Knowledge_Graph
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AROMA: Augmented Reasoning Over a Multimodal Architecture for Virtual Cell Genetic Perturbation Modeling
2026-04-22 07:10:45Zhenyu Wang, Geyan Ye, Wei Liu, Man Tat Alexander NgAbstract
Virtual cell modeling predicts molecular state changes under genetic perturbations in silico, which is essential for biological mechanism studies. However, existing approaches suffer from unconstrained reasoning, uninterpretable predictions, and retrieval signals that are weakly aligned with regulatory topology. To address these limitations, we propose AROMA, an Augmented Reasoning Over a Multimodal Architecture for virtual cell genetic perturbation modeling. AROMA integrates textual evidence, graph-topology information, and protein sequence features to model perturbation-target dependencies, and is trained with a two-stage optimization strategy to yield predictions that are both accurate and interpretable. We also construct two knowledge graphs and a perturbation reasoning dataset, PerturbReason, containing more than 498k samples, as reusable resources for the virtual cell domain. Experiments show that AROMA outperforms existing methods across multiple cell lines, and remains robust under zero-shot evaluation on an unseen cell line, as well as in knowledge-sparse, long-tail scenarios. Overall, AROMA demonstrates that combining knowledge-driven multimodal modeling with evidence retrieval provides a promising pathway toward more reliable and interpretable virtual cell perturbation prediction. Model weights are available at this https URL. Code is available at this https URL.
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URL
https://arxiv.org/abs/2604.20263
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Construction of a Battery Research Knowledge Graph using a Global Open Catalog
2026-04-22 06:45:42Luca Foppiano, Sae Dieb, Malik Zain, Kazuki Kasama, Keitaro Sodeyama, Mikiko TanifujiAbstract
Battery research is a rapidly growing and highly interdisciplinary field, making it increasingly difficult to track relevant expertise and identify potential collaborators across institutional boundaries. In this work, we present a pipeline for constructing an author-centric knowledge graph of battery research built on OpenAlex, a large-scale open bibliographic catalogue. For each author, we derive a weighted research descriptors vector that combines coarse-grained OpenAlex concepts with fine-grained keyphrases extracted from titles and abstracts using KeyBERT with ChatGPT (gpt-3.5-turbo) as the backend model, selected after evaluating multiple alternatives. Vector components are weighted by research descriptor origin, authorship position, and temporal recency. The framework is applied to a corpus of 189,581 battery-related works. The resulting vectors support author-author similarity computation, community detection, and exploratory search through a browser-based interface. The knowledge graph is then serialized in RDF and linked to Wikidata identifiers, making it interoperable with external linked open data sources and extensible beyond the battery domain. Unlike prior author-centric analyses confined to institutional repositories, our approach operates at cross-institutional scale and grounds similarity in domain semantics rather than citation or co-authorship structure alone.
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https://arxiv.org/abs/2604.20241
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Not All Memories Age the Same: Autodiscovery of Adaptive Decay in Knowledge Graphs
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Knowledge graphs used for retrieval treat all facts as equally current. Existing temporal approaches apply uniform decay, using a single forgetting curve regardless of knowledge type. We show this is fundamentally misspecified: different knowledge types exhibit different temporal dynamics, and the core retrieval problem is not latency or throughput but identifying what is important at query time. We propose a hierarchical framework that replaces uniform decay with a continuous decay surface parameterized by two orthogonal signals: velocity (how frequently a concept is observed) and volatility (how much the value changes between observations, measured via embedding distance). The decay surface is decomposed into three learnable levels: domain-level parameters capture universal patterns (some predicates are inherently permanent, others inherently transient), context-level parameters capture setting-dependent variation, and entity-level adaptation personalizes decay to specific subjects. All parameters emerge from data through survival analysis on observed value lifetimes, requiring no predefined taxonomies or domain expertise. We formulate edge lifetime as a survival problem where the event is value supersession (a meaningfully different value replacing the current one), distinct from mere re-observation. Experiments on synthetic temporal knowledge graphs demonstrate recovery of planted hierarchical parameters (HDBSCAN ARI = 1.0). Validation on 107 Wikipedia articles and 1,163 patient records from the Synthea clinical EHR simulator shows that velocity-volatility clusters emerge naturally, align with observable persistence patterns, and near-universally exhibit the Lindy effect (Weibull shape k < 1). Uniform decay performs 18x worse than no temporal weighting. Heterogeneous decay recovers from this, with each hierarchy level contributing measurable improvement.
