{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/openbiolink-a-resource-and-benchmarking","title":"OpenBioLink: A benchmarking framework for large-scale biomedical link prediction","arxiv_id":"1912.04616","date":"2019-12-10","proceeding":null,"authors":["Anna Breit","Simon Ott","Asan Agibetov","Matthias Samwald"],"abstract":"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","url_abs":"https://arxiv.org/abs/1912.04616v2","url_pdf":"https://arxiv.org/pdf/1912.04616v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"openbiolink-a-resource-and-benchmarking","repo_url":"https://github.com/OpenBioLink/OpenBioLink","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"jax","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"machine-learning","task_name":"BIG-bench Machine Learning"},{"task_slug":"benchmarking","task_name":"Benchmarking"},{"task_slug":"link-prediction","task_name":"Link Prediction"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/1912.04616","atlas_url":"https://app.syntology.ai/?focus=1912.04616","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"1912.04616"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-25T09:33:49+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. 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