LLM Reasoning with Graphs

We argue that pattern recognition and step-by-step reasoning are two ends of a spectrum. A large language model (LLM) learns to reason step-by-step when data is structured such that the next token depends on a small amount of preceding context. Inference in LLMs resembles pattern recognition when the next token depends on a large amount of preceding context. If the next token depends on only the $c$ most recent tokens, reasoning traces are paths on a De Bruijn graph whose nodes are $c$-length contexts and edges are next-token transitions between contexts. The set of reasoning traces of a task forms a directed acyclic subgraph of the De Bruijn graph. An LLM that has learned all edges of this subgraph can compose them to solve longer, unseen tasks, i.e., it reasons step-by-step. We prove that the number of edges is vanishingly small compared to the number of reasoning traces. Empirically, the number of training samples a transformer needs is a power law in the number of edges, so learning to reason step-by-step is sample efficient. We can induce De Bruijn structure in any task by maintaining a ``state'' that makes future reasoning independent of the past. The frequency of states in the reasoning trace determines $c$. We show, by fine-tuning Qwen2.5-1.5B-Instruct to solve equations and answer questions about stories, that frequent states (small $c$) result in higher accuracy but greater fragility to perturbations at test time. LLMs trained with a large $c$ are only as good as models that perform pattern recognition without reasoning. A moderate density of states balances accuracy and robustness. We show that real-world data has De Bruijn structure: Qwen3-14B and Qwen3-32B retain over 75% of their accuracy on GSM8K, MATH-500 and GPQA-Diamond when attention is restricted to a sliding window less than 15% as long as the full reasoning trace.

Large language models (LLMs) have demonstrated strong capabilities in question answering, yet they still frequently suffer from hallucinations on knowledge-intensive tasks. Knowledge graphs (KGs) provide LLMs with structured, interpretable, and updatable factual grounding, making them a promising external knowledge source for reliable reasoning. However, existing LLM-guided graph reasoning methods typically rely on hop-wise greedy or beam-style pruning during evidence retrieval. Such local decision processes are inherently myopic: evidence that appears weak near the source may become crucial only after deeper graph context is explored, causing answer-critical branches to be discarded prematurely and making the reasoning chain difficult to recover. To address this limitation, we propose Foresight-over-Graph (FoG), a foresight-aware evidence retrieval framework for knowledge base question answering (KBQA). FoG iteratively constructs a question-relevant evidence subgraph and uses far-to-near feedback to guide path exploration, and maintains a compact memory subgraph to support continued exploration. Extensive experiments on widely used KBQA benchmarks demonstrate that FoG achieves state-of-the-art performance, with a particularly large improvement of 16.58% in Hit on CWQ, while also reducing LLM calls and token usage. Our code is available at https://github.com/yhong7/FoG .

Post-discharge risk prediction from electronic health records (EHRs) is difficult because many dependencies that link discharge-time observations to downstream complications, such as comorbidity cascades and drug-disease interactions, are absent from the record. External medical knowledge graphs (KGs) can supply these missing dependencies, but tracing them demands three properties: KG exploration must remain cost-bounded, retrieved evidence must be differentiated by source quality, and the resulting rationale must be citable for retrospective review. Large language models (LLMs) can plan and verify over structured evidence, making them natural candidates for KG reasoning, but existing LLM-based methods do not satisfy these three properties jointly. In this paper, we propose BAR, a Budget-Aware LLM Reasoning framework over medical KGs with three contributions. First, BAR refines the raw KG into disease-specific evidence graphs whose edges carry support scores and provenance records, turning the KG into a quality-annotated reasoning space rather than a static feature source. Second, an LLM then reasons over this graph through a plan-navigate-verify loop that decomposes the question into steps, retrieves evidence under a patient-specific budget, and revises when verification fails. Third, a reasoning policy is trained with a reward that compares predictions with and without acquired evidence, combined with acquisition cost and citation-integrity terms. Across 8 diseases and 3 prediction horizons on MIMIC-III and MIMIC-IV, BAR improves AUPRC by 3.4 points over the strongest baseline, raises citation precision from 59.8% to 77.9%, and consumes only 62-65% of the budget cap.

