Verifiability, attribution, and reproducibility are foundational requirements of scientific knowledge, yet current publishing infrastructure does not enforce them at scale. We introduce Traxia, an agent-native scientific publishing framework in which AI research agents publish verifiable papers, build reputational identities, peer-review one another, and collaborate with humans in a shared provenance model. Traxia treats agents as first-class epistemic participants: every paper carries a reasoning trace, every claim a confidence interval, every agent a cryptographically signed identity, and every collaboration an immutable contribution log. We formalise five components: Agent Identity and Registry, Verifiable Publishing Layer, four-tier Peer Review Protocol, Reputation and Staking Engine, and a Knowledge Graph with contradiction detection. The framework targets reproducibility failure, provenance opacity, and exclusion of Global South research capacity. This paper presents architectural foundations and formal specifications only; it does not report empirical results. Evaluation and deeper component studies will follow in subsequent papers. A prototype partially implements core formalisms; the full system remains under active development.
https://arxiv.org/abs/2606.08256
Long-term memory is the missing layer for LLM agents: across sessions they forget, and the common workaround -- replaying the whole history into the prompt -- is expensive, slow, and, as distractors accumulate, less accurate. Most memory systems win on cost or latency but still lose to the full-context baseline on accuracy, and benchmark numbers are reported on inconsistent, non-reproducible harnesses, so one system appears at wildly different scores across sources. We present Engram, an open-source, dual-process memory engine on a bi-temporal data model. A fast write path appends lossless episodes with no LLM on the critical path; an asynchronous path extracts atomic (subject, predicate, object) facts, builds a bi-temporal knowledge graph, and resolves contradictions without an LLM call per fact -- invalidating, never deleting, so every fact keeps provenance and a supersession chain. A hybrid read path fuses dense, lexical, graph, and recency/salience signals, applies a point-in-time ("as-of") filter, and assembles a compact, provenance-tagged context. On the full 500-question LongMemEval_S, graded by the official category-specific judge, Engram's lean configuration -- answering from a ~9.6k-token retrieved slice, never the full history -- scores 83.6% vs. 73.2% for full-context (+10.4 points, McNemar p < 10^-6) at ~8x fewer tokens (9.6k vs. 79k), with 0/500 errored. The gain needs a hybrid read path: facts alone lose recall, while facts plus retrieved chunks recover detail. We also contribute a neutral, in-repo evaluation harness with the official judge baked in and the full-context baseline in every table, publish the raw per-question logs, and document the measurement-integrity pitfalls (truncation, home-grown judges, full-history leaks) that silently distort memory benchmarks. Every number ships with a command to reproduce it.
https://arxiv.org/abs/2606.09900
Scientific workflows increasingly generate structured JSON data that is easy to exchange but difficult to interpret consistently across systems due to lacking semantic interoperability. While JSON Schema ensures structural validation, it provides no native support for Linked Data semantics. This paper presents an RDF Authoring View extending the open-source JSON Schema editor MetaConfigurator, enabling researchers to transform existing JSON, YAML, or CSV data into RDF using AI-assisted RML mappings, refine triples, execute SPARQL queries, visualize knowledge graphs, and export RDF serializations within a single integrated web interface. This workflow is supported by ontology-aware IRI auto-completion, bidirectional synchronization between JSON-LD text views and RDF triple tables, and AI-assisted SPARQL query generation from natural language hints. We demonstrate the workflow using laboratory data from metal-organic framework (MOF) synthesis experiments. Protocol data describing reagents, procedure steps, and quantities is converted from JSON to ontology-based JSON-LD via RML mappings. We then refine the semantic representation, query relationships between experimental conditions and outcomes, and explore the resulting knowledge graph interactively. This integrated environment bridges conventional structured data management with Semantic Web technologies while preserving experimental context and lowering technical barriers through AI assistance.
