Datalog rules are often used to define ontologies over Knowledge Graphs. Rule reasoners routinely optimise such ontologies by rewriting their rules into a form that can be evaluated more efficiently. These transformations preserve the entailed facts, but not the structure of the underlying derivations. A proof tree under the rewritten rules explains why a fact holds, but does not readily yield an explanation in terms of the original rules. We study the problem of constructing, from a proof of entailment under the rewritten rules, a proof under the original ones: we establish its computational complexity and identify two practically relevant languages for specifying proof transformations.
https://arxiv.org/abs/2608.06399
Recently Large Language Models (LLMs) have been increasingly deployed as autonomous agents in applications such as self-reflection, retrieval-augmented generation, and scientific discovery. In these settings, agents must act based on limited observations rather than full environmental states, leading to partial observability. This introduces several key challenges: belief state inference, task objective misalignment, and planning under uncertainty. Prior approaches typically condition actions on full or summarized action-observation histories whose redundant and irrelevant information can mislead the decision making of LLM agent. Inspired by human cognition, we propose a novel neuro-symbolic fast-slow thinking (NeSyFS) framework for LLM agent, addressing the challenges introduced by partial observability in a unified approach. We use a knowledge graph (KG) to represent the belief state, providing triplets as context for every module of NeSyFS. The fast-thinking module performs reactive action, while slow-thinking conducts a new uncertainty-aware planning by following the high-level structure of twisted sequential Monte Carlo (TSMC) algorithm. To mitigate the misalignment of task objective, a reflection module is used to reflect fast-thinking actions, and also switches to the slow-thinking module whenever reactive actions repeatedly fail. Experiments on three representative benchmarks, i.e. ALFWorld, Webshop, and ScienceWorld, demonstrate significant advantages over previous methods.
https://arxiv.org/abs/2607.28942
Autonomous research loops driven by large language models can run machine-learning experiments at scale but tend to drift toward local refinements of whichever metric they optimise rather than testing the hypotheses that motivate the experiments. We address this structurally and present an AI Scientist for studying generalisation in quadruped robot navigation policies in simulation. Building on the autoresearch paradigm of Karpathy, our loop adds three components: an immutable experiment card that pairs each iteration's prediction with its outcome under a fixed schema, so a falsified hypothesis cannot be retconned; specialised subagents restricted to mechanical roles; and kkanbu, a preference oracle that holds the user's research taste as a typed knowledge graph and is the only component permitted to make subjective judgements. To isolate the oracle we run the identical loop twice across eleven research streams, with and without kkanbu. Neither arm drifts: both falsify roughly three quarters of their own hypotheses, and the best trained policy comes from the oracle-less arm. What the oracle changes is direction, not score: it alone explores test-time adaptation, it authored the winning designs where its arm led, and it carried lessons across streams that the other arm repeatedly re-derived. The scaffold keeps the loop honest; kkanbu decides where it looks.
https://arxiv.org/abs/2608.07542
Retrieval-augmented generation (RAG) over knowledge graphs requires retrievers that can effectively capture both graph structure and semantic information. Recent approaches have explored graph neural network (GNN)-based retrievers to model graph topology in multi-hop reasoning tasks. In parallel, graph language models (GLMs) have emerged as a promising paradigm that integrates graph reasoning and the semantic capabilities of language models. In this work, we introduce a GLM-based retriever and investigate the comparative strengths of GLM-based, GNN-based, and traditional vector-search-based retrievers in single- and multi-hop RAG settings, and with a particular focus on transferability to unseen domains. Our findings suggest that finetuned GLM retrievers generalize better out of domain, achieving SOTA on two multi-hop benchmarks. On in-domain multi-hop QA datasets they remain comparable to prior work, with promising scaling as parameters and subgraph coverage increase. GNN-based retrievers achieve higher graph coverage with an efficient training setup, whereas the vector-search baseline excels at single-hop datasets.