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URL
https://arxiv.org/abs/2604.26970
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Overcoming the Impedance Mismatch: A Theoretical Roadmap for Fusing Foundation Models and Knowledge Graphs
2026-04-21 17:30:15Sahil Rajesh DhayalkarAbstract
Modern artificial intelligence remains fundamentally divided between the continuous, probabilistic spaces of Foundation Models and the discrete, deterministic structures of Knowledge Graphs. While Retrieval-Augmented Generation (RAG) attempts to connect them by serializing graph data into text, we argue this lexical bridging is merely a superficial patch. In this paper, we formalize the underlying structural and geometric friction as the \textit{Impedance Mismatch}. By categorizing current neuro-symbolic integration strategies into a three-tiered hierarchy, we demonstrate that neither surface-level prompt injection nor continuous representation alignment can preserve the strict logical motifs required for reliable multi-hop reasoning. We define the specific mathematical limits, such as the Lexical Bottleneck and Topological Collapse, that show current architectures will eventually hallucinate or conflate semantic nodes. To achieve true semantic fusion, we propose a rigorous theoretical roadmap. We advocate for natively internalizing discrete symbolic structures through Structured Residual Streams, utilizing Vector Symbolic Architectures for latent sub-graph injection, and performing model updates via Orthogonal Subspace Editing. This actionable framework paves the way for models that seamlessly fuse the precision of symbolic logic with the expressivity of parametric memory.
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URL
https://arxiv.org/abs/2606.15656
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Revisiting Catastrophic Forgetting in Continual Knowledge Graph Embedding
2026-04-21 12:26:56Gerard Pons, Carlos Escolano, Besim Bilalli, Anna QueraltAbstract
Knowledge Graph Embeddings (KGEs) support a wide range of downstream tasks over Knowledge Graphs (KGs). In practice, KGs evolve as new entities and facts are added, motivating Continual Knowledge Graph Embedding (CKGE) methods that update embeddings over time. Current CKGE approaches address catastrophic forgetting (i.e., the performance degradation on previously learned tasks) primarily by limiting changes to existing embeddings. However, we show that this view is incomplete. When new entities are introduced, their embeddings can interfere with previously learned ones, causing the model to predict them in place of previously correct answers. This phenomenon, which we call entity interference, has been largely overlooked and is not accounted for in current CKGE evaluation protocols. As a result, the assessment of catastrophic forgetting becomes misleading, and CKGE methods performance is systematically overestimated. To address this issue, we introduce a corrected CKGE evaluation protocol that accounts for entity interference. Through experiments on multiple benchmarks, we show that ignoring this effect can lead to performance overestimation of up to 25%, particularly in scenarios with significant entity growth. We further analyze how different CKGE methods and KGE models are affected by the different sources of forgetting, and introduce a catastrophic forgetting metric tailored to CKGE.
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URL
https://arxiv.org/abs/2604.19401
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The Structural Attention Tax: How Retrieval Format Hijacks In-Context Learning Independent of Content
2026-04-21 08:47:00Yuqi Zhang, Di ZhangAbstract
Retrieval-augmented generation (RAG) systems inject external knowledge to improve LLM outputs, yet the format of injected content -- distinct from its semantic relevance -- can independently distort the model's attention distribution. We identify and formalise a phenomenon we term the structural attention tax: knowledge graph (KG) triples, due to their relational delimiters and repeated slot patterns, capture 2-3x more attention per token than semantically equivalent natural-language text ($\hat{o}$(KG) $\approx$ 0.70 vs. $\hat{o}$(neutral) $\approx$ 0.25), compressing demonstration attention by up to 42% -- regardless of whether the triples are relevant or noise. We develop a formal framework decomposing attention scores into semantic and structural components (Eq. 2), derive a compression bound (Proposition 1) connecting token-level format bias to demonstration attention loss, and show that the structural term governs how much attention is diverted while the semantic term governs whether this helps or hurts. This decoupling reveals two orthogonal axes for improving retrieval-augmented ICL: optimising retrieval quality (semantic axis) and reducing format-driven attention capture (structural axis). Empirically, across two model families (Mistral-7B, LLaMA-3-8B) and three QA benchmarks, we observe that source-task alignment dominates: task-matched BM25 retrieval achieves 58-62% on HotpotQA vs. ConceptNet's 25-27%, a >30 pp gap that dwarfs all gating strategies ($\leq$2 pp). We derive five structure-aware mitigation strategies from the framework, ranging from zero-cost prompt modifications to training-time regularisation; format flattening (S3) is validated by both accuracy and attention-level evidence from a verbalized-triple control, while structural dispersal (S1) yields mixed results that illuminate the challenges of format-level intervention.
