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Facing small and biased data dilemma in drug discovery with federated learning

By Zhaoping Xiong, Ziqiang Cheng, Chi Xu, Xinyuan Lin, Xiaohong Liu, Dingyan Wang, Xiaomin Luo, Yong Zhang, Nan Qiao, Mingyue Zheng, Hualiang Jiang

Posted 20 Mar 2020
bioRxiv DOI: 10.1101/2020.03.19.998898

Artificial intelligence (AI) models usually require large amounts of high-quality training data, which is in striking contrast to the situation of small and biased data faced by current drug discovery pipelines. The concept of federated learning has been proposed to utilize distributed data from different sources without leaking sensitive information of these data. This emerging decentralized machine learning paradigm is expected to dramatically improve the success of AI-powered drug discovery. We here simulate the federated learning process with 7 aqueous solubility datasets from different sources, among which there are overlapping molecules with high or low biases in the recorded values. Beyond the benefit of gaining more data, we also demonstrate federated training has a regularization effect making it superior than centralized training on the pooled datasets with high biases. Further, two more cases are studied to test the usability of federated learning in drug discovery. Our work demonstrates the application of federated learning in predicting drug related properties, but also highlights its promising role in addressing the small data and biased data dilemma in drug discovery. ### Competing Interest Statement The authors have declared no competing interest.

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