), characteristic of many real-world networks. 5. **Sparse Tail:** Even in later iterations, the "tail" of the distribution (centrality > 0.1) is populated by only a handful of nodes, often just one. ### Interpretation This sequence of histograms likely depicts the evolution of a growing network model (e.g., a preferential attachment or spatial network model) where betweenness centrality is being recalculated at each major iteration. * **What the data suggests:** The data demonstrates a fundamental property of many evolving networks: as the network grows, the *relative* importance of any single node as a bridge (measured by betweenness centrality) tends to diminish for the vast majority of nodes. While new nodes are added, the "load" of being on shortest paths becomes more distributed. The decreasing maximum centrality suggests the network is becoming less reliant on a few critical "hub" nodes for global connectivity, potentially indicating increased robustness. * **How elements relate:** The four charts are snapshots in time. The shift in x-axis range and y-axis magnitude directly visualizes the network's growth and the changing statistical properties of its node centrality. The consistent log-scale y-axis allows for comparison of distribution shape across orders of magnitude in node count. * **Notable anomalies/trends:** The most striking trend is the compression of the centrality range. The outlier node with centrality ~0.69 in Iteration 2 is a significant anomaly compared to later stages. Its disappearance suggests a major structural change in the network between Iteration 2 and 100, where the initial "bottleneck" structure was broken or diluted by subsequent growth. The stabilization between Iterations 510 and 1024 suggests the network may be approaching a steady-state statistical distribution for betweenness centrality. </details> Figure S3: Distribution of betweenness centrality across four iterations, $G_1$ . The $y$ -axis is in log scale, indicating the number of nodes with a given centrality value. The evolution suggests a transition from an early centralized state to a more distributed knowledge structure in later iterations. | Graph Utilization | 5/5 (Explicit use of graph-based insights for material selection and optimization) | 0/5 (No reference to graph data) | | --- | --- | --- | | Depth of Reasoning | 4/5 (Multi-step reasoning including AI/ML integration, degradation adaptability, and bioinspiration) | 3/5 (Structured approach but mostly standard materials science reasoning) | | Scientific Rigor | 4/5 (Logical relationships between material properties, AI/ML, and impact resistance) | 4/5 (Follows well-established materials science principles with clear reasoning) | | Innovativeness | 5/5 (Proposes unique ideas such as AI/ML-driven discovery, urban ecosystems, and adaptive materials) | 3/5 (Uses conventional material design strategies without novel insights) | | Overall Score | 18/20 (Superior interdisciplinary and computational approach) | 10/20 (Limited to conventional material design strategies) | Table S1: Comparison of Responses on Impact-Resistant Material Design with Annotated Scores. Response 1 achieves a higher score due to its interdisciplinary approach, explicit graph-based insights, and innovative integration of AI/ML. Text Box S1: Answer of the graph-reasoning model to the task Describe a way to design impact resistant materials. In this case, we extract key insights from a knowledge graph using centrality measures, Louvain community detection, and key relationship identification, integrating structured graph-based context into LLM prompts to enhance reasoning and evaluate response quality. Iterative Reasoning $i<N$ Iterative Reasoning $i<N$ Answer of the graph-reasoning model ⬇ Based on the knowledge graph insights, I will outline a design strategy for impact - resistant materials. ** Design Strategy:** 1. ** Material Selection and Optimization **: Utilize advanced materials science and machine learning algorithms to identify and optimize materials with inherent impact resistance properties. This can be achieved by analyzing the relationships between materials, their properties, and impact resistance. 2. ** Self - Healing Materials **: Incorporate self - healing materials into the design, which can repair cracks and damages autonomously. This can be achieved through the use of microcapsules, polymers, or other materials that can release healing agents in response to impact. 