https://arxiv.org/abs/2607.28397
Large language models (LLMs) have demonstrated strong capabilities in structured query generation, making them a natural choice for Text-to-SPARQL, which translates natural language questions into executable SPARQL queries over knowledge graphs. However, their initial outputs remain unreliable: generated queries may be executable yet semantically misaligned with input questions, leading to incorrect retrieval. To address this issue, we propose Generator-Gate-Corrector (GGC), a framework for reliable LLM-based Text-to-SPARQL generation. GGC first uses a Generator to produce an initial query, then applies a Gate to predict whether correction is needed, and finally invokes a Corrector only for selected high-risk queries. This selective correction mechanism avoids unnecessary modifications and reduces the risk of degrading originally correct queries. Experiments on MCQA show that GGC improves query-level accuracy from 90.23\% to 98.33\% while reducing inference overhead by 45\% compared with correcting all generated queries. Ablation studies show that the Gate is robust across thresholds and that Corrector training data composition affects correction effectiveness and stability. Overall, the results demonstrate that selective correction enhances the accuracy, reliability, and efficiency of LLM-based text-to-SPARQL generation.
https://arxiv.org/abs/2607.28082
Scientific processes are often described in heterogeneous article discourse, with details needed for comparison, reproducibility, reuse, and automation dispersed across prose, tables, figures, protocols, and supplementary files. We present the first release of this http URL, a multidisciplinary collection of 16 expert-annotated schemas spanning Biology & Biotechnology, Materials & Chemistry, Imaging & Measurement, Physics, and Psychology. Each schema defines reusable fields for describing process instances, including inputs, outputs, materials, instruments or software, parameters, conditions, procedural steps, measurements, and provenance-related information. The schemas were created through a human-in-the-loop schema-mining workflow in which large language models generated candidate structures from process specifications, scientific articles, and expert feedback, followed by domain-expert construction of final master schemas. The dataset contains final schemas in JSON Schema and SHACL formats, intermediate model-generated schemas, expert-feedback records, source-paper metadata, community-development materials, and analysis scripts. Technical validation assessed schema structure, development provenance, expert review, and syntactic conformance. The collection supports structured annotation, metadata enrichment, scientific knowledge graphs, information extraction, semantic publishing, and cross-study comparison.
https://arxiv.org/abs/2607.27955
In clinical practice, patients often undergo multiple imaging examinations over successive visits, yielding longitudinal data. Modeling such temporal information is crucial for reliable assessment of disease progression and treatment response. However, despite the rapid advancement of multimodal large language models (MLLMs), longitudinal medical visual reasoning remains largely underexplored. To fill this gap, we propose LoMeVQA, a comprehensive benchmark consisting of 206K longitudinal visual question answering (VQA) pairs for temporal medical image analysis. LoMeVQA covers five tasks: progress classification, progress description, progress report generation, differential region grounding, and differential region description. To construct the dataset, we develop an automated pipeline that (1) organizes patient records chronologically, (2) extracts clinically meaningful entities via a medical knowledge graph, and (3) models their temporal evolution to guide large language models in generating high-quality longitudinal VQA pairs. Extensive evaluations demonstrate that both general-purpose and medical-domain MLLMs perform poorly on LoMeVQA, revealing substantial limitations in temporal reasoning. To address these limitations, we introduce MedLong-8B, which achieves state-of-the-art performance across all tasks. Beyond benchmarking, we conduct detailed analyses that uncover key failure modes and shed light on how to improve longitudinal medical visual reasoning. Our data is available at: this https URL
https://arxiv.org/abs/2607.27806
Knowledge graphs are usually integrated into question answering by encoding a retrieved subgraph with a graph neural network and fusing it with the language model in the online inference path. The same subgraph is therefore re-encoded from scratch every time a pair is scored, across training epochs, seeds, and evaluation runs, even though the knowledge graph never changes. We ask whether the retrieved knowledge graphs can instead be compiled once, offline, and then accessed as read-only memory. VisKG-LM shows that it can, by decoupling graph encoding from language reasoning. It serializes each retrieved candidate-specific subgraph as Relation-Labeled Paths and renders the result as an image whose two-dimensional layout preserves the branching structure of the paths. Each image is encoded once, offline, and cached for reuse. At inference, the language model contextualizes the question and candidate from text alone, and only its final layer consults the cached visual memory, reading both its global layout and its local relational detail. The graph information thus enters only after the text has been understood. On the test sets of CommonsenseQA, OpenBookQA, and MedQA-USMLE, VisKG-LMimproves over GreaseLM by $1.2$, $0.8$, and $4.3$ points, respectively, while matching or surpassing GraphVis, a $7$B vision-language model, with only about $400$M online parameters. Against a matched text-only control that receives the identical Relation-Labeled Paths, it gains $4.2$, $6.5$, and $5.1$ points across the three benchmarks. These gains show that the complete visual-memory interface adds value beyond path textualization alone and support compiled visual memory as an alternative to online graph propagation.
