Visualizing Graph-to-Answer Mechanism Recovery in Materials-Science Hypothesis Generation

AI co-scientists can generate fluent materials-science hypotheses, but fluency does not show that an answer preserves a scientifically meaningful mechanism. We present a graph-to-answer mechanism-tracing case study for Graph-PRefLexOR-8B, a Qwen3-8B model adapted to expose distinct stages for brainstorming, graph construction, pattern extraction, and synthesis. We organize semantic backtracking, graph corruption, activation-based recovery measurements, and layer-by-token-region grids into a visual diagnostic workflow for inspecting this pathway. Across 100 open-ended materials-science questions, final answers remain closest to the model's own structured stages, especially synthesis. Under graph corruption, a full sweep over 37 residual-stream checkpoints, the embedding output and 36 transformer blocks, shows little mechanism recovery in the earlier transition region at layers 7--10, recovery instead concentrates in late synthesis and answer-start regions around layers 30 and 36. The workflow is intended to help scientists and model developers identify where a generated hypothesis loses or regains mechanism support before it is passed to downstream experimental planning.

Reading and Steering Representations of Materials-Science Mechanisms in an Open-Weight Language Model

Large language models can answer scientific questions, yet a correct output does not reveal whether the model represents or uses the governing physics. Here we show that materials science mechanism information in the open-weight google/gemma-4-E4B-it model has three experimentally separable forms: concepts are readable in individual hidden states, constitutive orientation is carried by controlled transformations between states, and selected internal representations causally control engineering answers. We combine matched direct and Jacobian vocabulary readouts, option-free state geometry, a 60-law counterfactual benchmark and causal interventions. In 50 held-out materials descriptions, three independently fitted Jacobian lenses reproduced concept ranks, and target-free word sets from both readouts enabled blinded identification of 9 of 10 mechanism families. A separate 72-prompt benchmark produced mechanism-specific hidden-state neighborhoods, but an exact graph audit showed that this apparent physical organization was equally explained by numerical comparison. We therefore compared otherwise identical prompts in which only the direction of the physical input was reversed, asking whether the resulting hidden-state movement followed the supplied constitutive law. These state transformations ordered direct, physically neutral and inverse laws across 60 frozen relations and correctly oriented 39 of 40 directional laws, whereas lexical controls were near chance. Bidirectional interventions shifted answer probabilities toward or away from the physically appropriate outcome across all 12 matched cases, while counterfactual state patches transferred opposing decision signals across mechanisms and answer formats. Physical relationships were therefore more visible in controlled state changes than in absolute states alone.

Graph-Native Reinforcement Learning Enables Traceable Scientific Hypothesis Generation through Conceptual Recombination

Accelerating materials discovery requires AI systems that can generate scientifically valid hypotheses through multi-step, domain-grounded reasoning. Standard large language models often produce fluent but weakly traceable responses to open-ended materials design problems, making it difficult to determine whether final answers are supported by coherent intermediate reasoning. We develop Graph-PRefLexOR, a family of graph-native reasoning models fine-tuned with Group Relative Policy Optimization (GRPO) to organize reasoning into explicit phases for mechanism exploration, graph construction, pattern extraction, and hypothesis synthesis. This design links neural language generation with symbolic relational structure, enabling causal connections to be constructed, inspected, and reused. On 100 open-ended questions from materials science and mechanics literature, Graph-PRefLexOR achieves 40-65% improvements over corresponding base models, with the largest gains in reasoning traceability. Embedding analyses show broader semantic exploration and approximately 2-3 times greater semantic diversity than baselines. Semantic backtracking and layer-wise hidden-state analyses further show stronger alignment between structured reasoning and final answers. Finally, test-time graph expansion reveals that additional compute primarily increases long-range conceptual recombination within a bounded semantic space, rather than simply expanding semantic coverage. These results establish graph-native reinforcement learning as a pathway toward interpretable AI systems for scientific hypothesis generation in materials design and other scientific applications.