3. ** Adaptive Materials **: Design materials that can adapt to changing environmental conditions, such as temperature, humidity, or pressure. This can be achieved through the use of shape - memory alloys, polymers, or other materials that can change their properties in response to external stimuli. 4. ** Urban Ecosystems Integration **: Incorporate urban ecosystems into the design, which can provide a natural source of inspiration for impact - resistant materials. For example, studying the properties of urban algae farms or the self - healing properties of certain plants can inform the design of impact - resistant materials. 5. ** Artificial Intelligence (AI) and Machine Learning (ML) Integration **: Utilize AI and ML algorithms to analyze data from various sources, such as sensor data, material properties, and environmental conditions. This can help identify patterns and trends that can inform the design of impact - resistant materials. 6. ** Material Degradation and Adaptability **: Design materials that can adapt to material degradation over time. This can be achieved through the use of materials that can self - heal, self - repair, or self - renew. ** Key Materials and Technologies:** 1. ** Shape - Memory Alloys (SMAs)**: SMAs can be used to create adaptive materials that can change their properties in response to external stimuli. 2. ** Polymers **: Polymers can be used to create self - healing materials that can repair cracks and damages autonomously. 3. ** Graphene **: Graphene can be used to create ultra - strong and lightweight materials with high impact resistance. 4. ** Nanomaterials **: Nanomaterials can be used to create materials with enhanced impact resistance and self - healing properties. ** Design Considerations:** 1. ** Material Properties **: Consider the material properties, such as strength, stiffness, and toughness, when designing impact - resistant materials. 2. ** Environmental Conditions **: Consider the environmental conditions, such as temperature, humidity, and pressure, when designing impact - resistant materials. 3. ** Scalability **: Consider the scalability of the design, including the ability to manufacture and deploy the material at large scales. 4. ** Cost - Effectiveness **: Consider the cost - effectiveness of the design, including the cost of materials, manufacturing, and deployment. By following this design strategy, impact - resistant materials can be designed that are optimized for performance, scalability, and cost - effectiveness. Text Box S2: Answer of the base model to the task Describe a way to design impact resistant materials. Iterative Reasoning $i<N$ Iterative Reasoning $i<N$ Answer of the base model ⬇ Designing impact - resistant materials involves creating materials that can absorb and distribute the energy of an impact, reducing the likelihood of damage or failure. Here ’ s a step - by - step approach to designing impact - resistant materials: 1. ** Material Selection **: Choose a material with inherent properties that can absorb and dissipate energy, such as: * High - density materials (e. g., metals, ceramics) * Viscoelastic materials (e. g., rubber, polymers) * Energy - absorbing materials (e. g., foam, composites) 2. ** Microstructure Optimization **: Design the material ’ s microstructure to optimize energy absorption: * Create a hierarchical structure with multiple scales (e. g., nanoparticles, microparticles, macroscopic particles) * Incorporate defects or irregularities to increase the material ’ s energy - absorbing capacity * Use phase transformations or phase changes to absorb energy 3. ** Material Properties Engineering **: Engineer the material ’ s properties to enhance its impact resistance: * Increase the material ’ s stiffness and strength to resist deformation * Improve the material ’ s toughness by increasing its energy - absorbing capacity * Enhance the material ’ s viscoelastic properties to absorb and dissipate energy 4. ** Composite Materials **: Design composite materials that combine different materials to achieve enhanced impact resistance: * Use a matrix material (e. g., polymer, metal) to bind together reinforcement materials (e. g., fibers, particles) * Incorporate energy - absorbing materials (e. g., foam, rubber) into the composite * Use a hierarchical structure to optimize energy absorption 5. ** Testing and Validation **: Test and validate the material ’ s impact resistance using standardized tests (e. g., Charpy impact test, Izod impact test): * Measure the material ’ s energy absorption capacity * Evaluate the material ’ s ability to withstand different types of impacts (e. g., drop, impact, penetration) 6. ** Scaling and Optimization **: Scale