A single vulnerability in a widely used library can cascade through millions of dependent applications, yet more than half of vulnerability database entries contain missing or incorrect affected-library information. Existing automated approaches neglect the relational structure of vulnerability databases, treating identification as an isolated text retrieval problem. In this paper, we propose Athena, the first graph-based approach for vulnerability affected library identification. Athena models vulnerability databases as a knowledge graph and reformulates the identification problem as knowledge graph completion (KGC). It comprises three key modules: a Modeling module that constructs a security knowledge graph integrating CVEs, libraries, CWE weakness types, CPE products, and software ecosystems; a Completion module that applies a modular KGC backbone to predict missing affected libraries for a given CVE via link prediction; and a Re-ranking module that retrieves KGC candidates and rescores them using a fine-tuned LLM augmented with knowledge graph embeddings, jointly leveraging structural and textual information. Our experiments on VulLib demonstrate that Athena significantly outperforms four state-of-the-art baselines, achieving a 32% improvement in Avg. F1 over the best baseline (i.e., VulLibGen). Notably, our KGC backbone with only 110M parameters already surpasses VulLibGen's best configuration at 7B parameters, demonstrating the effectiveness of graph-based modeling; the re-ranking module then provides substantial further gains, consistently outperforming the best baseline across all evaluated LLM backbones.
https://arxiv.org/abs/2609.01187
We present the zbMATH Open Knowledge Graph, a large-scale RDF knowledge graph (KG) covering more than 250 years of mathematical scholarship. Unlike existing scholarly knowledge graphs that primarily capture bibliographic metadata and citation structures, the zbMATH Open KG integrates expert-curated semantic content, including reviews, keywords, subject classifications, software references, and disambiguated authorship. This combination of domain-specific representation of mathematical knowledge and extensive temporal coverage supports analyses that require fine-grained exploration of mathematical concepts, research fields, and scholarly relationships over time. The resulting graph comprises 34 million entities and 168 million RDF triples represented using established Semantic Web vocabularies, supporting interoperability and FAIR data principles. We further demonstrate its capabilities through query-driven historically grounded scholarly exploration use cases, illustrating how the knowledge graph can surface relationships and patterns that may be difficult to identify from bibliographic and citation information alone. The zbMATH Open KG provides an open semantic infrastructure for studying the development of mathematical knowledge and tracing scholarly connections across centuries of scholarship.
https://arxiv.org/abs/2609.00969
Effective humanitarian response depends on the rapid synthesis of heterogeneous, high-volume information sources - a task that routinely exceeds human analytical capacity in the critical early hours of a crisis. We present a pipeline that combines structured disaster records from EM-DAT with unstructured documents from ReliefWeb and the European Media Monitor (EMM) to produce source-grounded disaster storylines and causal knowledge graphs supporting situational awareness for responders and analysts. Using Retrieval-Augmented Generation, the pipeline extracts structured storylines - tabular event profiles covering 17 fields, from severity and key drivers to child-sensitive impact indicators - and constructs causal knowledge graphs where each node and edge is enriched with citation-grounded explanatory narratives, enabling full traceability back to primary sources. We evaluate the system on three diverse crisis use cases through a human evaluation involving 9 domain expert and 9 non-expert evaluators. Results confirm high retrieval precision, strong faithfulness of extracted causal relations, and a clear expert preference for citation-grounded components over ungrounded alternatives. The pipeline is designed to scale to the full EM-DAT catalogue, with the goal of publicly releasing a narrative-enriched version of the database.