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URL
https://arxiv.org/abs/2606.11198
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Construction of Knowledge Graph based on Language Model
2026-04-21 06:38:07Qiubai Zhu, Qingwang Wang, Haibin Yuan, Wei Chen, Tao ShenAbstract
Knowledge Graph (KG) can effectively integrate valuable information from massive data, and thus has been rapidly developed and widely used in many fields. Traditional KG construction methods rely on manual annotation, which often consumes a lot of time and manpower. And KG construction schemes based on deep learning tend to have weak generalization capabilities. With the rapid development of Pre-trained Language Models (PLM), PLM has shown great potential in the field of KG construction. This paper provides a comprehensive review of recent research advances in the field of construction of KGs using PLM. In this paper, we explain how PLM can utilize its language understanding and generation capabilities to automatically extract key information for KGs, such as entities and relations, from textual data. In addition, We also propose a new Hyper-Relarional Knowledge Graph construction framework based on lightweight Large Language Model (LLM) named LLHKG and compares it with previous methods. Under our framework, the KG construction capability of lightweight LLM is comparable to GPT3.5.
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URL
https://arxiv.org/abs/2604.19137
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LogosKG: Hardware-Optimized Scalable and Interpretable Knowledge Graph Retrieval
2026-04-20 23:32:13He Cheng, Yifu Wu, Saksham Khatwani, Maya Kruse, Dmitriy Dligach, Timothy A. Miller, Majid Afshar, Yanjun GaoAbstract
Knowledge graphs (KGs) are increasingly integrated with large language models (LLMs) to provide structured, verifiable reasoning. A core operation in this integration is multi-hop retrieval, yet existing systems struggle to balance efficiency, scalability, and interpretability. We introduce LogosKG, a novel, hardware-aligned framework that enables scalable and interpretable k-hop retrieval on large KGs by building on symbolic KG formulations and executing traversal as hardware-efficient operations over decomposed subject, object, and relation representations. To scale to billion-edge graphs, LogosKG integrates degree-aware partitioning, cross-graph routing, and on-demand caching. Experiments show substantial efficiency gains over CPU and GPU baselines without loss of retrieval fidelity. With proven performance in KG retrieval, a downstream two-round KG-LLM interaction demonstrates how LogosKG enables large-scale, evidence-grounded analysis of how KG topology, such as hop distribution and connectivity, shapes the alignment between structured biomedical knowledge and LLM diagnostic reasoning, thereby opening the door for next-generation KG-LLM integration. The source code is publicly available at this https URL, and an online demo is available at this https URL.
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URL
https://arxiv.org/abs/2604.18913
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One Pass for All: A Discrete Diffusion Model for Knowledge Graph Triple Set Prediction
2026-04-20 14:41:47Jihong Guan, Jiaqi Wang, Wengen Li, Hanchen Yang, Yichao Zhang, Shuigeng ZhouAbstract
Knowledge Graphs (KGs) are composed of triples, and the goal of Knowledge Graph Completion (KGC) is to infer the missing factual triples. Traditional KGC tasks predict missing elements in a triple given one or two of its elements. As a more realistic task, the Triple Set Prediction (TSP) task aims to infer the set of missing triples conditioned only on the observed knowledge graph, without assuming any partial information about the missing triples. Existing TSP methods predict the set of missing triples in a triple-by-triple manner, falling short in capturing the dependencies among the predicted triples to ensure consistency. To address this issue, we propose a novel discrete diffusion model termed DiffTSP that treats TSP as a generative task. DiffTSP progressively adds noise to the KG through a discrete diffusion process, achieved by masking relational edges. The reverse process then gradually recovers the complete KG conditioned on the incomplete graph. To this end, we design a structure-aware denoising network that integrates a relational context encoder with a relational graph diffusion transformer for knowledge graph generation. DiffTSP can generate the complete set of triples in a one-pass manner while ensuring the dependencies among the predicted triples. Our approach achieves state-of-the-art performance on three public datasets. Code: this https URL.