https://arxiv.org/abs/2609.19158
Knowledge graph completion (KGC) aims to infer missing facts in knowledge graphs (KGs), thereby improving their completeness and supporting downstream intelligent applications. However, emerging entities and relations in real-world deployments make inductive KGC difficult, especially under few-shot and zero-shot settings. Multimodal information and Large Language Model (LLM)-derived priors can enrich sparse relational contexts, but they may also introduce noisy or hallucinated evidence. To address these issues, we propose DuPLeR, a \textbf{Du}al-\textbf{P}ath \textbf{L}LM \textbf{R}easoning framework for multimodal few-shot KGC. DuPLeR builds a calibrated relation graph by combining multimodal LLM-derived type priors with factual support structures, and performs dual-level structural reasoning over the refined relation topology. Moreover, a dual-pathway multimodal enhancement module regulates message passing with query-relevant multimodal signals and supplements entity representations after graph propagation. Experiments on eight inductive variants of two multimodal KG (MMKG) benchmarks show that DuPLeR achieves robust performance in data-scarce KGC scenarios.
https://arxiv.org/abs/2607.26909
Text, knowledge graphs, and hypergraphs all have elements that play distinct roles within relation instances, structure that is lost when data is flattened into token sequences. We introduce labeled incidence structures (LIS), a uniform representation that encodes each endpoint as $(x_d, s, e)$: content $x_d$, a role or slot $s$, and the relation instance $e$ in which that role appears. Because every data type maps to the same $(x_d, s, e)$ representation without flattening, a single standard transformer can process them all natively, structural differences are carried entirely by the operators, not the architecture. LIS assigns a structural address to each endpoint by composing a slot operator and an instance operator, $A(s,e) = R_s R_e$. We characterize when this factorization gives every token a unique, path-independent address. When it does, the natural operator comparing endpoint $j$ to endpoint $i$ is the relative transport $P_{j\to i} = A_i^{-1} A_j$, which gives attention a role- and relation-aware inductive bias without imposing an arbitrary sequence order. Additive encodings of the form "position term plus relation term" can miss information that depends jointly on $s$ and $e$. We prove this in a controlled example family: when the journey operator is approximated by the sum of a position-only term and a relation-only term, the approximation cannot capture how position and relation combine, only their separate effects. We also analyze persistent knowledge repositories. Identifiers tied to storage locations make models sensitive to storage order, while freely learned identifiers can become harder to control as the repository size $M$ grows relative to the sample size $n$. Computing relation-instance operators from content avoids this storage-order issue and yields a capacity bound independent of $M$, under fixed architectural and Lipschitz assumptions.
https://arxiv.org/abs/2609.20278
Biomedical knowledge graphs (KGs) are pivotal for knowledge organization, yet traditional binary relations often struggle to represent the conditional nature of biomedical knowledge. Symptoms provide a shared phenotypic layer for linking Traditional Chinese Medicine (TCM), which relies on symptom patterns for syndrome differentiation and treatment selection, with modern biomedicine, which connects clinical manifestations to diseases and molecular mechanisms. We present LingShu, a large-scale symptom-centric contextualized knowledge graph designed to bridge TCM and modern biomedicine. The exported version of LingShu analyzed in this study comprises 17.33 million atom-level entity records and 39.47 million relation records, including 17.19 million semantic triples and 22.29 million contextualized quadruples. LingShu integrates multi-source data, including clinical electronic medical records, authoritative TCM texts, biomedical ontologies, and curated knowledge bases, through a pipeline combining natural language processing, terminology normalization, and human-in-the-loop verification. A key innovation of LingShu is its hybrid data model: it maintains 64 typed triple relation patterns to ensure broad connectivity, while incorporating 35 contextual quadruple relation patterns to capture conditional medical associations. This dual-structure approach explicitly encodes conditional knowledge, providing a granular representation of the contexts associated with medical relations. These contextualized relations cover syndrome-dependent herb efficacy, disease-contextualized drug effects, population-specific clinical associations, and mechanism-related therapeutic responses. Furthermore, we developed a web platform (this http URL) that integrates graph visualization, graph-based reasoning, and an evidence-grounded knowledge question-answering agent.