Large language models (LLMs) are increasingly explored for graph understanding and decision-making, while System One models such as Jev select directly from supplied options. However, the capabilities of System One models on graph-related tasks remain unclear. We introduce GraphDecide, a model-independent benchmark that combines structural task profiles, matched graph-text input contrasts and heuristic-proposal controls to diagnose graph decision performance. We evaluate Jev and related choice-based models alongside language-model baselines, covering fourteen model-interface configurations. Jev's results illustrate the benchmark's central distinctions: accurate adjacency recognition does not guarantee broader structural correctness, joint graph-text input does not consistently improve prediction, and feasible construction does not establish high solution quality. Its task contracts, candidate interfaces and scoring rules support comparison across native selectors and language-model adapters. Code and aggregate results are available at https://github.com/VictorYXL/JevGraphBench.

Continuous language flows generate text by denoising all positions of a target canvas together. The natural way to add reasoning to such a model is to write a trace ahead of the answer, but the trace length changes from question to question. The answer start is therefore unknown during denoising, and the model has to decide the trace length, the place of every trace token, and the answer at the same time. We propose Plan Canvas to fix the boundary between the trace and the answer. A plan region of fixed capacity holds a compact trace, supervised padding fills its unused positions, and the answer starts at a fixed position. The fixed regions also allow separate denoising clocks for the plan and for the answer. With the trace text, backbone, and canvas length of the free-trace baseline held fixed, Plan Canvas improves accuracy on ProsQA and on Deep ProsQA, a graph benchmark with longer proofs. On Deep ProsQA, accuracy rises from 73.0% to 87.0%, the share of questions answered with a valid path rises from 30.8% to 59.1%, and the gain is largest on the longest proofs.

Algorithmic mathematical reasoning requires reliable decomposition, computation, and aggregation. Final-answer rewards provide limited guidance on intermediate errors, while successful execution does not guarantee mathematical correctness. This work proposes Function-Structured Graph Reinforcement Learning (FSG-RL), connecting subproblem graphs and Python implementations with multi-verifier feedback. The policy first learns to generate code from function graphs through supervised fine-tuning (SFT). Group Relative Policy Optimization (GRPO) then optimizes the policy using answer-gated rewards and span-level credit assignment. The framework also supports teacher supervision and structured memory. A benchmark curated from Grade School Math 8K (GSM8K), MathQA, MATH, and Omni-MATH pairs public function graphs with private verification specifications. Under a unified evaluation protocol, GRPO improves final-answer accuracy from 43.25% to 67.50% and full solution success from 32.25% to 52.25% over SFT. Continued reinforcement learning (RL) with teacher supervision yields additional gains. The gains extend beyond producing correctly formatted code, supporting verifier-guided reinforcement learning for mathematical reasoning. Code is available at https://github.com/ZihanLiummyycc/FSG-RL.

Graph agents extend large language models (LLMs) with the ability to actively explore and reason over knowledge graphs through multi-step interactions with graph tools. However, training capable graph agents typically requires large collections of question-answer pairs and reasoning trajectories, whose manual construction is costly and difficult to scale. Moreover, employing proprietary LLMs to generate such supervision further risks exposing sensitive graph data to external services. Therefore, we propose GraphCert to bootstrap agentic graph reasoning with certified evidence rubrics during post-training. Specifically, the Bootstrapped Graph Quizzer guided by generation controls produces graph-grounded QA pairs and marks supporting evidence, which undergo execution certification and semantic curation. The accepted evidence is then canonicalized into certified evidence rubrics that later reward Graph Solver evidence alignment alongside answer correctness during GRPO training. Experiments on five graph reasoning domains in GRBENCH demonstrate that GraphCert consistently outperforms substantially larger LLM agents and post-training method. Furthermore, our analysis demonstrates that the learned policy transfers robustly across heterogeneous graph domains, suggesting that GraphCert acquires reusable graph-reasoning capabilities rather than domain-specific patterns. These results establish executable self-certification as an effective approach to self-training compact graph reasoning agents. Our code will be made publicly available.

When a materials LLM answers a question about crystal structure, does it reason from the structure or copy an answer already printed in its input? Accuracy cannot tell: a structural description often prints the very field it is scored against. CARAT holds question and gold answer fixed across eight matched views, names each structural relation separately in GraphSpace, and adds matched fine-tuning, answer masking, evidence injection, paired inference, and a rule that can withhold claims. First, on the benchmark's hardest families the grounded view is worth 17.3 points over formula inputs. Second, we turn that scrutiny on ourselves. GraphSpace beats a plain periodic graph by 19.3 points, but that margin is two effects at once: where the plain rendering carries everything the question needs it is 1.96 points, and where it omits those fields entirely, 46.7 points. The headline mostly measures what the baseline lacked, not how evidence is presented. Third, we attack our own benchmark. A rule that skips the link and reads the list directly answers four of seven hardened families, so we rebuilt it until eleven such shortcuts sat near chance. The frozen model quotes that link yet answers the same when we redirect it, on 95.6% of paired cases: it repeats the relation without using it. After matched supervision it reaches 99.8%, and deleting the link drops it to 23.4%, below the 27.0% the best shortcut reaches: both steps are learnable.