https://arxiv.org/abs/2609.00858
Large language models (LLMs) excel at reasoning but struggle with knowledge-intensive questions due to limited context and parametric knowledge. However, existing methods that rely on finetuned LLMs or GNN retrievers are limited by dataset-specific tuning and scalability on large or unseen graphs. We propose the LLM-KGFR collaborative framework, where an LLM works with a structured retriever, the Knowledge Graph Foundation Retriever (KGFR). KGFR encodes relations using LLM-generated descriptions and initializes entities based on their roles in the question, enabling zero-shot generalization to unseen KGs. To handle large graphs efficiently, it employs Asymmetric Progressive Propagation (APP)- a stepwise expansion that selectively limits high-degree nodes while retaining informative paths. Through node-, edge-, and path-level interfaces, the LLM iteratively requests candidate answers, supporting facts, and reasoning paths, forming a controllable reasoning loop. Experiments demonstrate that LLM-KGFR achieves strong performance while maintaining scalability and generalization, providing a practical solution for KG-augmented reasoning.
https://arxiv.org/abs/2511.04093
Hierarchical Knowledge graph (KG)-based retrieval augmented generation (RAG) has emerged as a powerful approach for supporting large language models with structured knowledge. However, there are primary challenges: (i) the lack of methods for automatic KG construction using ontology expansion for low-resource languages such as Vietnamese, (ii) the absence of systematic evaluation for knowledge retrieval strategies leveraging the hierarchical structures. In this paper, we propose an end-to-end pipeline for KG construction and retrieval strategies evaluation. In the KG construction, we employ a three-phase hybrid relation extraction pipeline: intra-batch deduplication via Union-Find, approximate cross-batch search, and LLM extraction with a centroid filter that reduces prompts combined with a five-step dual-LLM validator to prevent bloated ontology. A two-tier architecture consists of unmergeable structural nodes to preserve the document structure and mergeable content nodes. The retrieval evaluation consists of three graph traversal strategies: Top-Down, Horizontal, and Bottom-Up, which are evaluated on a synthetically generated benchmark of 1,210 Vietnamese queries from 109 subgraphs, categorized by five query directions. In this paper, we construct the tree knowledge graph from Vietnamese high school History textbooks (nearly 400 pages) to produce 750 nodes and 4,341 semantic edges with controlled ontology growth from 40 to 41 types. Among experimental graph traversal strategies, the Top-Down strategy with structure surpasses the vector baseline by 4.7 percentage points in NDCG@10. As a result, tree-structural information provides valuable information beyond flat cosine similarity but degrades performance when the query does not require structural context.
https://arxiv.org/abs/2609.00763
Security teams and researchers choose knowledge-graph extraction tooling for threat reports on the strength of published triple-F1 scores, yet those scores depend on how predicted triples are matched to gold annotations. We could reimplement the stated matching rule for only five of twelve inspected systems. Re-scoring ten system outputs on shared documents under eight protocols reverses eleven of forty-five pairwise orderings; one fixed prediction set spans 0.16-0.70 F1. On GRID's external 378-item calibration set, no mechanical matcher (lexical, embedding, or entailment) agrees with multi-reviewer adjudication above 71%, whereas an LLM judge reaches 86%. To separate component effects from matcher rewards, we build CTIForge, whose deterministic validation layer can vary while extraction is held byte-identical. Across seven tested deployment configurations, validation raises precision for all four hosted backbones and lowers it for all three offline backbones. Because backbone, decoding, and backend-specific prompting covary, this is a descriptive split rather than an isolated serving effect. It coincides with a roughly 2.8-fold increase in actions explicitly disputing entity type, consistent with hand-written rules encoding the conventions of the extractor against which they were developed. We release the pipeline, protocol suite, and per-triple audit records.
https://arxiv.org/abs/2609.01671
Large Vision-Language Models (LVLMs) achieve strong performance on image-grounded text generation and visual question answering. However, it remains difficult for them to comprehensively and accurately describe the factual relations among the entities and concepts associated with the objects depicted in an image. In this work, we propose a framework that efficiently exploits factual information from a knowledge graph via retrieval-augmented generation (RAG), with the goal of enabling LVLMs to generate detailed and accurate image explanations. Specifically, our method alternates between answer generation and knowledge-graph retrieval, and controls the search using a correctness judgment, thereby acquiring the necessary and sufficient factual information efficiently. We also construct a knowledge graph for the artwork domain (ExpArt-KG), in which the correspondence between images and entities is unambiguous. Applying the proposed method to this knowledge graph, we show experimentally that it improves the level of detail of artwork explanations and reduces the retrieval cost of external knowledge while maintaining generation quality comparable to that of iterating a fixed number of times.