https://arxiv.org/abs/2608.20402
Wikipedia and Wikidata are widely used for information access, LLM pre-training, and retrieval-augmented generation. Their knowledge is deeply connected but scattered across text, tables, and knowledge graphs. This raises a practical question: when these modalities disagree, how can we detect and explain the conflict? We study this problem as \emph{modality-level inconsistency detection}. We first introduce a taxonomy of cross-modal knowledge inconsistencies, covering information granularity differences, direct conflicts, temporal changes, and KG incompleteness. We then present \textsc{Kontrast}, an automatic framework that uses Text-to-SPARQL and LLM reasoning to compare table-based answers with KG evidence and categorize the resulting inconsistencies. Experiments on various Table-QA datasets show that cross-modal inconsistencies are common and informative. They reveal not only true knowledge conflicts, but also missing KG structure and temporal mismatches while being limited by Text-to-SPARQL errors and noise. Our analysis shows that text, tables, and KGs can complement and correct one another through systematic comparison. \textsc{Kontrast} provides a practical tool for large-scale knowledge auditing and establishes a benchmark for future work on cross-modal knowledge consistency. Code and data are available at this https URL.
https://arxiv.org/abs/2607.25959
While text-to-image models exhibit remarkable visual fidelity, they frequently violate fundamental physical commonsense. Existing benchmarks often rely on coarse-grained descriptions, failing to diagnose the mastery of specific physical principles. Moreover, the high stochasticity of generative processes causes current prompt optimization methods to suffer from gradient hallucinations, where optimizers are misled by transient visual artifacts rather than systemic flaws. To address these challenges, we introduce OmniPhys, a rigorous benchmark of 1,551 samples grounded in a Physical Knowledge Graph. By aligning PhET simulations with standard curricula, OmniPhys operationalizes a knowledge-to-scenario pipeline that performs diagnostic stress tests via a dual-path verification protocol. We further propose OmniPrompt, an iterative framework that treats physical alignment as a discrete optimization problem. For each query, OmniPrompt aggregates K stochastic images into a per-query feedback buffer. Across training, it further merges feedback from batches of B queries before each meta-policy update, filtering seed and query-local noise. Evaluations across 12 representative text-to-image models reveal universal physical bottlenecks. Results demonstrate that OmniPrompt significantly enhances physical consistency across diverse backbones, proving the transferability and efficacy of our evolved meta-policies. The code and data are available at this https URL
https://arxiv.org/abs/2607.25641
Entity alignment (EA) identifies entities across knowledge graphs (KGs) that refer to the same real-world object. Conventional EA methods mainly exploit explicit graph structures and textual fields, which often provide insufficient semantic understanding to recognize the same entity under heterogeneous descriptions and distinguish it from semantically similar entities. Although large language models (LLMs) offer deeper entity understanding, existing LLM-based EA methods largely use this capability for auxiliary generation or candidate-conditioned decisions. Consequently, such understanding is not distilled into a stable and directly comparable identity space, leaving alignment tied to specific KG pairs or candidate sets and requiring repeated processing as the matching context changes. To address these limitations, we propose IRIS (Identity Representations from Internal States), a training-free framework that constructs for each entity an iris-like signature encoding its distinctive and stable identity characteristics. IRIS derives these signatures by eliciting identity-oriented contextual representations from a frozen LLM, thereby forming a shared space in which each entity is encoded once and can be aligned across different KGs through direct similarity comparison, without pair-dependent representation construction or candidate-wise LLM inference. Across four established EA benchmarks and two frozen LLM backbones, the best IRIS variants achieve Hits@1 scores of 100.00, 99.38, 98.31, and 97.99 on D-Y-15K V2, DBP-WIKI, ICEWS-WIKI, and ICEWS-YAGO, respectively.