https://arxiv.org/abs/2606.07094
Graph neural networks (GNNs) applied to drug-drug interaction (DDI) prediction rely exclusively on molecular structure encoded as SMILES-derived graphs. Prior work in this series demonstrated that model performance is bounded by the structural information content of training labels -- an Information Ceiling -- that architectural refinements alone cannot overcome. The present study investigates whether pharmacogenomic prior knowledge from the PharmGKB database partially closes this ceiling by providing metabolic pathway context that is independent of, and complementary to, molecular structure. Cytochrome P450 (CYP) enzyme substrate, inhibitor, and inducer annotations for four clinically relevant isoforms (CYP2D6, CYP3A4, CYP2C19, CYP2C9) are extracted and incorporated as a 12-dimensional feature vector concatenated to the molecular embedding prior to interaction prediction. Experiments are conducted under both pair-level and drug-level data splits to quantify generalization to unseen drugs. Results indicate that knowledge graph (KG) augmentation substantially improves DDI type classification under pair-level split conditions (F1-macro: 0.532 vs. 0.241 baseline), while binary interaction detection and drug-level generalization remain bounded by the Information Ceiling (AUC inflation: 0.224 vs. 0.250 baseline). Mechanistic validation on strictly held-out compounds confirms that augmentation preferentially improves CYP2C9-mediated interaction prediction, with probabilities increasing from 0.033-0.117 (baseline) to 0.560-0.586 (KG-augmented). An extension to single-molecule toxicity prediction on the Tox21 benchmark confirms that the effect is contingent on pharmacogenomic annotation coverage. These findings motivate the multimodal framework proposed for the subsequent study in this series.
https://arxiv.org/abs/2606.07698
Policymakers in defence and defence-aligned sectors must monitor rapidly evolving research alongside sector priorities relevant to operational and strategic needs. In practice, these sources are fragmented across heterogeneous formats, disjoint repositories, and siloed update streams, making capability discovery slow and difficult to audit. We present Didact, a prototype that integrates publicly available defence reports and policy documents from Australia with a purpose-built knowledge graph derived from Australian research publications. Didact provides natural language conversations for policy-oriented workflows, and leverages a composite retrieval-augmented generation (RAG) pipeline. A key feature of Didact is an interactive Evidence Rail that visualises retrieved evidence and source relationships. Our evaluation of the output quality and runtime of Didact highlights its utility. While Didact has been co-developed as an academia-industry project for the Australian context, it is adaptable to other domains where knowledge is similarly fragmented. A demonstration video is available here:
https://arxiv.org/abs/2606.06942
Aim: Existing AI-assisted traditional Chinese medicine diagnostic tools suffer from opaque reasoning processes, passive interaction, and limited treatment plan presentation. This study proposes a knowledge-enhanced visual diagnostic system to improve the transparency and interpretability of syndrome differentiation and treatment. Methods: The system is built upon a Neo4j knowledge graph comprising 241 syndromes, 1,263 symptoms, and 2,485 relations. It incorporates a four-stage symptom matching pipeline (exact, semantic, fuzzy, and large language model verification), an information gain-driven proactive questioning strategy optimized with genetic algorithms, and a multimodal treatment presentation integrating artificial intelligence-generated illustrations, three-dimensional meridian-acupoint models, and evidence-based literature. Results: Knowledge graph constraints reduced non-standard outputs by 32%. Case studies validated the effectiveness of the interactive workflow across patient self-assessment, clinician-assisted diagnosis, and traditional Chinese medicine education. Automated paired-comparison evaluation across 30 cases further demonstrated significant improvements in diagnostic trust (Cohen's d = 1.82, p < 0.001), reduced cognitive load (improvements in four of five dimensions), and higher credibility of evidence-based references (4.21 vs. 2.95). Conclusions: The proposed system enhances the transparency of traditional Chinese medicine diagnostic reasoning and the interpretability of treatment plans through knowledge graph-driven visualization and multimodal interaction, offering a practical solution for trustworthy artificial intelligence-assisted traditional Chinese medicine applications.
