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

12/10/2019 ∙ by Anna Breit, et al. ∙ 0

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

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OpenBioLink

OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.


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