Large Language Models can perform multi-step reasoning and improve task performance through different forms of intermediate computation, from token-based traces to computation carried out in latent space. However, a question remains open: do these different forms of thinking rely on the same underlying mechanism? To address this, we train and compare five variants of the same GPTNeoX backbone from scratch on an extended multi-hop reasoning task (ProsQA-Ext): a vanilla model, a Chain-of-Thought (CoT) model, a Pause Token model, and two latent-reasoning models that are optimized end-to-end without intermediate reasoning traces. We find that, strong in-distribution (ID) performance does not guarantee depth generalization. Vanilla, CoT, and Pause Token models solve ID problems well, but rely largely on local graph features and generalize poorly to out-of-distribution (OOD) problems with longer hops. In contrast, latent variants generalize better and show internal dynamics consistent with forward reachability propagation on the graph. Causal interventions and circuit analysis localize this computation to a sparse recurrent search circuit in the bottleneck latent model: an attention head retrieves graph relations, an MLP and the residual stream update the reachability state across recurrent steps, while multiple attention heads together then do the candidate matching. Together, these results show that different thinking mechanisms can learn distinct computational solutions, even at similar ID performance. In this setting, latent recurrence supports a reusable forward-search algorithm that generalizes beyond the training depth.

Rare-disease diagnosis is a long-tail reasoning problem: phenotypes are incomplete, individual disorders are sparsely documented, and relevant evidence is distributed across ontologies, gene annotations, and biomedical text. Language models consequently favor common conditions, miss rare candidates, or produce plausible but invalid names. We introduce RareDx, which couples controlled evidence use with knowledge-graph-grounded policy optimization. RareDx-Harness normalizes heterogeneous records into one ranked-diagnosis task and compares direct inference, static retrieval, adaptive tools, and structured phenotype-gene-disease reasoning over a shared knowledge layer. The training pipeline combines Top-10 post-training with RareDx-KGPO, our knowledge-graph-grounded policy optimization method. Its reward projects predictions into a canonical disease graph and integrates curated graded relevance, ontology proximity, biomedical similarity, and phenotype consistency. Vocabulary and output-budget constraints prevent dense partial credit from rewarding fabricated or overlong differentials. Across eight benchmarks, the complete RareDx system centered on Qwen3.5-9B reaches 38.34 macro Hit@10, 1.60 points above GPT-5.5 under the archived protocol; a disjoint validation-selection audit retains a 6.80-point routing gain over Direct on held-out cases. The 27B system reaches 23.53/36.56/40.76 at Hit@1/5/10. Controlled ablations show that retrieval is not uniformly helpful and that controlled routing is central to the gain. These results indicate that structured medical knowledge can turn a compact model into a competitive diagnostic ranker across heterogeneous long-tail settings in clinical practice.

Does structured mathematical knowledge help LLMs prove theorems in Lean 4? If so, for which models, and does the answer vary by problem? Formal libraries such as Mathlib encode 285,000+ verified theorems with syntactic dependencies, but the semantic layer mathematicians rely on for discovery (analogies, generalizations, cross-domain bridges) remains implicit. We introduce MathAgent, which builds this layer as a knowledge graph, MathKG, and uses it to augment LLM theorem provers. MathKG connects 364 Mathlib theorems and definitions by 9,434 typed semantic edges inferred via LLM-based relation extraction anchored to verified Mathlib declarations. We run a controlled ablation across four augmentation modes (no context, knowledge-graph context, Mathlib retrieval, both) and five models: Qwen3-8B/32B, their Lean-specialized derivatives Goedel-Prover-V2-8B/32B, and Claude Sonnet 4.6, on miniF2F, plus PutnamBench and MathOlympiadBench for Sonnet. Three findings emerge. (i) Specialization dominates augmentation: Lean fine-tuning adds 33-38 percentage points of solve rate in every mode, and a specialized 8B model beats a $4\times$ larger general one by 29-35 points, while no augmentation mode improves solve rate by more than 3 points. (ii) Augmentation is capability-conditioned: knowledge-graph context helps small models but hurts large ones, with the specialized model gaining more relative to its general base at every scale. (iii) Yet the augmentation modes solve different problems: an oracle selecting the best mode per problem solves 6% to 58% more than the unaugmented prover, a complementarity effect that strengthens on harder problems (32% more on PutnamBench). These results motivate adaptive strategies that select augmentation by model capability and problem. Code, data, and artifacts are available at https://github.com/sarehnabi/mathagent