https://arxiv.org/abs/2609.00629
Retrieval-Augmented Generation (RAG) mitigates large language models (LLMs) hallucinations, yet conventional dense retrieval struggles with the complex reasoning paths of multi-hop question answering (QA). Graph-based RAG captures multi-step relationships but suffers from severe semantic drift and high online latency due to noisy global graph traversals. Thus, we propose ISO-RAG (ISOperimetric Retrieval-Augmented Generation), a geometry-aware RAG framework. By projecting the underlying knowledge graph into a hyperbolic Poincare ball to precompute node-wise isoperimetric profiles, ISO-RAG prunes spurious edges during retrieval, restricting the search space to a strictly localized subgraph. This topological purification regulates Personalized PageRank (PPR) diffusion driving the retrieval process, ensuring exact and low-latency convergence. Experiments on multi-hop QA benchmarks demonstrate that ISO-RAG outperforms state-of-the-art baselines by average absolute gains of 10.0% in retrieval recall and 4.3% in downstream exact match, achieving a superior accuracy-efficiency trade-off by fundamentally eliminating the latency bottleneck of global traversals. Our source code is available at this https URL.
https://arxiv.org/abs/2609.00513
For emerging scientific research domains, local Small Language Models (SLMs) are becoming more attractive, as they offer stronger privacy control and more stable deployment pipelines than Large Language Models. However, in practice, scientific question-answering on SLMs often operates under inevitable constraints: small literature collections, fragmented evidence, limited context window and reasoning abilities. We propose the Evidence-Grounded Typed Knowledge Graph (EGT-KG), a retrieval framework to improve information retrieval with local SLMs. We assessed three question-answering settings: a vanilla Retrieval-Augmented Generation (RAG) workflow and two EGT-KG workflows: an automatically generated relation schema (AS) and an expert-defined relation schema (ES). Our experiments were evaluated with a six-dimensional evaluation framework (S3CRF: Soundness, Correctness, Completeness, Conciseness, Relevance, Fluency) on a Biopolymer-bound Soil Composite literature benchmark, showing that EGT-KG outperforms the vanilla RAG method in most settings, with the best improvement from llama3:8b: a Final Score of 70.37 (+14.67%) and 68.82 (+12.14%) by AS/ES EGT-KG variants.
https://arxiv.org/abs/2609.00479
General-purpose NLP embedding models perform well on linguistic tasks, but their ability to capture symbolic ontological structure remains unclear. We introduce AVA, a systematic framework for evaluating whether embeddings distinguish logic-sensitive relational semantics in ontologies and knowledge graphs. AVA comprises 171,007 contrastive triplets derived from 163 heterogeneous ontologies using hierarchy inversion, relation substitution, and disjointness injection. Each triplet contains an ontology statement, a semantically equivalent paraphrase, and a logic-sensitive hard negative with contradictory relational meaning. We evaluate more than 25 state-of-the-art embedding models and find substantial limitations: the best model achieves only 0.739 triplet accuracy, while hard negative accuracy falls to 0.135. Fine-tuning improves discrimination by a large margin but transfers poorly to downstream Semantic Web tasks, including taxonomy discovery and ontology alignment. Further analysis suggests that improvements stem partly from perturbation-specific pattern recognition rather than robust ontological understanding. These findings reveal a persistent gap between linguistic representation learning and ontology-level discrimination, challenging the assumption that strong NLP benchmark performance translates to Semantic Web competence.
