Biomedical KGs

KG: Knowledge Graph

Overview

Biomedical knowledge graphs connect entities such as genes, diseases, drugs, pathways, and patient findings, often combining literature, databases, and clinical records. Researchers build and refine these graphs with information extraction, ontologies, provenance tracking, and temporal or patient-specific context, then use graph embeddings and neural networks to predict associations or rank candidates. Retrieval-augmented language models and graph-based agents use relevant subgraphs to answer biomedical questions, explain mechanisms, and support tasks such as diagnosis and drug discovery. A central challenge is ensuring that graphs are complete and reliable, and that models use retrieved evidence correctly rather than producing plausible but unsupported conclusions.

Latest papers

CardsList

71 papers9 papers in the last four weeks, up 13% on the four weeks before. 0.1% of all new papers.

  1. AskGLP1: A Knowledge Graph LLM Agent for Exploring GLP-1 Experience from Online Patient Narratives

    Oct 26, 2026Zhaoqian Xue, Anay Somani, Siddhartha Singh +10Clinical Information ExtractionBiomedical KGs

  2. Are We Done with UMLS Injection into Language Models for Medical Question Answering?

    Oct 24, 2026Yiran Zeng, Giacomo Frisoni, Lorenzo Molfetta +1Knowledge Augmentation for Language ModelsMedical QA

  3. Trust the Edge, Doubt the Arrow: Auditing Validation Signals for Text-Mined Clinical Causal Knowledge Graphs

    Oct 17, 2026Su Lan, Shicheng Zhou, Yiqi Wang +3Biomedical KGsClinical Information Extraction

  4. Beyond Reachability: A Relation-Semantic Reasoning Framework for Biomedical Multi-hop QA

    Oct 14, 2026Ziyang Ling, Ziyi Chen, Ronald X. Xu +1Multi-Hop QABiomedical QA

  5. CircuitATLAS: Agentic reasoning over a systems neuroscience knowledge graph for target discovery in circuitopathies

    Oct 7, 2026Gabriel Ocana-Santero, Marko TvrdicDrug DiscoveryBiomedical KGs

  6. Cite What You Explore: Budget-Aware LLM Reasoning over Medical KGs with Verifiable Evidence

    Oct 6, 2026Chen Chen, Dongjie Wang, Mei Liu +1LLM Reasoning with GraphsEvidence-Grounded Reasoning

  7. Aligning Multimodal Patient Evidence with Biomedical Knowledge Graphs for Clinical LLMs

    Oct 5, 2026Jiawen Du, Arshan Ali Khan, Chenhao Zhang +7KG ConstructionGraph-Based Retrieval

  8. ColdDDI: Evaluating Knowledge Utilization in Cold-Start Drug-Drug Interaction Prediction

    Oct 4, 2026Jiheng Liang, Chen Zhao, Di Wu +4Drug-Drug Interaction PredictionBiomedical KGs

  9. RareDx: Controlled Knowledge Integration and Graph-Grounded Policy Optimization for Rare-Disease Diagnosis

    Sep 28, 2026Bo Zhang, Yuchen Wang, Dongbai Li +6Rare Disease DiagnosisLLM Reasoning with Graphs

  10. TCMaster: Confidence-Aware Querying and Workload-Guided Physical Design for Multi-Source Traditional Chinese Medicine Knowledge Graphs

    Sep 22, 2026Zheng Chen, Yuzhu Li, Haoxuan Li +3Graph-Based RetrievalKnowledge Graphs

  11. TRACE: Deployable Tree-Relational Structure Enhancement for Oncology LLMs

    Sep 20, 2026Jizheng Lai, Yingyun Li, Ying Qin +1Medical LLMsLLM Grounding

  12. Hyperbolic Graph Representation Learning for Differential Diagnosis on Biomedical Knowledge Graphs

    Sep 16, 2026Pietro Miotto, Lucia Mellini, Tommaso Marzi +5KG EmbeddingKnowledge Graphs

  13. HypoKG: Evidence-Disciplined Biomedical Hypothesis Generation Beyond Endpoint Knowledge

    Sep 10, 2026Dominic Okonkwo, Adetayo Okunoye, Ismailcem Budak ArpinarLLM Reasoning with GraphsEvidence-Grounded Reasoning

  14. Hakken: Predicting future discoveries to fill the gaps in today's knowledge

    Sep 3, 2026Tarek R. Besold, Uchenna Akujuobi, Pablo Sanchez +21Scientific Hypothesis GenerationAI-Assisted Scientific Research

  15. Expert Knowledge & Machine Understanding: Bridging Reactome's Ontology with LLM Semantic Embeddings

    Aug 28, 2026Susanna Bravi, Riccardo De Luca, Rosa Sicilia +2BioinformaticsBiomedical KGs

  16. Surgical Alignment in Knowledge Graph Training for Clinical Diagnosis with Large Language Models

    Aug 27, 2026Saksham Khatwani, He Cheng, Majid Afshar +2LLM Reasoning with GraphsLLM Alignment

  17. Aligning Biomedical Texts and Knowledge Graphs: A Systematic Comparison of Lightweight Alignment Strategies

    Aug 24, 2026Artem Bisliouk, Elizaveta Nosova, Heiko Paulheim +2Biomedical KGsBiomedical IR

  18. Clinical Graph-JEPA: Predictive Patient-State Knowledge Graphs for Cognitive Decision Support

    Aug 23, 2026Kushagra Yadav, Nalin Prabhath, Amit Lamba +3KG ConstructionBiomedical KGs

  19. AutoSchema: Live Schema Grounding for Agentic Text-to-Sparql over Heterogeneous Knowledge Graphs

    Aug 14, 2026Yiming Zhang, Koji TsudaNatural Language to SPARQLSchema Linking

  20. MolBioKG: Grounding Out-of-Graph Molecules in Biomedical Knowledge Graphs via Multi-Resolution Structural Anchoring

    Aug 7, 2026Yiming Zhang, Hikaru Shindo, Shuan Chen +5Knowledge GraphsDrug Discovery

  21. THBKG: A Temporal Biomedical Knowledge Graph for Decision-Aligned Clinical Advancement Prediction

    Aug 6, 2026Pui Chung Siu, Claudia Cabrera, Mani Mudaliar +1KG ConstructionClinical Outcome Prediction

  22. Plausibility-Driven Prioritization of Candidate Biomedical Annotations

    Jul 22, 2026Emanuele Cavalleri, Miad Alavinezhad, Dario Malchiodi +1Human-in-the-Loop AnnotationKnowledge Graphs

  23. Canopy: A Heterograph Foundation Model for Metabolic Engineering

    Jul 7, 2026Jake Bowden, Laurence Legon, Satnam SuraeHeterogeneous GNNsGraph SSL

  24. MKGR: Multimodal Knowledge-Graph Representation Learning for Cold-Start Protein-Protein Interaction Prediction

    Jul 2, 2026Wenbo ZhangKG EmbeddingProtein-Protein Interaction Prediction