up the material design and optimize it for specific applications: * Use computational models (e. g., finite element analysis, molecular dynamics) to simulate the material ’ s behavior under impact * Optimize the material ’ s design for specific applications (e. g., aerospace, automotive, sports equipment) Some examples of impact - resistant materials include: * Kevlar - reinforced polymers * Carbon fiber - reinforced polymers * High - density polyethylene (HDPE) foam * Rubber - based composites * Ceramic matrix composites By following these steps, designers can create impact - resistant materials that can withstand various types of impacts and reduce the risk of damage or failure. <details> <summary>x24.png Details</summary>  ### Visual Description ## [Multi-Panel Line Chart]: Network Metric Evolution Over Iterations ### Overview The image displays three separate line charts arranged horizontally, labeled (a), (b), and (c). Each chart plots a different network metric against the number of iterations (from 0 to 500) of an algorithm, likely a community detection or network optimization process. The charts share a common x-axis but have different y-axes and data series colors. ### Components/Axes * **Common X-Axis (All Charts):** * **Label:** `Iteration` * **Scale:** Linear, from 0 to 500. * **Major Tick Marks:** 0, 100, 200, 300, 400, 500. * **Chart (a) - Left Panel:** * **Title:** `Louvain Modularity vs. Iteration` * **Y-Axis Label:** `Modularity` * **Y-Axis Scale:** Linear, from 0.2 to 0.7. * **Data Series:** Magenta line with circular markers. * **Chart (b) - Center Panel:** * **Title:** `Avg Shortest Path vs. Iteration` * **Y-Axis Label:** `Avg SPL` (presumably Average Shortest Path Length) * **Y-Axis Scale:** Linear, from 2.0 to 5.0. * **Data Series:** Blue line with circular markers. * **Chart (c) - Right Panel:** * **Title:** `Diameter vs. Iteration` * **Y-Axis Label:** `Diameter` * **Y-Axis Scale:** Linear, from 4 to 16. * **Data Series:** Red line with circular markers. ### Detailed Analysis **Chart (a) - Louvain Modularity:** * **Trend:** The magenta line shows a very rapid, near-vertical increase from a low starting point, followed by a period of high-frequency fluctuation and a gradual, noisy ascent to a plateau. * **Data Points (Approximate):** * Iteration 0: Modularity ≈ 0.22 * Iteration ~10: Sharp rise to ≈ 0.65 * Iteration ~50: Reaches a local peak near 0.70 * Iteration 100-300: Fluctuates between ≈ 0.63 and 0.68 * Iteration 300-500: Gradually climbs and stabilizes near 0.70. **Chart (b) - Average Shortest Path Length (Avg SPL):** * **Trend:** The blue line exhibits a steep initial increase, a distinct peak, a subsequent decline to a trough, and then a final rise to a stable high value. * **Data Points (Approximate):** * Iteration 0: Avg SPL ≈ 1.7 * Iteration ~50: Sharp rise to a peak of ≈ 4.7 * Iteration ~150: Declines to a trough of ≈ 4.0 * Iteration ~300: Rises again to ≈ 5.0 * Iteration 350-500: Stabilizes with minor fluctuations around 4.9. **Chart (c) - Network Diameter:** * **Trend:** The red line demonstrates a step-like, discontinuous increase. It features sharp vertical jumps followed by extended horizontal plateaus. * **Data Points (Approximate):** * Iteration 0: Diameter = 3 * Iteration ~10: Jumps to 7 * Iteration ~20: Jumps to 9 * Iteration ~30: Jumps to 11 * Iteration ~50: Jumps to 13 * Iteration ~80-280: Plateaus at 10 (with a brief spike to 11 around iteration 180) * Iteration ~290: Jumps to 12 * Iteration ~300: Jumps to 15 * Iteration ~350-500: Drops to and stabilizes at 13. ### Key Observations 1. **Phase Transition:** All three metrics undergo dramatic changes within the first 100 iterations, suggesting a rapid restructuring of the network. 2. **Modularity vs. Path Length Correlation:** The initial spike in modularity (a) coincides with the spike in average shortest path length (b). This is a known trade-off in community detection: forming tight communities can increase the distance between nodes in different communities. 3. **Diameter Behavior:** The diameter (c) shows the most discrete, step-wise changes, indicating specific iterations where the longest shortest path in the network increases or decreases abruptly. 