https://arxiv.org/abs/2607.25579
Recent advances in RAG aim to optimize for performance by paying high ingestion costs for knowledge ingestion: building knowledge graphs or extracting SQL tables. In this work we show that the operations that such knowledge bases allow can be replicated with zero ingestion costs (not even a vector database); in fact our solution, Zero-Ingestion ScalableRAG, handily out-performs all baselines (including knowledge graph approaches) in three out of the six corpora considered here, and only marginally missing maximum performance on the other three, with average accuracy across all six datasets 7.36% above the next most competitive baseline. It achieves this by keeping a workspace of document sets and values sets that it can write into and read from, allowing for on-the-fly aggregative reasoning in all situations where grouping is required on a primary key that is in one to one correspondence with a subset of the total document set. Capping the number of LLM calls by a constant independent of the corpus size, we also introduce Limited-Ingestion ScalableRAG, which does use a minimal vector database as well as an automated pattern discovery from a sample of documents, to further improve accuracy at scale. Our code is available at this https URL .
https://arxiv.org/abs/2607.25135
In recent years, the number of events in earthquake catalogs has significantly increased due to the utilization of more effective deep learning based detectors and phase pickers but answering open ended questions such as what characterizes this sequence? remains constrained by rigid spatiotemporal windowing and subjective expert interpretation. We present the first systematic application of graph based retrieval augmented generation GraphRAG directly to raw, tabular catalog records across three independently featured catalogs, a reservoir adjacent swarm, the 2019 Ridgecrest tectonic sequence, and the 2021 Maduo Mw7.4 aftershock sequence. Without the need for manual data structuring, the pipeline builds structurally complete, queryable knowledge graphs for all three. Rigorous evaluation individually verified against catalog derived ground truth and a rule based reference graph exposes failure modes, and four seismology informed prompt fixes eliminate all targeted fabrications while sharply improving mechanism reasoning. A vector RAG baseline demonstrates the graph layers distinctive value, catalog wide summarization and temporal stage comparison. In addition, we have identified two main pitfalls that need attention. GraphRAG thus offers a practical, transferable, near zero cost query interface for earthquake catalogs, where careful prompting ensures the results are consistently accurate and trustworthy.
https://arxiv.org/abs/2607.24984
Security Operations Centers increasingly rely on automated mapping of Cyber Threat Intelligence reports to MITRE ATT&CK, yet extractor outputs remain fallible and are often stored without the evidence, provenance, and validation history needed to decide whether an individual mapping should be trusted. We present TRACE- CTI, a post-extraction claim-governance framework that preserves run-level Predictions, aggregates them into configuration-level GraphAssertions, materializes setup-deduplicated corroboration as ConsensusAssertions, and exposes only GraphAssertions backed by policy-compliant validation grounds. The framework retains native evidence granularity, complete extraction provenance, versioned trust decisions, and non-destructive revocation history. We evaluate TRACE-CTI on two public CTI corpora comprising 65 reports and 5,303 sentences, using a controlled 2 x 3 matrix of retrievers and generator families, incrementally ingested across six GraphVersions. All setups are incorporated without schema modification; provenance paths remain complete, operational scopes remain disjoint, and every trusted GraphAssertion has an active qualifying validation ground. Cross-generator-family setup pairs exhibit greater output diversity than same-family pairs. At the final graph state, increasing setup support from k >= 1 to six-setup unanimity raises gold-aligned precision from 25.3% to 90.6%, while recall decreases from 88.2% to 16.3%. The graph also directly answers seven questions about provenance, trust, versioning, dependency, disagreement, and review-queue that the evaluated minimal flat output cannot fully answer without enrichment or reprocessing. These results support explicit, auditable governance of extracted TTP claims; the observed corroboration trajectory is descriptive and does not establish statistical independence or a causal model-family effect.
