Biomedical KGs

KG: Knowledge Graph

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6 papers in the last four weeks, against 1 the four weeks before. 0.1% of all new papers.

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

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

    Exin Therapeutics, Inc., 2261 Market Street STE 22614, San Francisco, California 94114, United States

  2. 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

    Electrical Engineering and Computer Science, University of Kansas, USA · Health Outcomes and Biomedical Informatics, University of Florida, USA

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

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

    University of North Carolina at Chapel Hill · Siddaganga Institute of Technology · Foci Labs +1

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

    Oct 4, 2026Jiheng Liang, Chen Zhao, Di Wu +4Biomedical KGs

    Data Science, William & Mary · Computer Science, Baylor University · Southwest University +2

  5. 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

    Xi’an Jiaotong University · UIUC · Tsinghua University +4

  6. DoAtlas-2: A Foundation for Self-Evolving Causal Biomedical Discovery

    Sep 28, 2026Yulong Li, Rong Xia, Yuxuan Zhang +12Causal DiscoveryCausal Attribution

    MBZUAI

  7. 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

    Tsinghua University, China · Beijing University of Chinese Medicine, China · Guangdong Provincial Laboratory of Traditional Chinese Medicine, China

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

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

    Department of Computer Science, Università degli Studi di Milano, Milan, Italy · Università della Svizzera italiana (USI), Lugano, Switzerland · Politecnico di Milano, Milan, Italy +2

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

    Sep 14, 2026Dominic Okonkwo, Adetayo Okunoye, Ismailcem Budak ArpinarLLM Reasoning with GraphsEvidence-Grounded Reasoning

    School of Computing University of Georgia

  10. AdaPath: Query-Adaptive Path-Finding via Path-Bank for Multi-Hop Implicit Biomedical KGQA

    Aug 31, 2026Jun Hyeong Kim, Dongki Kim, Yinhua Piao +1Multi-Hop QABiomedical QA

    KAIST

  11. 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

    1The University of Tokyo · 2SB Intuitions · Department of AI Systems Medicine, Institute of Science Tokyo

  12. 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

    Recursion Pharmaceuticals Inc. Salt Lake City, UT, USA · Queen Mary University of London Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry London, United Kingdom

  13. Plausibility-Driven Prioritization of Candidate Biomedical Annotations

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

    Department of Computer Science, University of Milano, Milano, Italy

  14. Canopy: A Heterograph Foundation Model for Metabolic Engineering

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

    Twig Bio, London, United Kingdom

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

    Jul 2, 2026Wenbo ZhangKG EmbeddingProtein-Protein Interaction Prediction

    College of Computer and Information Science, Southwest University, Chongqing, Chongqing, China

  16. Knowledge-augmented Agentic AI for Mental Health Medication Information Seeking

    Jun 24, 2026Huizi Yu, Jian Liu, Wenkong Wang +10KG ConstructionHealthcare

    Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China · Department of Psychiatry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China · School of Control Science and Engineering, Shandong University, Ji’nan, Shandong, China +5

  17. Knowledge-Graph Grounding Helps LLMs Only for Out-of-Training Knowledge: A Controlled Study on Clinical Question Answering

    Jun 21, 2026Madhulatha Mandarapu, Sandeep KunkunuruLLM GroundingLLM Reasoning with Graphs

    samyama

  18. Weaving Multi-Source Evidence for Biomedical Reasoning: The BioMedHop Benchmark and BioWeave Framework

    Jun 15, 2026Xingyu Tan, Shiyuan Liu, Xiaoyang Wang +5Multi-Hop QAEvidence-Grounded Reasoning

    University of New South Wales, Australia · 2CSIRO, Australia · University of Technology Sydney, Australia

  19. DeepRoot: A KG-Coordinated Multi-Agent System for Therapeutic Reasoning over Historical Medical Texts

    Jun 14, 2026Zijian Carl Ma, Sean J. Wang, Sijbren Kramer +1Historical Document AnalysisMulti-Agent LLM Systems

    Department of Bioengineering · Stanford University · Amazon AWS AI

  20. Semantic Reasoning in Medicine: The Role of Knowledge Graphs Across Five Key Domains

    Jun 13, 2026Haniye Sherafatmandjoo, Mohammad Akbari, Zahed RahmatiKG ConstructionHealthcare

    Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran

  21. Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors

    Jun 7, 2026Jake Fawkes, Liam Hodgson, Jason HartfordRL for Language Model ReasoningSingle-Cell Perturbation Modeling

    Department of Computer Science, University College London, UK · Valence Labs, London, UK · Recursion, London, UK +1

  22. A Multi-modal Agentic Co-pilot for Evidence Grounded Computational Pathology

    Jun 6, 2026Zhe Xu, Zhengyu Zhang, Zhiyuan Cai +12Computational PathologyClinical Decision Support

    Department of Computer Science and Engineering, Hong Kong University of Science and Technology, Hong Kong, China · Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China · Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China +7

  23. Pharmacogenomic Knowledge Graph Augmentation for Graph Neural Network-Based Drug-Drug Interaction Prediction

    Jun 5, 2026Juergen DietrichGraph Neural NetworksKnowledge Graphs

    AI Solutions Berlin

  24. UniD3^3: A Knowledge Graph-Enhanced RAG Framework for Drug-Disease Discovery and Reasoning

    May 31, 2026Qing Wang, Tianshi Liu, Minghao Zhou +5Relation ExtractionKG Construction

    Department of Health Outcomes and Biomedical Informatics, University of Florida, Florida, USA · Department of Hematology, H. Lee Moffitt Cancer Center and Research Institute, Florida, USA · Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, TX, USA +2

  25. Knowledge Graph Modulated Deep Learning for Limited-Sample Clinical Data Analysis

    May 22, 2026Yuwei Xue, Sakib Mostafa, James Zou +5Graph Representation LearningMedical Diagnosis

    Department of Radiation Oncology, Stanford University, Stanford, California, USA · Department of Electrical Engineering, Stanford University, Stanford, California, USA · Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California, USA +6

  26. ChronoMedKG: A Temporally-Grounded Biomedical Knowledge Graph and Benchmark for Clinical Reasoning

    May 21, 2026Md Shamim Ahmed, Farzaneh Firoozbakht, Lukas Galke Poech +2KG ConstructionHealthcare

    University of Southern Denmark · University of Hamburg

  27. MHGraphBench: Knowledge Graph-Grounded Benchmarking of Mental Health Knowledge in Large Language Models

    May 15, 2026Weixin Liu, Congning Ni, Shelagh A. Mulvaney +4LLM EvaluationHealthcare

    Vanderbilt University, Nashville, TN, USA · Vanderbilt University Medical Center, Nashville, TN, USA · Virginia Tech, Blacksburg, VA, USA

  28. ClinicalBench: Stress-Testing Assertion-Aware Retrieval for Cross-Admission Clinical QA on MIMIC-IV

    May 11, 2026Alex StinardHealthcareClinical QA

    Department of Clinical Sciences, College of Medicine · University of Central Florida, Orlando, FL 32816

  29. PrimeKG-CL: A Continual Graph Learning Benchmark on Evolving Biomedical Knowledge Graphs

    May 11, 2026Yousef A. Radwan, Yao Li, Qing Qing +5KG EmbeddingKnowledge Graph Question Answering

    Technology, Innovation, Entrepreneurship Department King Abdullah University of Science and Technology · School of Computing and Information Systems The University of Melbourne · College of Computer Science and Technology Jilin University +3

  30. CMKL: Modality-Aware Continual Learning for Evolving Biomedical Knowledge Graphs

    May 11, 2026Yousef A. Radwan, Yao Li, Qing Qing +5Continual LearningKG Embedding

    Technology, Innovation, Entrepreneurship Department King Abdullah University of Science and Technology · School of Computing and Information Systems The University of Melbourne · College of Computer Science and Technology Jilin University +2

  31. LLM-Guided Monte Carlo Tree Search over Knowledge Graphs: Composing Mechanistic Explanations for Drug-Disease Pairs

    May 10, 2026Rishabh Jakhar, Michel Dumontier, Remzi CelebiLLM Reasoning with GraphsScientific Discovery

    Institute of Data Science, Department of Advanced Computing Sciences, Maastricht University, The Netherlands