Large language models (LLMs) have demonstrated strong capabilities in biological reasoning; however, genomic disease inference remains largely dependent on memorized gene-disease associations rather than understanding biological pathways. This shortcut learning undermines robustness and generalization, and breaks down when molecular identifiers are unavailable. We present GenoMorph, a multimodal genomic reasoning framework that shifts disease prediction from associative gene-disease mapping toward pathway-grounded reasoning. GenoMorph couples a frozen DNA foundation model with question-conditioned cross-attention fusion, self-adaptive latent reasoning (LatentSp), a residual reasoning gate for iterative genomic evidence reinjection, and rejection sampling fine-tuning regularized by hierarchical optimal transport (OT). Rather than learning direct gene-disease mappings, GenoMorph aligns genomic sequence representations with latent pathway dynamics, enabling reasoning trajectories that follow molecular interactions before producing disease predictions. LatentSp dynamically allocates computation according to reasoning confidence, reducing unnecessary reasoning steps and improving inference efficiency. We further construct an anonymized benchmark from the Kyoto Encyclopedia of Genes and Genomes (KEGG), replacing every gene and molecular identifier with anonymous symbols while preserving sequences and pathway topology, thereby removing memorization shortcuts. GenoMorph raises the weighted F1 from 0.7863 (BioReason) to 0.9412, and rejection sampling fine-tuning with self-adaptive latent reasoning pushes it to 0.9725 while cutting latency nearly 60%. On the anonymized benchmark it reaches 0.9465 F1, substantially outperforming prior systems and confirming that accurate disease prediction can arise from pathway reasoning rather than memorized gene-disease associations.

Legal contracts are structurally complex documents in which contradictions may emerge across distant and interconnected provisions. Although large language models (LLMs) improve legal language understanding, contradiction analysis remains a human-centered and evidence-grounded review task. We present ContraVis, a visual analytics system for human-in-the-loop contradiction analysis in legal contracts. The system models contracts as typed paragraph graphs that combine explicit contractual references with semantic relationships between paragraphs. This graph plays a dual role: it conditions LLM reasoning and serves as the interactive representation the analyst explores, keeping model context and human inspection aligned across coordinated views. In a controlled comparison, graph-conditioned reasoning recovered more injected contradictions than standalone LLM analysis as contract length grew, while surfacing additional candidates for analyst validation. A formative study with contract-domain lawyers indicated that in-context evidence comparison supported contradiction validation, and we distill design implications for evidence-grounded, LLM-assisted document review.

Large language models are increasingly applied to high-risk domains such as law, yet complex legal reasoning remains limited by two structural challenges. First, existing RAG and GraphRAG methods emphasize lexical or semantic similarity while overlooking normative relations among legal provisions. Second, vanilla Chain-of-Thought prompting may generate plausible rationales without enforcing the normative structure of legal reasoning. To deal with the bottleneck of pipelines in the legal reasoning domain, we propose LEGO, a dual-module framework that synergizes Legal Expert GraphRAG and expert Chain-of-thought for complex legal reasoning. ExpertGraphRAG uses an expert-annotated civil code graph encoding these normative relations with a greedy normative-coverage retrieval algorithm to dynamically extract instance-specific provision subgraphs, while ExpertCoT organizes the retrieved provisions and case facts into structured Provision-Fact-Conclusion reasoning. With a Qwen3-8B backbone, LEGO achieves 40.53% exact-match accuracy on LawExamQA_Civil, outperforming the evaluated RAG and CoT baselines and performing comparably to the evaluated larger models, while remaining robust on multi-hop questions. It also achieves the best results among the evaluated baselines on the open-ended benchmarks. Ablation studies confirm the individual and complementary contributions of both modules, demonstrating LEGO's effectiveness in improving LLMs' complex legal reasoning ability. Code and dataset can be found in the link: https://github.com/BLK-WHT/LEGO

Propagation structures provide crucial evidence for fake news detection, yet existing approaches primarily rely on supervised GNN-based models, which require substantial labeled data and exhibit limited generalization. Although large language models (LLMs) exhibit strong reasoning capabilities, directly feeding them raw propagation graphs creates a significant modality mismatch and severe information overload, making structure-aware reasoning unreliable in zero-shot and few-shot settings. To bridge this gap, we propose MAGER, a multi-agent genetic evolution framework that automatically discovers meta-paths optimized for LLM reasoning. By compressing complex propagation graphs into informative subgraphs, the evolved meta-paths alleviate both information overload and modality mismatch, enabling frozen LLMs to perform structure-aware veracity reasoning. We further introduce a graph in-context learning strategy that retrieves semantically and structurally similar demonstrations to strengthen classification and reasoning. Extensive experiments show that MAGER substantially improves frozen LLMs as standalone fake news detectors in data-efficient settings. Our code is available at https://github.com/SenticNet/MAGER.