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URL
https://arxiv.org/abs/2604.18344
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Towards a New Grammar of Reasoning for Artificial Legal Intelligence and the Mecelle as Its Semantic Protocol
2026-04-20 08:20:24Ali Goksu, F. Gozde Kardes, Mustafa YaylaliAbstract
This article examines the enduring epistemic and methodological crisis of traditional legal practice in light of the opportunities and constraints introduced by artificial intelligence. It proposes an ontologically grounded framework termed the Mecellem semantic protocol as a response to this crisis. The analysis focuses on the structural tension within law between maintaining normative coherence and adapting to evolving social and institutional conditions, and shows why approaches based solely on codification, positivist systematization, or quantitative methods such as jurimetrics are insufficient. The article argues that legal reasoning cannot be reduced to data retrieval or statistical pattern recognition. Instead, it is grounded in the premise that meaning is context-dependent and must be dynamically reconstructed through ontologically defined entity categories and differentiated layers of knowledge. Within this perspective, Mecellem reconceptualizes law not as a fixed system of rules, but as an ontodynamic architecture structured along the interconnected axes of ontology, epistemology, and methodology. The transition from jurimetrics to a semantic protocol is presented not merely as a technical shift, but as a transformation in the foundations of legal knowledge. The article further argues that neurosymbolic systems, knowledge graphs, and agentic artificial intelligence can effectively address persistent legal challenges only when embedded within such an ontodynamic framework. By understanding law as a domain of ongoing formation rather than a completed rational totality, Mecellem advances a context-sensitive, auditable, and coherent model for legal meaning production at both human and machine levels, offering a comprehensive framework for rethinking legal reasoning in the age of artificial intelligence.
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https://arxiv.org/abs/2608.04011
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VeriGraphi: A Multi-Agent Framework of Hierarchical RTL Generation for Large Hardware Designs
2026-04-19 19:11:10Sazzadul Islam, Tasnim Tabassum, Hao ZhengAbstract
Generating synthesizable Verilog for large, hierarchical hardware designs remains a significant challenge for large language models (LLMs), which struggle to replicate the structured reasoning that human experts employ when translating complex specifications into RTL. When tasked with producing hierarchical Verilog, LLMs frequently lose context across modules, hallucinate interfaces, fabricate inter-module wiring, and fail to maintain structural coherence - failures that intensify as design complexity grows and specifications involve informal prose, figures, and tables that resist direct operationalization. To address these challenges, we present VeriGraphi, a framework that introduces a spec-anchored Knowledge Graph as the architectural substrate driving the RTL generation pipeline. VeriGraphi constructs a HDA, a structured knowledge graph that explicitly encodes module hierarchy, port-level interfaces, wiring semantics, and inter-module dependencies as first-class graph entities and relations. Built through iterative multi-agent analysis of the specification, this Knowledge Graph provides a deterministic, machine-checkable structural scaffold before code generation. Guided by the KG, a progressive coding module incrementally generates pseudo-code and synthesizable RTL while enforcing interface consistency and dependency correctness at each submodule stage. We evaluate VeriGraphi on a benchmark of three representative specification documents from the National Institute of Standards and Technology and their corresponding implementations, and we present a RV32I processor as a detailed case study to illustrate the full pipeline. The results demonstrate that VeriGraphi enables reliable hierarchical RTL generation with minimal human intervention for RISC-V, marking a significant milestone for LLM-generated hardware design while maintaining strong functional correctness.
