DOI: 10.1101/2023.05.22.540599

BioModelsML: Building a FAIR and reproducible collection of machine learning models in life sciences and medicine for easy reuse

D. D.Tiwari N. Hoffmann K. Didi S. Deshpande S. Ghosh T. V. N. Nguyen K. Raman H. Hermjakob R. S. Malik Sheriff

D. D.Tiwari N. Hoffmann K. Didi ...+5 R. S. Malik Sheriff

摘要

Machine learning (ML) models are widely used in life sciences and medicine; however, they are scattered across various platforms and there are several challenges that hinder their accessibility, reproducibility and reuse. In this manuscript, we present the formalization and pilot implementation of community protocol to enable FAIReR (Findable, Accessible, Interoperable, Reusable, and Reproducible) sharing of ML models. The protocol consists of eight steps, including sharing model training code, dataset information, reproduced figures, model evaluation metrics, trained models, Dockerfiles, model metadata, and FAIR dissemination. Applying these measures, we aim to build and share a comprehensive public collection of FAIR ML models in the BioModels repository through incentivized community curation. In a pilot implementation, we curated diverse ML models to demonstrate the feasibility of our approach and we discussed the current challenges. Building a FAIReR collection of ML models will directly enhance the reproducibility and reusability of ML models, minimizing the effort needed to reimplement models, maximizing the impact on the application and significantly accelerating the advancement in the field of life science and medicine.

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