https://arxiv.org/abs/2606.06869
Multimodal generative models produce fluent outputs but remain unreliable when generation must respect structured, domain-specific, or safety-critical knowledge. Existing methods incorporate knowledge through mechanisms such as prompt augmentation, guidance, latent editing, or fine-tuning, yet they are typically categorized by technique rather than by the component of the generative process they modify. We argue that knowledge infusion in iterative generative models is fundamentally anintervention-layer problem. Since thegenerative process unfolds as a trajectory of internal states, knowledge can act on four structurally distinct components of this process: the input/output boundary, the transition function, the intermediate state, and the model parameters. This maps to four intervention layers: surface, trajectory, latent, and parametric infusion. We instantiate the framework in diffusion models, map representative methods to all four layers, and derive design principles for multi-layer composition. In a controlled safety-alignment experiment using a multimodal knowledge graph with two diffusion backbones, we implement three of the four layers cumulatively, surface (input-side and output-side) and trajectory--latent (mid-generation). We show empirically that each additional layer addresses failure classes that prior layers cannot reach, reducing knowledge-violating outputs by 70.97% compared to vanilla generation and empirically confirming the framework's complementarity prediction.
https://arxiv.org/abs/2606.06356
Large language model (LLM) deployments for long-horizon tasks face a fundamental constraint: context windows are finite while productive work sessions are not. When history exceeds the Maximum Effective Context Window (MECW), critical structured information - architectural decisions, task transitions, file histories - is silently discarded. Existing mitigations treat history as flat text, destroying the relational structure that makes sessions resumable. We present TokenMizer, an open-source proxy system that models LLM session history as a typed knowledge graph. The schema defines 14 node types and 7 edge types. A hybrid extraction pipeline populates the graph incrementally, while a three-tier checkpoint system serializes it into compact resume blocks. An 8-layer compression pipeline reduces context overhead, and a semantic cache reduces repeated-query latency. Evaluated on a controlled benchmark of 21 sessions spanning 5 domains, TokenMizer demonstrates significant token economy. It produces resume blocks averaging 78 tokens (range: 42-124) - 2x smaller than evaluated baselines (159-170 tokens) - while achieving higher decision recall (+9-17 percentage points). Crucially, baselines only preserve that a technology was mentioned; TokenMizer preserves the rationale. Across all sessions, TokenMizer achieves mean task recall 51.0%, decision recall 46.6%, and file recall 58.7%. Variance reflects domain heterogeneity: explicit imperative phrasing (software engineering) scores higher than implicit reasoning (research). Ablation studies show fuzzy label matching is the dominant improvement factor (+33 pp task recall). The heuristic compression achieves 47.3% token reduction with zero external dependencies. TokenMizer provides a queryable alternative to text-retention baselines at half the token cost.
https://arxiv.org/abs/2606.06337
Entity alignment (EA) aims to identify equivalent entities across heterogeneous knowledge graphs (KGs) and is a key component of knowledge fusion and cross-KG reasoning. The recent EA foundation model demonstrates that alignment knowledge, once pretrained, can be directly applied to diverse previously unseen KG pairs. However, it still underuses structural context in two places: cross-KG interaction is weak during encoding, and final candidate ranking still relies too heavily on coarse similarity. We address these limitations with ContextEA, an enhanced encoder-decoder framework for transferable EA. On the encoder side, we introduce a cross-KG interaction encoder that unifies the two KGs with anchor bridges and performs earlier relation-aware cross-graph propagation. On the decoder side, we introduce a structural calibration decoder that calibrates alignment scores with entity-level, neighborhood-level, relation-level, and anchor-aware structural evidence. This design strengthens both structural context construction and structural context exploitation while remaining lightweight. Experiments on 29 EA datasets in OpenEA, SRPRS, and DBP show consistent gains over strong transferable baselines. Notably, the pretrained ContextEA already surpasses the finetuned baselines on all three benchmark groups, demonstrating substantially stronger transfer to unseen KGs. These results suggest that explicitly harnessing structural context is an effective direction for improving EA foundation models.