A large language model (LLM) agent can follow more graph paths without acquiring more independent evidence. GraphEcho tests whether agents mistake these repeated encounters for additional corroboration. The benchmark varies path counts and evidential origins while holding evidence content fixed, and evaluates both judgments and active exploration. Controlled synthetic experiments reveal model-dependent judgment shifts, but redundant supporting paths increase the share of repeated walks across all evaluated frozen agents. Provenance-aware post-training (PAPT) reduces revisits and improves synthetic accuracy, yet covers fewer distinct sources. On scientific claims, it continues to reduce repetition while accuracy declines. These findings expose a gap between efficient exploration and effective evidence use: an agent can learn to stop repeating itself while overlooking information it needs. GraphEcho provides a controlled way to evaluate both what graph agents conclude and whether their exploration reaches distinct evidential sources.

Puns are a challenging form of figurative language that exploit phonetic similarity and semantic ambiguity to convey multiple meanings. Although large language models (LLMs) demonstrate strong language understanding capabilities, they still struggle with pun reasoning due to limited phonetic modeling and uncontrolled end-to-end generation. We propose \textbf{PunGraph}, a retrieval-enhanced knowledge graph framework for pun understanding. PunGraph constructs a phonetic-semantic lexical graph using the Unisyn phonetic dictionary, IPA and G2P representations, and WordNet definitions, and retrieves candidate words or senses to constrain LLM reasoning within a structured candidate space. We further introduce \textbf{WebPun}, a new large-scale dataset containing 5,730 annotated heterographic and homographic puns. Experiments on SemEval-2017 and WebPun show that PunGraph consistently improves the performance of small-scale LLMs and achieves competitive results against strong proprietary models. Further analysis shows that retrieval-guided phonetic and semantic constraints effectively reduce common reasoning errors in pun interpretation, highlighting the benefits of integrating structured knowledge with LLMs. We release our code and dataset at https://github.com/ysu132/PunGraph.

Large language models (LLMs) can generate biomedical hypotheses, but it remains unclear whether they truly reason from scientific evidence or simply produce convincing-sounding ideas. To study this, we combine three major biological databases: the Kyoto Encyclopedia of Genes and Genomes (KEGG), Rhea, and UniProt, into a unified biochemical knowledge graph and construct a benchmark of 550 paths connecting enzyme sources to rare disease endpoints, yielding 13,200 hypotheses from six LLMs under four conditions varying the biological information each model receives: source enzyme only, full biological path, or source and disease endpoint only. Hypotheses are scored using an expert-derived five-criterion rubric on a 1-5 scale per criterion. We find that models given both the source and disease endpoint often produce the highest-scoring hypotheses, showing that LLMs can generate compelling ideas from minimal information. However, these hypotheses are less grounded in the evidence. In contrast, models given the full biological path generate hypotheses more consistent with known mechanistic relationships. We call this evidence-disciplined reasoning. To confirm this effect, we shuffled intermediate path steps while keeping endpoints fixed. Evidence grounding dropped significantly (delta = -0.793, p < 0.001), confirming models genuinely used path structure during reasoning. Our findings show that knowledge graphs support hypothesis generation in two ways: they identify biological endpoint pairs absent from the literature, and their mechanistic paths guide how LLMs reason between them.

Large Language Models (LLMs) are increasingly asked to reason over structured data such as graphs, yet how reliably they can carry out multi-step graph algorithms in language remains unclear. Existing evaluations tend to use simple tasks on small graphs, to score code generation rather than reasoning over the graph itself, or to fix a single input format. We introduce Graph Theory Bench (GT Bench), a benchmark covering 24 classical graph problems in 44 task-structure settings, with over 100,000 examples across four representations: natural language, structured language, adjacency list, and adjacency matrix. Evaluating eight LLMs on GT Bench shows that accuracy is strongly tied to the input representation, that the best representation shifts with graph density, size, and topology as well as with the model, and that this sensitivity persists, attenuated, in the strongest reasoning models. Building on these observations, we propose the Graph Theory Agent (GTA), which pairs a preference-trained representation selector with plan-and-decompose scaffolding around a frozen executor LLM. GTA lifts Phi-4 from 53.5% to 69.1% on the benchmark's easy split and from 33.0% to 41.5% on its hard split, outperforming eight prompting and agent baselines, and transfers without retraining to GraCoRe and NLGraph. Code for benchmark generation and evaluation: https://github.com/xzx34/GTA. The project homepage is available at https://xzx34.github.io/gta/.