Self-Revising Discovery Systems for Science: A Categorical Framework for Agentic Artificial Intelligence

Scientific discovery is not only answer generation but revision of the representational regime in which evidence, artifacts, operations, and verifiers are typed. We develop a category-theoretic account of agentic discovery for materials science. In a fixed regime b with schema category S_b, the system state is a copresheaf I_t: S_b -> Set, and provenance is the category of elements \int_{S_b} I_t. Fixed-regime operation is an update on such states, endofunctorial only when provenance-preserving refinements are specified and preserved. Discovery is instead a verified regime transition u: S_b -> S_b': old artifacts are preserved, transported by the left Kan extension Lan_u I_t, and compared with the post-transition state to identify residual content beyond functorial transport. This separates retrieval, search, and discovery without subjective novelty. We instantiate the framework in two systems. In Builder/Breaker, a protein-mechanics world model is revised under a Minimum Description Length gate; the accepted law expresses within-chain flexibility as all-mode elastic compliance conditioned by slow collective-mode participation, or mode-conditioned compliance. In CategoryScienceClaw, typed skills, artifacts, open needs, workflow mutation, gates, stress tests, and public discourse become a proof-carrying knowledge-computation graph. A fiber-network example records candidate models, rejected alternatives, an AIC gate, perturbation tests, and an accepted orientation-tensor anisotropic stiffness surrogate over an isotropic fiber-count descriptor. Together, the cases show how category theory can be both a mathematical language for discovery and an engineering specification for self-revising AI discovery systems.

LEIA: Learned Environment for Interactive Architected Materials

World models have enabled interactive exploration of game environments and robotic manipulation, but physical engineering remains beyond their reach: real materials exhibit nonlinear constitutive laws, carry history-dependent internal state, undergo inertial dynamics, and may possess hierarchical structures spanning multiple length scales. We present LEIA (Learned Environment for Interactive Architected materials), a world model that lets engineers apply boundary conditions step by step and observe the resulting deformation and stress fields in real time. LEIA handles large three-dimensional unstructured meshes and generates autoregressive responses to user-specified loading. We introduce MicroPlate, a benchmark of architected plates spanning two regimes of microstructure modeling: architected lattices that resolve microstructure explicitly through three-dimensional geometry, and a homogeneous plate where microstructural change is modeled implicitly through internal degrees of freedom. MicroPlate is used to assess LEIA alongside four baseline methods across both regimes. Finally, we demonstrate that LEIA enables efficient candidate generation and ranking for fast surrogate-guided search for de novo designs of architected materials, with stress-accurate candidate ranking validated by finite element ground truth.

Cross-domain benchmarks reveal when coordinated AI agents improve scientific inference from partial evidence

Scientific evidence often spans instruments, databases, and disciplines, so no single source records the full phenomenon. This makes it difficult to determine when coordinated AI agents add value over simpler scientific workflows. We evaluate this question with a cross-domain benchmark spanning four scientific tasks: mapping molecular structure into musical representations, detecting historical paradigm shifts in science, identifying vector-borne disease emergence, and vetting transiting-exoplanet candidates. Each case uses a frozen evaluation panel, predefined scoring protocols, explicit baselines, ablations or null controls, and stated limitations. The results define three operating regimes. When different disciplines each capture only part of the phenomenon, cross-channel composites improve over single-channel baselines: climate-vector emergence reaches AUROC 0.944 and exoplanet vetting reaches AUROC 0.955. However, the exoplanet workflow is effectively tied with a strong combined-summary baseline, showing that decomposition does not always improve top-line performance. When one signal dominates, as in paradigm-shift detection, coordination mainly improves interpretation and traceability. For molecular sonification, the gain is representational rather than predictive. ScienceClaw x Infinite provides the auditable artifact and provenance layer for this evaluation. The benchmark therefore assigns value to coordination only when the corresponding performance, provenance, or representation claim is supported by explicit comparators.

Recursive Multi-Agent Systems

Recursive or looped language models have recently emerged as a new scaling axis by iteratively refining the same model computation over latent states to deepen reasoning. We extend such scaling principle from a single model to multi-agent systems, and ask: Can agent collaboration itself be scaled through recursion? To this end, we introduce RecursiveMAS, a recursive multi-agent framework that casts the entire system as a unified latent-space recursive computation. RecursiveMAS connects heterogeneous agents as a collaboration loop through the lightweight RecursiveLink module, enabling in-distribution latent thoughts generation and cross-agent latent state transfer. To optimize our framework, we develop an inner-outer loop learning algorithm for iterative whole-system co-optimization through shared gradient-based credit assignment across recursion rounds. Theoretical analyses of runtime complexity and learning dynamics establish that RecursiveMAS is more efficient than standard text-based MAS and maintains stable gradients during recursive training. Empirically, we instantiate RecursiveMAS under 4 representative agent collaboration patterns and evaluate across 9 benchmarks spanning mathematics, science, medicine, search, and code generation. In comparison with advanced single/multi-agent and recursive computation baselines, RecursiveMAS consistently delivers an average accuracy improvement of 8.3%, together with 1.2$\times$-2.4$\times$ end-to-end inference speedup, and 34.6%-75.6% token usage reduction. Code and Data are provided in https://recursivemas.github.io.