https://arxiv.org/abs/2606.06109
Retrieval-Augmented Generation (RAG) fails systematically on queries requiring structural reasoning over interconnected entities. We compare eight retrieval architectures for aerospace supply chain intelligence, progressing from text retrieval through graph traversal to graph computation. Using a 46-node knowledge graph with 64 typed edges, we evaluate 23 queries across 10 intent categories and demonstrate that five query classes are structurally unreachable for vector retrieval. Our central finding is the operator vocabulary thesis: the barrier to LLM-based graph reasoning is not model intelligence but the computational operators available as tools. An LLM Query Planner with 9 typed traversal primitives outperforms bespoke handlers (F1 = 0.632 vs. 0.472) while generalizing to unseen queries. Adding 6 graph computation tools, the LLM selectively adopts them for exactly the query categories where traversal fails. We also identify a measurement gap: entity-level F1 systematically underscores structural queries where comprehensive answers are correct.
https://arxiv.org/abs/2606.06003
Graph Retrieval-Augmented Generation (Graph-RAG) enhances multihop question answering by organizing corpora into knowledge graphs and routing evidence through relational structure. However, practical deployments face two persistent bottlenecks: (i) mixed-difficulty workloads where one-size-fits-all retrieval either wastes cost on easy queries or fails on hard multihop cases, and (ii) extraction loss, where graph abstraction omits fine-grained qualifiers that remain only in source text. We present A2RAG, an adaptive-and-agentic GraphRAG framework for cost-aware and reliable reasoning. A2RAG couples an adaptive controller that verifies evidence sufficiency and triggers targeted refinement only when necessary, with an agentic retriever that progressively escalates retrieval effort and maps graph signals back to provenance text to remain robust under extraction loss and incomplete graphs. Experiments on HotpotQA and 2WikiMultiHopQA demonstrate that A2RAG achieves +9.9/+11.8 absolute gains in Recall@2, while cutting token consumption and end-to-end latency by about 50% relative to iterative multihop baselines.
https://arxiv.org/abs/2601.21162
Real-world data spans tables, documents, and semi-structured files with implicit semantics. Querying this data requires integrating evidence across inconsistent schemas and formats, yet existing approaches either demand costly manual engineering or bypass structure entirely. We present a system that automatically discovers an executable schema from raw multi-source data and uses it as a shared contract for knowledge graph construction and query-time retrieval. A closed-world field catalog constrains LLM-based schema discovery to attested fields; deterministic structural analysis infers identity keys, foreign keys, and source hierarchy; and the resulting schema drives extraction, deduplication, and cross-source linking into a provenance-aware knowledge graph. At query time the schema -- optionally extended via a monotonic protocol -- conditions a multi-tool agent routing retrieval across structured lookup, graph traversal, and vector search, returning grounded answers with traceable citations. In controlled zero-shot comparisons using the same LLM, data, and evaluation harness, the system improves over retrieval-only and decomposition-based baselines across four QA benchmarks, with ablations showing that schema-conditioned routing, structural intelligence, and schema-guided construction each contribute to the gains.
https://arxiv.org/abs/2606.05415
We describe a practical architecture for making the Maritime Information Exchange Model (MIEM) and the broader Rich Semantic Track model tractable using current large language model (LLM) technology. The barrier to adoption of semantic track models in defense and law enforcement has been the requirement that operators learn formal ontology languages and manually encode observations as typed logical assertions. We propose eliminating this barrier entirely: operators contribute observations in natural language; an LLM translates these into typed Semantic Assertion Records (SARs), which are named case frames that capture n-ary relations in a single compact structure; a knowledge graph accumulates the SARs; and a second LLM pass performs inference, anomaly detection, and hypothesis ranking over the graph. We work through two detailed examples (a 9/11-era pre-attack indicator scenario and a maritime cargo inspection scenario) showing the full pipeline from natural language input to SAR representation to inference output. We argue that this architecture makes the Track Model and MIEM immediately deployable with current technology, establishes prior art against proprietary enclosure of the approach, and grounds the method in a theoretical framework connecting semantic track representations to neural manifold geometry.