Agentic graph learning (AGL) has recently achieved promising results on graph reasoning tasks, where an agent powered by a large language model (LLM) sequentially samples the graph as evidence to support its final prediction. Existing methods either employ a single agent or orchestrate multiple role-based agents to reason and learn over the entire graph, but both essentially rely on a shared reasoning policy across different graph regions, which can be suboptimal for graphs with heterogeneous structural and semantic patterns. Inspired by the progress of multi-agent collaboration on complex reasoning tasks, a natural remedy is to let multiple agents own different memory and collaborate; however, applying this paradigm to graphs directly faces two challenges. First, existing AGL methods typically verbalize graph structures into natural-language descriptions for LLM agents, making the reasoning process sensitive to the ordering of structural information and thereby breaking the permutation-invariant nature of graphs. Second, incorporating increasingly large sampled neighborhoods leads to rapidly growing contexts. To address these challenges, this paper introduces a multi-agent agentic graph learning (i.e., MAAGL) framework. MAAGL partitions the graph into communities and assigns an independent agent to each community for region-specific specialization. MAAGL represents structural and semantic evidence separately. Structural evidence is summarized by a dynamically updated structural signature that is permutation-invariant and fixed in size, while semantic evidence is filtered to the top-k nodes ranked by relevance. Based on historical trajectories with similar signatures, agents estimate their confidence and trigger debate-style collaboration when needed. Extensive experiments on four benchmark datasets show that MAAGL outperforms SOTA AGL methods.

Large Language Models (LLMs) demonstrate impressive performance across diverse NLP tasks, yet their ability to exhibit genuine contextual understanding remains uncertain. Traditional evaluation metrics such as perplexity, BiLingual Evaluation Understudy (BLEU), or surface-level accuracy fail to reveal how well LLMs extract, integrate, and reason over contextual information--a gap particularly critical in question answering, where models must align responses with contextually grounded knowledge rather than memorized associations. We propose a novel knowledge graph-based evaluation framework introducing Semantic Structural Similarity for KGs (S3KG), a hybrid similarity measure integrating structural and semantic similarity into a continuous evaluation score, alongside a diagnostic framework for categorizing reasoning errors. To validate this pipeline, we evaluate S3KG against established metrics on a curated question-answer (QA) benchmark, demonstrating its effectiveness in measuring correctness, faithfulness, and interpretability in LLM-generated responses.

Multi-step LLM reasoning lacks a machine-recheckable ledger: discarded reasoning paths leave no auditable record. We propose the Deposon scattering layer, which binds each node of an LLM-generated concept-decomposition graph to a two-parameter Deposon state; paths undergo three-channel scattering -- transmission, reflection, irreversible dissipation -- obeying T+R+A=1 for arbitrary parameters, with a maximum per-path energy-audit deviation of 2.2E-16 (machine epsilon). We report all three evidence tiers honestly. On synthetic trap benchmarks the path-filtering gain is closed (pre-registered): unified reaches 100% versus a decoy-capture baseline at 7%/10%. On real benchmarks the layer is indistinguishable from a trivial six-keyword rule filter (GSM8K 0.87 >= 0.85, McNemar p=0.5; StrategyQA 0.899 = 0.899); no difference is detected here, so we sharpen the claim to "the differential value lies solely in machine verifiability." Fusion yields a second negative result: convex combinations with a semantic prior never improve (physics 0.484 -> 0.452), and the apparent lambda=2 gain is an anti-field artifact; any fusion gain must be nonlinear. Modeling the reverse dynamics as a potential game on the graph, we evidence an auditable scalar's monotonicity and near-gradientness and quantify the empirical coordination ratio (ECR). The three formalized dynamical-equivalence propositions (P1a/P1b/T-P1c) are falsified under the pre-registered kill protocol, and the potential-game claim is downgraded to approximate (cyclic-graph median residual 0.669): only consistency-level evidence survives at the dynamical level. Code: github.com/zeroandcat/Deposon.