https://arxiv.org/abs/2607.24563
Maintenance regulations are complex legal texts that are difficult to exploit when addressing a specific case and challenging to integrate into operational systems. This paper presents a two-stage LLM-assisted workflow for French maintenance regulations: ontology engineering from a SEMLEG-based core ontology, followed by construction of an ontology-grounded French legal knowledge graph. The first stage consists in the open extraction of typed entities and triples from a stratified corpus sample, the normalization of labels through embedding-based fusion, and the induction of candidate object properties with their signature (domain and range). The second stage uses the resulting ontology to guide the closed extraction of triples and RDF graph construction over the full corpus. Experiments with GPT-4.1 and mistral-large-2512 show robust structured outputs, near-complete class alignment, and a substantial reduction of duplicated entities and predicates after fusion. Fewer than 20% of triples introduce unseen properties, while lower exact signature compliance reveals new domain-range combinations for existing predicates. These results point to predicate normalization and the validation of newly observed relation signatures as key refinement steps for industrial maintenance settings.
https://arxiv.org/abs/2607.24551
Mathematical models are central to formalizing research problems, yet their documentation often falls short of FAIR principles. Knowledge bases such as the Mathematical Model Database (MathModDB) address this gap by providing curated, semantically rich representations of mathematical models. Built on Wikibase, the same open-source infrastructure underlying Wikidata, MathModDB utilizes Semantic Web technologies to support Linked Open Data, collaborative editing, and the storage of semantically enriched metadata, making it a domain-specific knowledge graph within the broader Wikidata ecosystem. However, access to MathModDB currently requires either navigating a complex web interface or proficiency in SPARQL and Wikibase APIs, posing significant barriers for potential users. In addition, the combination of such curated knowledge bases with actual research data stored, e.g., in Dataverse repository instances, remains a challenge. To overcome these limitations, we propose integrating Large Language Models (LLMs) with MathModDB via a Model Context Protocol (MCP) server that exposes a vector-indexed schema retrieval and Steiner-tree-based join planner, combining dialogue-based natural language interaction with curated, epistemically grounded knowledge. Although instantiated on MathModDB, the architecture can be applied to other Wikibase-based systems. We demonstrate that this approach enables epistemically grounded LLM usage, improves model explainability and accessibility beyond what the standard Wikibase interface offers, and simplifies interoperability with external databases and tools, such as Dataverse data repositories. We illustrate the benefits of combining the accessibility of an LLM with the epistemic safety of a curated knowledge base through the adaptability of the MCP protocol by two use cases involving mathematical models in the fields of continuum mechanics and enzyme kinetics.
https://arxiv.org/abs/2607.24512
Integrating heterogeneous industrial knowledge, including factual relations and decision constraints, remains a core challenge in industrial information systems. Machining process planning exemplifies this problem because engineers must select operations by combining material properties, feature characteristics, and quality requirements. Existing methods rely mainly on similarity retrieval or classification, without a unified ranking objective or standardized evaluation. We propose PCA-GAT, which formulates machining process plan recommendation as a knowledge graph enhanced collaborative filtering problem. Bayesian Personalized Ranking provides the learning objective, while Recall@K and NDCG@K define evaluation. The knowledge graph supplies semantic structure when collaborative signals are sparse. Four domain constraints, material compatibility, precision requirements, feature applicability, and operation sequencing, are introduced as attention biases during graph propagation. Type-specific weights learn their importance, and an adaptive gate adjusts their influence using local context. On a real aerospace dataset with 115 parts and 507 plans, PCA-GAT achieves Recall@1 = 0.9087 and strong cold-start robustness, with about half the degradation of the strongest baseline under severe sparsity. Ablation studies show that knowledge graph enrichment is essential, constraints add value, and ungated constraint injection can hurt performance. The learned weights identify material-operation compatibility as the dominant factor, consistent with domain expertise. Results on three public benchmarks show no degradation when constraints are absent, supporting generalization beyond manufacturing. This study establishes a standardized recommendation protocol for engineering process planning and benchmarks seven methods across three categories, showing that knowledge representation is the main bottleneck.
https://arxiv.org/abs/2607.24213