https://arxiv.org/abs/2608.24892
Language models acting as agents over knowledge graphs generate Cypher queries that fail structurally (crashing at the database) or semantically (executing but returning wrong results). We place a pre-execution gate between query generation and a production Neo4j database. The gate validates structure through a four-backend chain culminating in execution against a mirror graph at 5.6 ms median latency. Structurally broken queries are routed to a corrector that iterates structured error feedback through a language model. On seven CypherBench schemas (2348 questions, ACL 2025) the pipeline maintains generation accuracy on every model tested, confirming it operates as a safe defensive layer. The corrector achieves 81% to 95% success across five models (mean 89%). On a template-generated corpus across nine schemas the gate catches 100% of parse errors, 100% of constraint violations, and 100% of schema-reference errors in path queries with labelled endpoints, at zero false positives across 1135 queries. Property sibling-swaps where the substituted name is valid on the target label score 0%, marking the formal boundary where structural validation ends and semantic validation must begin. A planner-based cost gate flags catastrophic plan structures before execution.
https://arxiv.org/abs/2606.04645
Large language models have shown strong performance in natural language generation and downstream reasoning tasks, but they still struggle with logical consistency, factual grounding, and interpretability in complex multi-step reasoning. To address these limitations, this paper proposes SGR, a stepwise reasoning enhancement framework that integrates large language models with external knowledge graphs through query-relevant subgraph generation. Given an input question, SGR first extracts key entities, relations, and constraints to construct a structured schema, then retrieves compact subgraphs from a knowledge graph using schema-guided querying. The generated subgraphs provide explicit relational evidence that guides the language model through step-by-step reasoning. In addition, SGR combines direct Cypher-based reasoning with collaborative reasoning integration, allowing candidate answers from multiple reasoning paths to be validated and aggregated according to both model confidence and graph consistency. Experiments on benchmark datasets including CWQ, WebQSP, GrailQA, and KQA Pro demonstrate that SGR improves reasoning accuracy and Hits@1 performance over standard prompting and several knowledge-enhanced baselines. Ablation studies further show that schema guidance and Neo4j-based retrieval are both crucial to the effectiveness of the framework. These results indicate that dynamically generated external subgraphs can improve the accuracy, robustness, and interpretability of LLM-based reasoning.
https://arxiv.org/abs/2606.04454
Traditional fake news detection methods are falling behind as multimodal misinformation grows more advanced, seamlessly blending deceptive text, manipulated visuals, and factually incorrect claims. Most prior work focuses on text-image fusion or applies external knowledge only as a post-processing step, limiting their ability to detect deeper semantic inconsistencies. In this paper, we introduce KITE (Knowledge-Integrated Text-Image Encoder), a tri-modal fake news detection framework that jointly models textual, visual, and factual knowledge representations. KITE leverages Roberta [23,14] and CLIP [24] for linguistic and visual encoding, while a Graph Attention Network (GAT) processes structured facts retrieved from Wikidata. KITE uses cross-modal attention [9] within a multimodal transformer to integrate text, visual, and knowledge features, helping it understand how each modality relates to one another. Modality-specific confidence scores are generated alongside the final prediction, offering interpretability by indicating which input type most influenced the decision. Evaluations on benchmark datasets demonstrate that KITE significantly outperforms unimodal and bimodal baselines, particularly in scenarios involving image-text mismatches or contradictions with external knowledge.