https://arxiv.org/abs/2609.00177
Ontology alignment (OA) has evolved through several methodological paradigms, ranging from lexical and structural aligners to knowledge graph embedding (KGE) models and, more recently, Large Language Model (LLM)-based approaches. Although modern OA frameworks provide unified ecosystems for deploying these heterogeneous aligners, mechanisms for systematically reconciling their complementary and sometimes conflicting predictions remain relatively underexplored. We present OntoAligner-Ensemble, a modular and aligner-agnostic framework that combines candidate correspondences through a configurable two-stage process comprising voting-based fusion strategies followed by post-fusion selection policies. The framework supports any aligner implemented within OntoAligner that produces candidate correspondences, enabling diverse alignment paradigms to be integrated through a unified decision process. To demonstrate its effectiveness, we instantiate the framework using representative lightweight string-aligner, KGE-based, and Retrieval-Augmented Generation aligners powered by both open-weight and API-based LLMs. We evaluate individual aligners and ensemble configurations across eight benchmark tasks from five OAEI tracks spanning biomedical to beyond-equivalence. The results show that ensemble fusion consistently improves the balance between precision and recall and frequently outperforms standalone aligners across diverse domains. Furthermore, our analysis reveals that ensemble composition directly affects the precision-recall trade-off: heterogeneous cross-paradigm ensembles generally improve precision, whereas homogeneous LLM ensembles more often achieve higher overall F1-scores. These findings demonstrate that systematic ensemble learning offers a robust and reproducible strategy for OA while providing practical guidance for selecting ensemble compositions under different alignment scenarios.
https://arxiv.org/abs/2608.31137
Despite the strong capabilities of multimodal large language models (MLLMs), their parametric knowledge remains incomplete and difficult to update, motivating multimodal retrieval-augmented generation (RAG) to ground responses in external text and images. However, existing benchmarks face two major limitations: (i) they typically emphasize single-hop retrieval or reasoning over a small set of provided contexts rather than open-domain evidence discovery; and (ii) they provide fragmented coverage of cross-modal reasoning paths, leaving complex multi-hop and multi-image reasoning underexplored. In this paper, we introduce CrossModalQA, an open-domain benchmark for evaluating multimodal retrieval and reasoning over heterogeneous corpora. CrossModalQA contains 1,863 question-answer pairs constructed from 4,987 Wikipedia articles and 4,431 Wikimedia Commons images. It covers five complementary reasoning paths: vision-to-text, text-to-vision, vision-to-text-to-vision, multi-image intersection, and image-set reasoning. Every question requires retrieving and composing distributed textual and visual evidence, with an average reasoning depth of 3.50 hops. We construct the benchmark through multimodal knowledge graph-guided subgraph sampling and apply rule-based consistency checking and LLM verification to ensure multimodal dependence and traceable evidence. Extensive experiments demonstrate that existing multimodal RAG systems struggle to recover complete evidence chains and can underperform closed-book models when incomplete retrieval introduces distracting context. Further analysis reveals that complete cross-modal retrieval contributes more to answer accuracy than generator scaling, while multi-image retrieval and reasoning remain the primary bottlenecks limiting end-to-end performance.
https://arxiv.org/abs/2609.05518
Artificial intelligence (AI) and natural language processing (NLP) are increasingly used to extract, integrate, and interpret biomedical knowledge relevant to cancer genomics, yet their translation into routine clinical oncology has been comparatively slow. The central challenge is not computational capability alone, but trustworthy integration into clinical workflows. This review examines how NLP and AI support the cancer genomics pipeline, from literature mining and automated variant interpretation to clinical trial matching, knowledge graph construction, and multimodal data integration. We identify four interrelated translational failure domains: evidence inconsistency, explainability and uncertainty, data governance and reproducibility, and interoperability. Rather than considering these challenges in isolation, we take a systems-level view, focusing on their interaction across the translational pathway. We propose a conceptual framework and roadmap for addressing these domains through rigorous validation, uncertainty-aware methods, interoperable infrastructures, regulatory alignment, and human oversight across the AI lifecycle. Progress toward routine clinical use will depend less on further improving model capability than on systematically addressing these interacting failure domains from development through deployment and post-deployment monitoring.