Autoregressive (AR) large language models formulate reasoning as token-level probabilistic sampling, which induces three fundamental defects in complex logical reasoning: error accumulation, probability substituting necessity, and the linear-chain information bottleneck. This paper proposes the Deterministic Operator-Driven Reasoning in Latent Space architecture (DODR), which reconstructs reasoning as reasoning-graph computation in a high-dimensional linear-algebraic space. Reasoning states are represented as snapshot vectors whose primitives are semantic units (phrases or sentences) rather than tokens, and each inference step is a deterministic matrix operation with no token sampling. Peirce's three inference types are formalized as three trainable matrix operators: a rank-deficient deduction operator (information collapse), a full-rank induction operator (information expansion), and an abduction operator defined as the Moore-Penrose pseudo-inverse of deduction (information hypothesizing). We prove that the operator set is minimal and complete given Peirce's trichotomy, that no single "super-operator" can realize all three types (a rank obstruction), and that reasoning graphs are Turing-complete with contractive backflow converging by Banach's fixed-point theorem. Experiments on 503 sample records (420 deduplicated samples) across dedicated and end-to-end settings show: deduction loss converges to 1.40e-05; induction achieves 0.9996 generalization coverage with 20/20 hard vetoes on counterexamples; abduction solutions exceed the random baseline by 28x with judgment accuracies of 72.5% (58/80, Wilson 95% CI [61.9%, 81.1%]) and 81.7% (49/60, CI [70.1%, 89.4%]); frozen operators attain 100% (60/60) on unseen cross-domain deduction. The architecture provides a structural zero-hallucination guarantee and a three-layer continual-learning mechanism. All data and code are released.

Networks describe systems in biology and beyond, from protein interactions and social relationships to power grids and citation records. Reasoning about such systems requires understanding their structure: which elements are central, which connections bridge separate communities, and how it changes when elements are removed. Although large language models (LLMs) excel at natural language, they struggle with such questions when networks are given as edge lists, sentences or measurement tables, because their structural meaning must be inferred. Here we introduce BioGlyph, which compiles network topology into an interpretable and transferable language of structural roles. BioGlyph combines graph partitioning and structural measurements to identify roles such as hubs, community cores and cross-community connectors, and fixed rules to translate them into a universal vocabulary. The representation describes each element through its structural role, supporting evidence and semantic consequences, leaving both the network and the LLM unchanged. Across twenty networks spanning five domains, BioGlyph substantially improves open LLMs' ability to answer structural reasoning questions, outperforming edge-based, numerical and learned representations by up to 26 percentage points in system accuracy. Ablations show that the gain comes from explicitly encoding structural roles in semantically interpretable terms. The gain is more prominent in dense, community-structured networks and diminishes in sparse networks whose topology is more readily inferred from text. In a budding-yeast protein-interaction network, BioGlyph exposes biological organization: cross-community connectors are enriched for essential genes, whereas peripheral proteins are depleted. BioGlyph thus provides an interpretable representation for both language models and scientists to reason about network structure.

Large Reasoning Models produce Long Chains-of-Thought (LCoTs) which involve breaking down the problem into smaller reasoning steps before reaching the conclusion. However, these steps often contain contradictions, unsupported inferences, or irrelevant steps, even when the final answer is correct. We propose Long Chain-of-Thought Graph Verifier (LCoT-GV), a graph-based framework that represents LCoTs as reasoning graphs. Each node in the graph represents a reasoning step and the edges encode semantic and logical relations. A Graph Attention Network is then trained to predict chain-of-thought correctness from the reasoning graph. We construct a new graph-oriented verification dataset from multiple reasoning benchmarks for question answering in various domains. The results show that our method is competitive with the most similar approaches.

Graph-augmented large language models often assume that graph evidence produced by external computation and placed in the input can be used by the native decoder. We test this assumption with HopQA, a deliberately bounded diagnostic that asks for the shortest-hop distance between two query nodes. Because the answer is a small integer and the target is purely topological, failure cannot be dismissed as open-ended generation or ambiguous evaluation. Yet existing graph-augmented baselines still fail on this setting, showing that providing graph evidence is not the same as making it usable. We introduce an intervention triangle with three matched conditions: readable graph evidence, shuffled graph evidence, and no-graph input. This separates evidence inclusion, structural readability, and decoder-usable topology. Guided by this diagnosis, we present S$^2$GE as an instance showing that diagnosis-driven interface design can improve native decoder usability. S$^2$GE uses query-aware sampling, endpoint and proximity-based ordering, and structure-preserving alignment. Across DBLP, Biomedical, GoodReads, and PubMed, S$^2$GE achieves strict exact-match scores of $36.5\%$, $57.8\%$, $76.6\%$, and $52.0\%$, improving over the strongest native-generation baseline by $53.5$ points on average. The interventions further reveal harmful-shuffle, shuffle-robust, and no-graph-saturated regimes.

