kMoL: an open-source machine and federated learning library for drug discovery

Abstract

Machine learning is quickly becoming integral to drug discovery pipelines, particularly quantitative structure-activity relationship (QSAR) and absorption, distribution, metabolism, and excretion (ADME) tasks. Graph Convolutional Network (GCN) models have proven especially promising due to their inherent ability to model molecular structures using graph-based representations. However, maximizing the potential of such models in practice is challenging, as companies prioritize data privacy and security over collaboration initiatives to improve model performance and robustness. kMoL is an open-source machine learning library with integrated federated learning capabilities developed to address such challenges. Its key features include state-of-the-art model architectures, Bayesian optimization, explainability, and federated learning mechanisms. It demonstrates extensive customization possibilities, advanced security features, straightforward implementation of user-specific models, and high adaptability to custom datasets without additional programming requirements. kMoL is evaluated through locally trained benchmark settings and distributed federated learning experiments using various datasets to assess the features and flexibility of the library, as well as the ability to facilitate fast and practical experimentation. Additionally, results of these experiments provide further insights into the performance trade-offs associated with federated learning strategies, presenting valuable guidance for deploying machine learning models in a privacy-preserving manner within drug discovery pipelines. kMoL is available on GitHub at https://github.com/elix-tech/kmol.

Scientific contribution The primary scientific contribution of this research project is the introduction and evaluation of kMoL, an open-source machine learning library with integrated federated learning capabilities. By demonstrating advanced customization and security capabilities without additional programming requirements, kMoL represents an accessible yet secure open-source platform for collaborative drug discovery projects. Additionally, the experiment results provide further insights into the performance trade-offs associated with federated learning strategies, presenting valuable guidance for deploying machine learning models in a privacy-preserving manner within drug discovery pipelines.