  32. EpiGraph: Building Generalists for Evidence-Intensive Epilepsy Reasoning in the Wild

    May 10, 2026Yuyang Dai, Zheng Chen, Jathurshan Pradeepkumar +4KG ConstructionRetrieval-Augmented Generation

    Florida State University · The University of Osaka · University of Illinois Urbana-Champaign

  33. GATHER: Convergence-Centric Hyper-Entity Retrieval for Zero-Shot Cell-Type Annotation

    May 7, 2026Zhonghui Zhang, Feng Jiang, Shaowei Qin +2Zero-Shot LearningGraph Retrieval-Augmented Generation

    Artificial Intelligence Research Institute, Shenzhen University of Advanced Technology Shenzhen, China · Software College, Northeastern University Shenyang, China

  34. A Unified Benchmark for Evaluating Knowledge Graph Construction Methods and Graph Neural Networks

    May 6, 2026Othmane Kabal, Mounira Harzallah, Fabrice Guillet +2KG ConstructionGraph Neural Networks

    Nantes University, LS2N, Nantes, 44300, France · National Institute of Informatics, Chiyoda-ku, Tokyo, 101-8430, Japan · Institute of Science Tokyo, Tokyo, 152-8550, Japan

  35. Robustness of Graph Self-Supervised Learning to Real-World Noise: A Case Study on Text-Driven Biomedical Graphs

    May 6, 2026Othmane Kabal, Mounira Harzallah, Fabrice Guillet +2Graph SSLText-Attributed Graph Learning

    Nantes University, LS2N, Nantes, 44300, France. · National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku,2026 Tokyo 101-8430 Japan. · Institute of Science Tokyo, Tokyo 152-8550 Japan.

  36. Graph Neural Network based Hierarchy-Aware Embeddings of Knowledge Graphs: Applications to Yeast Phenotype Prediction

    May 5, 2026Filip Kronström, Alexander H. Gower, Daniel Brunnsåker +2Graph Neural NetworksRepresentation Learning

    Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Sweden · Department of Life Sciences, Chalmers University of Technology, Sweden · Department of Industrial Biotechnology, KTH Royal Institute of Technology, Sweden +1

  37. Unifying biomedical knowledge in a modern multimodal graph

    Apr 29, 2026Lucas Vittor, Ayush Noori, Iñaki Arango +5KG ConstructionMultimodal KGs

    Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA · Department of Engineering Science, University of Oxford, Oxford, UK · Edison Scientific Inc., San Francisco, CA, USA +4

  38. Quantum Knowledge Graph: Modeling Context-Dependent Triplet Validity

    Apr 27, 2026Yao Wang, Zixu Geng, Jun YanKG ConstructionKnowledge Representation

    HKAI-Sci, City University of Hong Kong · Department of Automation, Tsinghua University · Pratt School of Engineering, Duke University

  39. Large Language Models Meet Biomedical Knowledge Graphs for Mechanistically Grounded Therapeutic Prioritization

    Apr 17, 2026Chih-Hsuan Wei, Chi-Ping Day, Zhizheng Wang +8LLM GroundingLarge Language Model-Guided Scientific Discovery

    Division of Intramural Research (DIR), National Library of Medicine (NLM), National Institutes of Health (NIH); Bethesda, MD 20894, USA · Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20894, USA · Dartmouth Health, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA +2

  40. From Literature to Hypotheses: An AI Co-Scientist System for Biomarker-Guided Drug Combination Hypothesis Generation

    Feb 28, 2026Raneen Younis, Suvinava Basak, Lukas Chavez +1Scientific Hypothesis GenerationOncology

    Peter L. Reichertz Institute for Medical Informatics (PLRI), Hannover Medical School · Lower Saxony Center for Artificial Intelligence and Causal Methods in Medicine (CAIMed) · Sanford Burnham Prebys (SBP) Medical Discovery Institute

  41. BioPIE: A Biomedical Protocol Information Extraction Dataset for Experiment Understanding

    Jan 8, 2026Haofei Hou, Shunyi Zhao, Fanxu Meng +3KG ConstructionDocument Information Extraction

    School of Advanced Manufacturing and Robotics, Peking University · School of Integrated Circuits, Peking University