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URL
https://arxiv.org/abs/2604.14550
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The Provenance Gap in Clinical AI: Evidence-Traceable Temporal Knowledge Graphs for Rare Disease Reasoning
2026-04-18 19:10:12Md Shamim Ahmed, Maja Dusanic, Moritz Nikolai Kirschner, Elisabeth Nyoungui, Jana Zsch\"untzsch, Lukas Galke Poech, Richard R\"ottgerAbstract
Frontier large language models generate clinically accurate outputs, but their citations are often fabricated. We term this the Provenance Gap. We tested five frontier LLMs across 36 clinician-validated scenarios for three rare neuromuscular disease pairs. No model produced a clinically relevant PubMed identifier without prompting. When explicitly asked to cite, the best model achieved 15.3% relevant PMIDs; the majority resolved to real publications in unrelated fields. We present HEG-TKG (Hierarchical Evidence-Grounded Temporal Knowledge Graphs), a system that grounds clinical claims in temporal knowledge graphs built from 4,512 PubMed records and curated sources with quality-tier stratification and 1,280 disease-trajectory milestones. In a controlled three-arm comparison using the same synthesis model, HEG-TKG matches baseline clinical feature coverage while achieving 100% evidence verifiability with 203 inline citations. Guideline-RAG, given overlapping source documents as raw text, produces zero verifiable citations. LLM judges cannot distinguish fabricated from verified citations without PubMed audit data. Independent clinician evaluation confirms the verifiability advantage (Cohen's d = 1.81, p < 0.001) with no degradation on safety or completeness. A counterfactual experiment shows 80% resistance to injected clinical errors with 100% detectability via citation trace. The system deploys on-premise via open-source models so patient data never leaves institutional infrastructure.
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https://arxiv.org/abs/2604.17114
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Comparing Human and Large Language Model Interpretation of Implicit Information
2026-04-18 17:43:59Antonio De Santis, Tommaso Bonetti, Andrea Tocchetti, Marco BrambillaAbstract
The interpretation of implicit meanings is an integral aspect of human communication. However, this framework may not transfer to interactions with Large Language Models (LLMs). To investigate this, we introduce the task of Implicit Information Extraction (IIE) and propose an LLM-based IIE pipeline that builds a structured knowledge graph from a context sentence by extracting relational triplets, validating implicit inferences, and analyzing temporal relations. We evaluate two LLMs against crowdsourced human judgments on two datasets. We find that humans agree with most model triplets yet consistently propose many additions, indicating limited coverage in current LLM-based IIE. Moreover, in our experiments, models appear to be more conservative about implicit inferences than humans in socially rich contexts, whereas humans become more conservative in shorter, fact-oriented contexts. Our code is available at this https URL.
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https://arxiv.org/abs/2604.17085
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RLM-on-KG: Heuristics First, LLMs When Needed: Adaptive Retrieval Control over Mention Graphs for Scattered Evidence
2026-04-18 16:25:39Andrea Volpini, Elie RaadAbstract
When does an LLM controller outperform rule-based traversal for knowledge graph exploration? We study this question through RLM-on-KG, a retrieval system that treats an LLM as an autonomous navigator over an RDF-encoded mention graph for grounded question answering. Unlike GraphRAG pipelines that rely on offline LLM indexing, RLM-on-KG performs entity-first, multi-hop exploration at query time using deterministic graph construction and a fixed tool set. Our central finding is a conditional advantage: the value of LLM control depends on evidence scatter and tool-calling sophistication. The paper's core claim is LLM control versus heuristic traversal, not a generic win over GraphRAG. On GraphRAG-Bench Novel (519 questions), Gemini 2.0 Flash achieves +2.47 pp F1 over a rule-based heuristic baseline (p < 0.0001), but only +0.16 pp over a GraphRAG-local variant (not significant). With a stronger controller, Claude Haiku 4.5, the gain over heuristic grows to +4.37 pp (p < 0.001) and extends to a +2.42 pp significant improvement over GraphRAG-local (p < 0.001). The gain is largest when gold evidence is scattered across 6-10 chunks (+3.21 pp) and smallest for concentrated evidence (+1.85 pp). Cross-scale validation on MuSiQue confirms that the LLM-over-heuristic advantage transfers, with expected attenuation on smaller per-question graphs. The core architectural insight is the separation of candidate discovery from ranking: the LLM adds value through exploration breadth, while final evidence selection is best handled by pure vector re-ranking. Beyond retrieval, exploration traces provide a proposed stress-test harness for structured data quality, yielding diagnostics for coverage, connectivity, provenance, and queryability.