https://arxiv.org/abs/2606.07651
Multi-Document Summarization (MDS) plays a critical role in distilling essential information from collections of textual data. Existing approaches often struggle to capture complex inter-document relationships, rely heavily on large amounts of labeled data for supervised training, or exhibit limited generalization across domains and languages. To address these limitations, we present a training-free mixture-of-agents framework for MDS that leverages the complementary strengths of large language models (LLMs) and knowledge graphs. Our approach decomposes summarization into specialized agent tasks: extractive selection, knowledge-aware abstraction, and iterative refinement, each operating without task-specific fine-tuning. We unify their outputs using a multi-perspective consistency mechanism guided by LLMs. Experiments across four datasets in English and Vietnamese demonstrate state-of-the-art or competitive performance, validating the effectiveness and adaptability of our modular design.
https://arxiv.org/abs/2606.03867
Knowledge Graph-based Retrieval-Augmented Generation (KG-RAG) enables natural language interaction with structured enterprise knowledge, yet existing agentic approaches that perform well on public benchmarks often fail to generalize to real-world enterprise Knowledge Graphs (KGs), which are dense, schema-driven, and operationally constrained. To address these limitations, we propose SCAIR (Schema-Conditioned Agentic Iterative Reasoning), a training-free framework that integrates structured planning with controlled iterative reasoning by injecting schema-conditioned structural priors and enforcing schema-aware traversal during multi-hop reasoning. Experiments on an enterprise-oriented benchmark constructed from a real-world Configuration Management DataBase (CMDB) demonstrate that SCAIR substantially improves performance over existing KG-RAG methods. Crucially, our study highlights that reliable enterprise graph reasoning cannot rely on generic agentic designs; instead, it must explicitly incorporate the target domain's structural and operational constraints into the reasoning process. We demonstrate that by aligning agent design with business logic, substantial performance gains can be achieved without the need for costly model retraining.
https://arxiv.org/abs/2607.22571
Knowledge Graphs (KGs) are widely used to mitigate the limitations of Large Language Models (LLMs), such as outdated knowledge and hallucinations. Existing LLM-KG integration frameworks typically rely on predefined operators to retrieve factual knowledge from KGs and inject it into prompts for answer generation. This paradigm faces two critical bottlenecks: 1) Inflexibility: The predefined operators are limited in scope and thus lack sufficient compositional expressiveness to fully capture the complex semantics required by KG questions. 2) Unscalability: Direct injection of factual knowledge into prompts limits scalability in handling large-scale factual knowledge. To address these two bottlenecks, we propose Code-on-Graph (CoG), a programmatic reasoning framework for LLM-KG integration. Specifically, given the factual knowledge retrieved at each reasoning step, CoG first identifies the corresponding KG schemas and represents these schemas as Python classes, which serve as abstract interfaces to the retrieved facts. It then generates executable code grounded in these classes, with the retrieved facts instantiated as objects of the corresponding classes during execution. This design enables flexible code-based reasoning while avoiding the direct injection of large-scale factual knowledge into prompts. Experiments on WebQSP, CWQ, and GrailQA demonstrate that CoG outperforms prior state-of-the-art models by up to 10.5%.
https://arxiv.org/abs/2606.03705
Large Reasoning Models (LRMs) have demonstrated impressive capabilities in many tasks, yet they struggle with reliably following multiple instructions, either by failing to satisfy individual constraints or by struggling to balance competing constraints simultaneously. We formalize this challenge as the Constraint Adherence Problem (CAP). This paper introduces a novel framework that addresses CAP by representing instructions as a structured knowledge graph of constraints. Our approach, Constraint Relationship Graph Completion (CRGC), explicitly models relationships between constraints, identifies adherence challenges, and discovers ``bridge constraints'' that help the model better focus on and reconcile requirements. Bridge constraints act as auxiliary instructions that make primary constraints more salient and compatible. Unlike existing approaches that enhance instruction following through general training methods, CRGC specifically improves constraint satisfaction by leveraging the model's own knowledge to create better pathways for generation. Experiments across three popular instruction following datasets demonstrate that our approach reduces constraint violations by 39% compared to standard prompting while maintaining reasoning abilities of large reasoning models.
https://arxiv.org/abs/2606.03624