4. **Convergence:** All three metrics appear to reach a relatively stable state after approximately 350-400 iterations, suggesting the algorithm has converged. ### Interpretation This set of charts visualizes the evolution of a network's structural properties during an iterative optimization process, likely the Louvain method for community detection. * **What the data suggests:** The process successfully increases modularity (a measure of community strength) from a low value to a high, stable value (~0.7). However, this comes at the cost of increasing the average distance between nodes (Avg SPL) and the overall network diameter, especially in the early phases. The step-like changes in diameter are particularly insightful, revealing critical moments where the global connectivity of the network is reconfigured. * **How elements relate:** The three metrics are interconnected. As the algorithm partitions the network into more defined communities (rising modularity), it initially makes the network more "stretched" (rising SPL and diameter). The later dip in SPL while modularity remains high might indicate a secondary optimization phase where inter-community connections are refined without breaking apart the communities. * **Notable anomalies:** The temporary drop in diameter to 10 between iterations ~80-280, while modularity and SPL are still evolving, is interesting. It suggests a period where the network became more compact globally, even as its community structure was still being optimized. The final stabilization of all metrics indicates a robust, final community structure has been found. </details> Figure S4: Evolution of key structural properties in the recursively generated knowledge graph ( $G_2$ , focused on Describe a way to design impact resistant materials.): (a) Louvain modularity, showing stable community formation; (b) average shortest path length, highlighting efficient information propagation; and (c) graph diameter, demonstrating bounded hierarchical expansion. <details> <summary>x25.png Details</summary>  ### Visual Description ## Multi-Panel Figure: Network Metric Evolution Over Iterations ### Overview The image is a composite figure containing six distinct subplots arranged in a 2x3 grid. Each subplot is a line or scatter plot tracking a different network metric against a common x-axis labeled "Iteration," ranging from 0 to 500. The figure appears to document the evolution of various topological properties of a network (likely a graph) during an iterative process, such as a simulation, optimization, or growth algorithm. The plots are labeled (a) through (f) in the top-left corner of each panel. ### Components/Axes * **Layout:** 2 rows, 3 columns. * **Common X-Axis:** All six plots share the same x-axis label: "Iteration". The axis is marked with major ticks at 0, 100, 200, 300, 400, and 500. * **Individual Plot Titles & Y-Axes:** * **(a) Top-Left:** Title: "Degree Assortativity vs. Iteration". Y-axis Label: "Assortativity". Y-axis scale: -0.6 to 0.0 (with ticks at -0.6, -0.4, -0.2, 0.0). * **(b) Top-Center:** Title: "Global Transitivity vs. Iteration". Y-axis Label: "Transitivity". Y-axis scale: 0.00 to 0.20 (with ticks at 0.00, 0.05, 0.10, 0.15, 0.20). * **(c) Top-Right:** Title: "Max k-Core Index vs. Iteration". Y-axis Label: "Max k". Y-axis scale: 1 to 9 (integer ticks). * **(d) Bottom-Left:** Title: "Size of Largest k-Core vs. Iteration". Y-axis Label: "#Nodes in max k-core". Y-axis scale: 10 to 50 (with ticks at 10, 20, 30, 40, 50). * **(e) Bottom-Center:** Title: "Avg Betweenness vs. Iteration". Y-axis Label: "Betweenness". Y-axis scale: 0.00 to 0.35 (with ticks at 0.00, 0.05, 0.10, 0.15, 0.20, 0.25, 0.30, 0.35). * **(f) Bottom-Right:** Title: "#Articulation Points vs. Iteration". Y-axis Label: "Count". Y-axis scale: 0 to 500 (with ticks at 0, 100, 200, 300, 400, 500). * **Data Series Colors:** Each plot uses a distinct color for its data points/line: (a) Blue, (b) Green, (c) Red, (d) Purple, (e) Orange, (f) Teal/Dark Cyan. ### Detailed Analysis **Subplot (a): Degree Assortativity vs. Iteration (Blue)** * **Trend:** The series begins with high volatility in the first ~50 iterations, then stabilizes into a near-constant, slightly negative value. * **Data Points:** Starts at approximately -0.7 at iteration 0. Spikes sharply to a peak of ~0.1 at a very low iteration (<10). Fluctuates between -0.2 and 0.0 until iteration ~50. From iteration ~100 onward, it settles into a stable plateau at approximately -0.07 to -0.08, showing minimal variation through iteration 500. **Subplot (b): Global Transitivity vs. Iteration (Green)** * **Trend:** Shows a rapid initial increase to a peak, followed by a steady, decaying decline that eventually plateaus. * **Data Points:** Starts at 0.0 at iteration 0. Peaks rapidly at approximately 0.21 within the first ~20 iterations. Enters a consistent downward trend, crossing 0.15 around iteration 50, 0.10 around iteration 150. The decline