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https://arxiv.org/abs/2604.17056
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A phenotype-driven and evidence-governed framework for knowledge graph enrichment and hypotheses discovery in population data
2026-04-18 12:49:57Adela B\^ara, Simona-Vasilica OpreaAbstract
Current knowledge graph (KG) construction methods are confirmatory, focusing on recovering known relationships rather than identifying novel or context-dependent nodes. This paper proposes a phenotype-driven and evidence-governed framework that shifts the paradigm toward structured hypothesis discovery and controlled KG expansion. The approach integrates graph neural networks (GNNs) for phenotype discovery, causal inference, probabilistic reasoning and large language models (LLMs) for hypothesis generation and claim extraction within a unified pipeline. The framework prioritizes relationships that are both structurally supported by data and underexplored in the literature. KG expansion is formulated as a multi-objective optimization problem, where candidate claims are jointly evaluated in terms of relevance, structural validation and novelty. Pareto-optimal selection enables the identification of non-dominated claims that balance confirmation and discovery, avoiding trivial or redundant knowledge inclusion. Experiments on heterogeneous population datasets demonstrate that the proposed framework produces more interpretable phenotypes, reveals context-dependent causal structures and generates high-quality claims that align with both data and scientific evidence. Compared to rule-based and LLM-only baselines, the method achieves the best trade-off across plausibility, novelty, validation and relevance. In retrieval-augmented settings, it significantly improves performance (Recall@5=0.98) while reducing hallucination rates (0.05), highlighting its effectiveness in grounding LLM outputs.
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https://arxiv.org/abs/2604.16982
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From 'Strings' to 'Things' for Personal Knowledge Graphs: Evaluating LLM Triple Extraction for Recommendation Systems
2026-04-18 12:23:42Abhirup Dasgupta, Fernando Spadea, Oshani SeneviratneAbstract
Personal Knowledge Graphs (PKGs) offer a privacy-preserving framework for modeling user preferences, yet constructing them from unstructured, decentralized conversational data remains a challenge. This paper bridges the gap between conversational "strings" and semantic "things" by presenting a reproducible pipeline for extracting structured user-preference triples using lightweight Large Language Models. We evaluate Qwen- and Gemma-based models on their ability to extract RDF-compliant triples linked to Wikidata identifiers from conversational data for PKG construction. Our evaluation assesses both the semantic extraction fidelity and the utility of the resulting graphs in a downstream recommendation task. We found that certain models performed well and had proportionally high downstream performance relative to their triple extraction performance.
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https://arxiv.org/abs/2607.00003
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AutoPKG: An Automated Framework for Dynamic E-commerce Product-Attribute Knowledge Graph Construction
2026-04-18 10:19:10Pollawat Hongwimol, Haoning Shang, Chutong Wang, Zhichao Wan, Yi Gao, Yuanming Li, Lin Gui, Wenhao Sun, Cheng YuAbstract
Product attribute extraction in e-commerce is bottlenecked by ontologies that are inconsistent, incomplete, and costly to maintain. We present AutoPKG, a multi-agent Large Language Model (LLM) framework that automatically constructs a Product-attribute Knowledge Graph (PKG) from multimodal product content. AutoPKG induces product types and type-specific attribute keys on demand, extracts attribute values from text and images, and consolidates updates through a centralized decision agent that maintains a globally consistent canonical graph. We also propose an evaluation protocol for dynamic PKGs that measures type and key validity, consolidation quality, and edge-level accuracy for value assertions after canonicalization. On a large real-world marketplace catalog dataset from Lazada (Alibaba), AutoPKG achieves up to 0.953 Weighted Knowledge Efficiency (WKE) for product types, 0.724 WKE for attribute keys, and 0.531 edge-level F1 for multimodal value extraction. Across three public benchmarks, our method improves edge-level exact-match F1 by 0.152 and yields a precision gain of 0.208 on the attribute extraction application. Online A/B tests show that AutoPKG-derived attributes increase Gross Merchandise Value (GMV) in Badge by 3.81 percent, in Search by 5.32 percent, and in Recommendation by 7.89 percent, supporting the practical value of AutoPKG in production.