Graph RAG connects facts no single passage states, but implementations pay three times: in infrastructure, keeping vector store, graph database and document store in sync; in quality, because a pipeline that never refuses extractor output stores edges that assert nothing; and over time, because a graph that only accumulates treats superseded and current facts alike. post-graph-rag is an open-source engine addressing all three. Chunks with embeddings, a canonical entity graph and community summaries live in one PostgreSQL database, with pgvector for search and edge tables for traversal. Extraction output is validated before writing: vague predicates, pronominal names and bare quantities are rejected, predicates normalise onto an optional vocabulary, entities resolve to one vertex per canonical name, and denials keep the positive predicate under a negation flag. A bi-temporal layer records when a relation held and when the system believed it, superseding incompatible earlier assertions from document order. Against LightRAG on three corpora with extraction and embedding models fixed, it builds a denser graph everywhere, up to $2.4\times$ the relations per entity, and a more queryable one: 0.46-0.58 distinct edge labels per relation against 0.77-1.33. It supersedes 13 and 8 relationships where the baseline, having no temporal model, supersedes none. On LongMemEval, 500 questions of long-horizon chat memory, it scores 85.8 percent with gemini-3.6-flash against 71.2 for Zep's gpt-4o and 60.2 for a full-context baseline, leading on all six question types. The largest single contribution is temporal grounding in the prompt: carrying each relation's validity period through to synthesis moves temporal reasoning from 0.496 to 0.881, ablated paired on one graph per instance. Code: post-graph-rag https://github.com/crajah/post-graph-rag; post-graph https://github.com/crajah/post-graph

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.

Graph reasoning provides a promising testbed for evaluating the reasoning ability of large language models (LLMs), as graph instances can be programmatically generated, structurally controlled, and naturally scaled to long-input settings. However, existing graph reasoning benchmarks have limited coverage of data complexity, rely heavily on manual construction, and lack unified evaluation across text-based and code-based reasoning modes. To address these limitations, we propose {\dataset}, a five-stage \textit{semi-automatic} framework for constructing complex graph reasoning benchmarks. It expands benchmark coverage along five dimensions: \textit{Graph Size}, \textit{Task Complexity}, \textit{Task Description}, \textit{Graph Loading}, and \textit{Task Source}. The framework uses an LLM-based data generator to automatically produce task descriptions, graph data, reference solutions, graph-loading scripts, question forms, and evaluation scripts, while retaining human validation at key quality-control stages. Based on it, we construct a benchmark with $202$ tasks and evaluate LLMs under text-based, code-based, and augmented reasoning settings. Experiments show that the complexity dimensions reveal model limitations that are less visible in existing benchmarks; existing fine-tuned models struggle to generalize to GraphGym, whereas retrieval-augmented methods show scenario-dependent adaptability, improving textual reasoning but not consistently improving coding reasoning. These findings suggest that ours serves as a challenging and diagnostic benchmark for graph reasoning and provides empirical guidance for future enhancement methods. Code and dataset will be published soon.

Deep search has become a fundamental capability of large language models (LLMs) for solving open-domain complex tasks. However, existing approaches typically rely on linear sequential reasoning for both trajectory generation and inference, making it difficult to consistently preserve intermediate states and constraints throughout long-horizon multi-hop search. Consequently, they often suffer from context forgetting, search drift, and inefficient exploration. To address these limitations, we propose $\textbf{G-ReAct}$, a reasoning framework for deep search that organizes reasoning as $\textbf{state evolution over a fixed-topology query graph}$. The evolving graph state explicitly tracks search progress and guides subsequent decisions, transforming exploratory search driven by textual history into graph-guided reasoning under explicit constraints. G-ReAct supports both training and inference: it generates high-quality deep-search trajectories for supervised fine-tuning and provides structured guidance for inference-time search without additional fine-tuning. Experiments demonstrate that with only 1.9K generated trajectories for fine-tuning, Qwen3-30B-A3B-Thinking-2507 achieves $52.6\%$ accuracy on BrowseComp-ZH and $79.0\%$ on XBench, outperforming comparable open-source methods trained on substantially larger datasets, including RL-enhanced methods. Furthermore, when applied at inference time, G-ReAct consistently improves the performance of existing strong LLMs on deep-search tasks. We will publicly release all code and model weights.