Autonomous Agents Coordinating Distributed Discovery Through Emergent Artifact Exchange

We present ScienceClaw + Infinite, a framework for autonomous scientific investigation in which independent agents conduct research without central coordination, and any contributor can deploy new agents into a shared ecosystem. The system is built around three components: an extensible registry of over 300 interoperable scientific skills, an artifact layer that preserves full computational lineage as a directed acyclic graph (DAG), and a structured platform for agent-based scientific discourse with provenance-aware governance. Agents select and chain tools based on their scientific profiles, produce immutable artifacts with typed metadata and parent lineage, and broadcast unsatisfied information needs to a shared global index. The ArtifactReactor enables plannerless coordination: peer agents discover and fulfill open needs through pressure-based scoring, while schema-overlap matching triggers multi-parent synthesis across independent analyses. An autonomous mutation layer actively prunes the expanding artifact DAG to resolve conflicting or redundant workflows, while persistent memory allows agents to continuously build upon complex epistemic states across multiple cycles. Infinite converts these outputs into auditable scientific records through structured posts, provenance views, and machine-readable discourse relations, with community feedback steering subsequent investigation cycles. Across four autonomous investigations, peptide design for the somatostatin receptor SSTR2, lightweight impact-resistant ceramic screening, cross-domain resonance bridging biology, materials, and music, and formal analogy construction between urban morphology and grain-boundary evolution, the framework demonstrates heterogeneous tool chaining, emergent convergence among independently operating agents, and traceable reasoning from raw computation to published finding.

BeamPERL: Parameter-Efficient RL with Verifiable Rewards Specializes Compact LLMs for Structured Beam Mechanics Reasoning

Can reinforcement learning with hard, verifiable rewards teach a compact language model to reason about physics, or does it primarily learn to pattern-match toward correct answers? We study this question by training a 1.5B-parameter reasoning model on beam statics, a classic engineering problem, using parameter-efficient RLVR with binary correctness rewards from symbolic solvers, without teacher-generated reasoning traces. The best BeamPERL checkpoint achieves a 66.7% improvement in Pass@1 over the base model. However, the learned competence is anisotropic: the model generalizes compositionally (more loads) but fails under topological shifts (moved supports) that require the same equilibrium equations. Intermediate checkpoints yield the strongest reasoning, while continued optimization degrades robustness while maintaining reward. These findings reveal a key limitation of outcome-level alignment: reinforcement learning with exact physics rewards induces procedural solution templates rather than internalization of governing equations. The precision of the reward signal - even when analytically exact - does not by itself guarantee transferable physical reasoning. Our results suggest that verifiable rewards may need to be paired with structured reasoning scaffolding to move beyond template matching toward robust scientific reasoning.

GraphAgents: Knowledge Graph-Guided Agentic AI for Cross-Domain Materials Design

Large Language Models (LLMs) promise to accelerate discovery by reasoning across the expanding scientific landscape. Yet, the challenge is no longer access to information but connecting it in meaningful, domain-spanning ways. In materials science, where innovation demands integrating concepts from molecular chemistry to mechanical performance, this is especially acute. Neither humans nor single-agent LLMs can fully contend with this torrent of information, with the latter often prone to hallucinations. To address this bottleneck, we introduce a multi-agent framework guided by large-scale knowledge graphs to find sustainable substitutes for per- and polyfluoroalkyl substances (PFAS)-chemicals currently under intense regulatory scrutiny. Agents in the framework specialize in problem decomposition, evidence retrieval, design parameter extraction, and graph traversal, uncovering latent connections across distinct knowledge pockets to support hypothesis generation. Ablation studies show that the full multi-agent pipeline outperforms single-shot prompting, underscoring the value of distributed specialization and relational reasoning. We demonstrate that by tailoring graph traversal strategies, the system alternates between exploitative searches focusing on domain-critical outcomes and exploratory searches surfacing emergent cross-connections. Illustrated through the exemplar of biomedical tubing, the framework generates sustainable PFAS-free alternatives that balance tribological performance, thermal stability, chemical resistance, and biocompatibility. This work establishes a framework combining knowledge graphs with multi-agent reasoning to expand the materials design space, showcasing several initial design candidates to demonstrate the approach.