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URL
https://arxiv.org/abs/2604.16950
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Using Large Language Models and Knowledge Graphs to Improve the Interpretability of Machine Learning Models in Manufacturing
2026-04-17 17:41:17Thomas Bayer, Alexander Lohr, Sarah Wei{\ss}, Bernd Michelberger, Wolfram H\"opkenAbstract
Explaining Machine Learning (ML) results in a transparent and user-friendly manner remains a challenging task of Explainable Artificial Intelligence (XAI). In this paper, we present a method to enhance the interpretability of ML models by using a Knowledge Graph (KG). We store domain-specific data along with ML results and their corresponding explanations, establishing a structured connection between domain knowledge and ML insights. To make these insights accessible to users, we designed a selective retrieval method in which relevant triplets are extracted from the KG and processed by a Large Language Model (LLM) to generate user-friendly explanations of ML results. We evaluated our method in a manufacturing environment using the XAI Question Bank. Beyond standard questions, we introduce more complex, tailored questions that highlight the strengths of our approach. We evaluated 33 questions, analyzing responses using quantitative metrics such as accuracy and consistency, as well as qualitative ones such as clarity and usefulness. Our contribution is both theoretical and practical: from a theoretical perspective, we present a novel approach for effectively enabling LLMs to dynamically access a KG in order to improve the explainability of ML results. From a practical perspective, we provide empirical evidence showing that such explanations can be successfully applied in real-world manufacturing environments, supporting better decision-making in manufacturing processes.
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URL
https://arxiv.org/abs/2604.16280
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Large Language Models Meet Biomedical Knowledge Graphs for Mechanistically Grounded Therapeutic Prioritization
2026-04-17 15:29:52Chih-Hsuan Wei, Chi-Ping Day, Zhizheng Wang, Christine C. Alewine, Betty Tyler, Hasan Slika, David Saraf, Chin-Hsien Tai, Joey Chan, Robert Leaman, Zhiyong LuAbstract
Drug repurposing is often framed as a candidate identification task, but existing approaches provide limited guidance for distinguishing biologically plausible candidates from historically well-connected ones. Here we introduce DrugKLM, a hybrid framework that integrates biomedical knowledge graph structure with large language model-based mechanistic reasoning to enable mechanistically grounded therapeutic prioritization. Across benchmark datasets, DrugKLM outperforms knowledge graph-only and language model-only baselines, including TxGNN. Beyond improved recall, DrugKLM confidence scores exhibit functional alignment with molecular phenotypes: higher scores are associated with transcriptional signatures linked to improved survival across 12 TCGA cancers. The scoring framework preferentially captures biologically perturbational signals rather than historical indication patterns. Expert curation across five cancers further reveals systematic differences in prioritization behavior, with DrugKLM elevating candidates supported by coherent mechanistic rationale and disease-specific clinical context. Together, these results establish DrugKLM as an evidence-integrative framework that translates heterogeneous biomedical data into mechanistically interpretable and clinically grounded therapeutic hypotheses.
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URL
https://arxiv.org/abs/2604.19815
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Integrating Graphs, Large Language Models, and Agents: Reasoning and Retrieval
2026-04-17 11:12:55Hamed Jelodar, Samita Bai, Mohammad Meymani, Parisa Hamedi, Roozbeh Razavi-Far, Ali GhorbaniAbstract
Generative AI, particularly Large Language Models, increasingly integrates graph-based representations to enhance reasoning, retrieval, and structured decision-making. Despite rapid advances, there remains limited clarity regarding when, why, where, and what types of graph-LLM integrations are most appropriate across applications. This survey provides a concise, structured overview of the design choices underlying the integration of graphs with LLMs. We categorize existing methods based on their purpose (reasoning, retrieval, generation, recommendation), graph modality (knowledge graphs, scene graphs, interaction graphs, causal graphs, dependency graphs), and integration strategies (prompting, augmentation, training, or agent-based use). By mapping representative works across domains such as cybersecurity, healthcare, materials science, finance, robotics, and multimodal environments, we highlight the strengths, limitations, and best-fit scenarios for each technique. This survey aims to offer researchers a practical guide for selecting the most suitable graph-LLM approach depending on task requirements, data characteristics, and reasoning complexity.
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https://arxiv.org/abs/2604.15951
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