mlsanityData to 14 Oct 2026

OpenBioLink: A benchmarking framework for large-scale biomedical link prediction

arXiv 1912.04616 ↗First posted 10 Dec 2019cs.AI cs.IRcited by 28

Not on the map. Why?

Abstract (arXiv)

SUMMARY: Recently, novel machine-learning algorithms have shown potential for predicting undiscovered links in biomedical knowledge networks. However, dedicated benchmarks for measuring algorithmic progress have not yet emerged. With OpenBioLink, we introduce a large-scale, high-quality and highly challenging biomedical link prediction benchmark to transparently and reproducibly evaluate such algorithms. Furthermore, we present preliminary baseline evaluation results. AVAILABILITY AND IMPLEMENTATION: Source code, data and supplementary files are openly available at https://github.com/OpenBioLink/OpenBioLink CONTACT: matthias.samwald ((at)) meduniwien.ac.at

Key facts. Cited by 28 papers in the map (data through 14 Oct 2026). First posted on arXiv 10 Dec 2019.

Builds on

No reference list yet.

Built on by

Cited by year (2026 to 14 Oct)

Citing papers per year: 2021: 6; 2022: 3; 2023: 9; 2024: 5; 2025: 3; 2026: 2.

28 papers.

Sort:

By area:

  1. 2022A Survey of Knowledge Graph Reasoning on Graph Types: Static, Dynamic, and Multimodalcited by 106
  2. 2021A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspectivecited by 38
  3. 2021Understanding the Performance of Knowledge Graph Embeddings in Drug Discoverycited by 18
  4. 2022Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completioncited by 13
  5. 2025Graph Neural Networks in Modern AI-aided Drug Discoverycited by 12
  6. 2021A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarkscited by 11
  7. 2021Implications of Topological Imbalance for Representation Learning on Biomedical Knowledge Graphscited by 11
  8. 2023An Open-Source Knowledge Graph Ecosystem for the Life Sciencescited by 11
  9. 2023Comprehensive evaluation of deep and graph learning on drug-drug interactions predictioncited by 10
  10. 2023Accurate and interpretable drug-drug interaction prediction enabled by knowledge subgraph learningcited by 9
  11. 2021Explainable Biomedical Recommendations via Reinforcement Learning Reasoning on Knowledge Graphscited by 7
  12. 2023Knowledge-augmented Graph Machine Learning for Drug Discovery: A Surveycited by 6
16 more
  1. 2025Biomedical Knowledge Graph: A Survey of Domains, Tasks, and Real-World Applicationscited by 6
  2. 2024MOTIVE: A Drug-Target Interaction Graph For Inductive Link Predictioncited by 5
  3. 2023Clinical Trial Recommendations Using Semantics-Based Inductive Inference and Knowledge Graph Embeddingscited by 4
  4. 2021Prediction of Adverse Biological Effects of Chemicals Using Knowledge Graph Embeddingscited by 2
  5. 2023Know2BIO: A Comprehensive Dual-View Benchmark for Evolving Biomedical Knowledge Graphscited by 2
  6. 2024TWIG: Towards pre-hoc Hyperparameter Optimisation and Cross-Graph Generalisation via Simulated KGE Modelscited by 2
  7. 2024The Role of Graph Topology in the Performance of Biomedical Knowledge Graph Completion Modelscited by 2
  8. 2024MARS: A neurosymbolic approach for interpretable drug discoverycited by 2
  9. 2023Decoding Virtual Healthcare Success through Knowledge-Aware and Multimodal Predictive Modelingcited by 1
  10. 2023Knowledge Graphs are not Created Equal: Exploring the Properties and Structure of Real KGscited by 1
  11. 2025On the Theoretical Limitations of Embedding-based Link Predictioncited by 1
  12. 2026Unifying biomedical knowledge in a modern multimodal graphcited by 1
  13. 2022OntoMerger: An Ontology Integration Library for Deduplicating and Connecting Knowledge Graph Nodescited by 0
  14. 2023A Review of Link Prediction Applications in Network Biologycited by 0
  15. 2024Improving rule mining via embedding-based link predictioncited by 0
  16. 2026THBKG: A Temporal Biomedical Knowledge Graph for Decision-Aligned Clinical Advancement Predictioncited by 0