https://arxiv.org/abs/2608.30912
Embedding methods have become popular due to their scalability on link prediction and/or triple classification tasks on Knowledge Graphs (KGs). Embedding models are trained relying on both positive and negative samples of triples. However, since KGs generally contain only positive assertions, negative samples are artificially generated through negative sampling strategies, ranging from simple random corruption to more sophisticated approaches that exploit structural, semantic, or embedding information. The design and implementation of advanced negative samplers remains challenging, as most popular Knowledge Graph Embedding (KGE) libraries provide support only for basic strategies and lack a unified framework for developing more advanced and customized solutions. To address this gap, we introduce PyKEEN-NSX, an extension of PyKEEN, the popular KGE framework, that provides a modular engineered abstraction for negative sampling. The proposed architecture separates the generation of candidate negative pools, conditioned on an explicit context, from the selection strategy, enabling the development and integration of static, schema-aware and dynamic approaches within a consistent framework. Based on this abstraction, we implement six negative samplers, while remaining fully compatible with existing PyKEEN workflows and pipelines. As a proof of concept, we study negative availability across four datasets, showing that constrained pools frequently fall below the requested number of negatives, so that the encoded criterion is to a large extent replaced by the random fallback that supplements them.
https://arxiv.org/abs/2608.30652
Path-finding over knowledge graphs has become an effective way to ground LLM reasoning on multi-hop questions. However, biomedical QA introduces two distinct challenges that general-domain methods are not designed for: (i) queries do not expose intermediate reasoning and can be answered through multiple valid pathways, and (ii) biomedical knowledge graphs are densely connected, so path-finding methods easily take wrong turns. To address these challenges, we propose AdaPath, a path-finding framework that retrieves query-adaptive meta-paths from Path-Bank, which captures both query semantics and biomedical knowledge graph structure. AdaPath provides the missing cues in biomedical queries while effectively pruning dense knowledge graph neighborhoods during multi-hop reasoning. We further release BioStrat-QA, a biomedical KGQA benchmark that stratifies multi-hop queries by how much intermediate reasoning they expose. Across biomedical KGQA benchmarks, AdaPath consistently outperforms baselines, sustaining meaningful path-finding even when multi-hop queries expose less surface information. The source code is available at this https URL.
https://arxiv.org/abs/2608.30556
Biomedical artificial intelligence (AI) systems increasingly extract, organize, and reuse scientific claims from literature, clinical trials, and regulatory documents. But automatic extraction alone does not make a claim reliable evidence: a claim becomes useful only when it can be traced to its source, linked to the quantitative details that support it, and read within its biomedical context and uncertainty. This matters as large language models (LLMs) and increasingly autonomous systems drive evidence synthesis, knowledge graph (KG) construction, and decision support. Many text-mining and LLM pipelines remain relation-centric: they capture entities and relations such as Drug--TREATS--Disease, but drop the dose, effect size, population, comparator, uncertainty, and conditions under which a claim holds. Such relations can look actionable yet remain hard to verify, compare, or reuse. In this perspective, we argue for a shift toward quantitative evidence mining---extracting values, units, measured entities and properties, context, uncertainty, provenance, and plausibility as structured evidence units that populate evidence-aware KGs and can be checked for source grounding, unit consistency, completeness, and biological plausibility. We outline a framework for plausibility-aware AI that treats extracted claims not as final answers but as auditable evidence objects, making clear what was measured, how much it changed, in which setting, with what uncertainty, and from which source. The central risk is not only incorrect extraction, but claims that look like evidence while lacking the structure needed to trust them.