slows, reaching a minimum of ~0.08 around iteration 300. It then shows a very slight recovery and stabilizes at approximately 0.09 from iteration 400 to 500. **Subplot (c): Max k-Core Index vs. Iteration (Red)** * **Trend:** A step function that increases monotonically in discrete jumps, with long plateaus. * **Data Points:** Starts at k=1. Jumps to k=2, then k=4, then k=6 in rapid succession within the first ~20 iterations. Plateaus at k=6 until approximately iteration 250. At iteration ~250, it jumps to k=8 and remains constant at k=8 until iteration 500. **Subplot (d): Size of Largest k-Core vs. Iteration (Purple)** * **Trend:** A complex, non-monotonic step function with periods of increase, sharp drops, and plateaus. * **Data Points:** Starts at ~10 nodes. Drops to ~5 nodes and plateaus until iteration ~80. Jumps to ~15 nodes, plateaus until iteration ~150. Experiences a rapid, multi-step increase, peaking at approximately 55 nodes around iteration 250. Suffers a sharp drop to ~27 nodes, plateaus briefly. Jumps to ~35 nodes, plateaus until iteration ~450. Finally, jumps to ~43 nodes and plateaus through iteration 500. **Subplot (e): Avg Betweenness vs. Iteration (Orange)** * **Trend:** A sharp, exponential-like decay from a high initial value to a near-zero asymptote. * **Data Points:** Starts at a very high value of ~0.34 at iteration 0. Plummets rapidly, falling below 0.10 by iteration ~20. The decay continues at a slower rate, reaching ~0.02 by iteration 100. From iteration 200 onward, the value is extremely close to zero (approximately 0.005 or less) and remains flat. **Subplot (f): #Articulation Points vs. Iteration (Teal)** * **Trend:** A steady, near-linear increase with minor fluctuations, showing no signs of plateauing. * **Data Points:** Starts at 0 at iteration 0. Increases consistently, reaching ~100 by iteration 100, ~200 by iteration 200, ~300 by iteration 300, ~400 by iteration 400, and ~500 by iteration 500. The line is not perfectly smooth but has small, frequent variations around the linear trend. ### Key Observations 1. **Phase Transition:** Most metrics (a, b, c, d, e) exhibit a volatile or rapidly changing "transient phase" within the first 50-100 iterations, followed by a more stable "steady-state phase." 2. **Correlated Events:** The sharp drop in the size of the largest k-core (d) around iteration 250 coincides exactly with the jump in the max k-core index (c) from 6 to 8. This suggests a major structural reorganization of the network's core at that point. 3. **Divergent Behavior:** The number of articulation points (f) is the only metric that shows continuous, unbounded growth throughout the entire process, unlike the others which stabilize or fluctuate within bounds. 4. **Inverse Relationship:** The average betweenness (e) decays to near-zero as the number of articulation points (f) grows large. This makes intuitive sense, as a network with many articulation points (whose removal disconnects the graph) likely has a more fragmented, less centralized path structure. ### Interpretation This figure collectively illustrates the topological evolution of a network undergoing an iterative process. The data suggests the process initially creates a dense, highly connected, and centralized structure (high transitivity, high betweenness, low articulation points). However, this structure is unstable. A critical reorganization occurs around iteration 250, where the core becomes more exclusive (higher k) but smaller in size, while the network simultaneously becomes more fragmented (increasing articulation points). The end state (iteration 500) is a network with a small, tight-knit core (high k-core index), low global clustering (transitivity), minimal central brokerage (betweenness), and a high number of vulnerable connection points (articulation points). This profile is characteristic of a network that has evolved or been optimized for a specific, possibly modular or hierarchical, function at the expense of robustness and global connectivity. The steady rise in articulation points is a particularly strong indicator of increasing fragility or specialization in the network's architecture. </details> Figure S5: Evolution of graph properties over recursive iterations, highlighting the emergence of hierarchical structure, hub formation, and adaptive connectivity (Graph $G_2$ , focused on Describe a way to design impact resistant materials.). See pages - of discovery_sample.pdf See pages - of compositional_1_20250217_140156.pdf See pages - of compositional_2_20250217_140156_o1-pro.pdf See pages - of proposal_1.pdf