https://arxiv.org/abs/2608.30393
Knowledge graph completion requires models to use both textual descriptions and relational structure. Existing LLM-based methods either encode KG structure as discrete tokens or refine a restricted set of candidate entities, and these two directions have largely been studied separately. We propose CoSC for LLM-based KGC, which combines discrete structural coding with similar entity information. Specifically, an LLM generates an initial candidate entity ranking from discrete structural codes, after which information from entities with structures similar to that of the query entity refines the ranking. Experiments on FB15k-237 show that CoSC outperforms existing baselines on MRR and Hits@10 while remaining competitive on Hits@1.
https://arxiv.org/abs/2608.30235
This paper introduces a hybrid fact-checking framework that integrates Knowledge Graph-based semantic memory with adversarial multi-agent reasoning for explainable misinformation detection. The proposed system follows a memory-first, web-fallback architecture, in which input claims are initially evaluated against a dual-index Knowledge Graph through Sentence-BERT-based semantic retrieval and Natural Language Inference. When the evidence retrieved from the graph is insufficient to support a reliable decision, the framework collects information from trusted web sources and assesses it using an adversarial tribunal composed of support, contradiction, and judging agents. A graph-aware confidence mechanism combines semantic similarity, NLI confidence, and structural graph evidence to determine whether internal knowledge is sufficient, thereby reducing unnecessary web retrieval. Following verification, validated information is transformed into structured triples and incorporated into the Knowledge Graph, supporting the incremental expansion of the system's semantic memory. Experimental evaluation on a curated COVID-19 misinformation benchmark demonstrates that the proposed framework achieves an accuracy of 97.4\% and a macro-averaged F1-score of 92.6% on resolved claims, outperforming a Llama~3.3~70B baseline, which obtains an accuracy of 87.7% and a macro-averaged F1-score of 86.3%.
https://arxiv.org/abs/2608.29617
Large language model (LLM) agents need durable, faithful memory of everything a user or organization has said and stored, yet most memory systems commit to a single organizing structure (a fact store, a vector index, or a knowledge graph) and inherit its blind spots. We present Agent Zero Memory, a provenance-aware long-term memory system that distils a user's conversations, files, and connected sources into three parallel memory systems, each capturing a different facet of the same history: an episodic Memory Events timeline that makes when and what changed first-class, an associative entity-event knowledge graph that links people and projects across sessions, and a semantic, curated, citation-locked Hierarchical Documentary Memory (HDM) of durable facts. A retrieval turn runs an intent gate (so self-contained turns add no latency), a source router, and three concurrent agentic searches, one per system, each a tool-using loop over hybrid (embedding + lexical) search under agent-controlled filters; their grounded, cited answers are integrated into one answer with a single confidence. We formalize the reading discipline: every learned item is a provenanced item carrying its origin, timestamp, and evidence pointer, and every answer is read under a citation lock, so it may cite only evidence its reader actually opened; fabrication is structurally excluded and the system abstains rather than guesses. On two public benchmarks the system sets a new state of the art: 95.60% on LongMemEval and 93.60% on LoCoMo, improving over the strongest prior systems by +0.73 and +1.10 points. A controlled study across eight backbone LLMs characterizes the accuracy-cost-latency frontier: accuracy varies by only 3.4 points while per-query cost varies by ~30x, with near-state-of-the-art quality at up to 20x lower cost per query, the signature of memory-driven, rather than model-driven, quality.
https://arxiv.org/abs/2608.29606
The most disruptive step that enterprises of small-medium size and maturity can take to make the most of the latest technological advances in AI is to step back from the hype and focus on establishing or reviving a good knowledge foundation layer. It is a hard message to present to the executive team; therefore, it needs to be backed by evidence, and its implementation needs to be of minimal impact on the existing processes. In this vision statement, we discuss how we need to rethink what evidence speaks to the decision-makers and propose a low-impact data strategy that adapts to the existing and ever-changing data flows and processes across the company. We firmly believe that knowledge graph techniques will increasingly become non-negotiable in the data strategy of an AI-powered enterprise, provided that we approach their design in a modular, dynamic and cross-functional way.
https://arxiv.org/abs/2608.29368