As training volume increases predictive model quality, leveraging existing external data sources holds the promise of time- and cost-efficiency. In a drug discovery setting, pharmaceutical companies all own substantial but confidential datasets. The MELLODDY project develops a privacy-preserving federated machine learning solution and deploys it at an unprecedented scale (more than 100,000 tasks across ten major pharmaceutical companies), while ensuring the security and privacy of each partner’s sensitive data. Each partner builds models that benefit from a shared representation, for their own private assays. Established predictive performance metrics such as AUC ROC or AUC PR are constrained to unseen labelled chemical space. However, they cannot gauge performance gains in unlabelled chemical space. Federated learning indirectly extends labelled space, but in a privacy-preserving context, a partner cannot use this label extension for performance assessment. Metrics that estimate uncertainty on a prediction can be calculated even where no label is known. Practically, the chemical space covered with predictions of sufficient confidence, reflects the applicability domain of a model. After establishing a link to established performance metrics, we propose the efficiency from the conformal prediction framework (‘conformal efficiency’) as a proxy to the applicability domain size. A documented extension of the applicability domain would qualify as a tangible benefit from federated learning. In interim assessments, MELLODDY partners report a median increase in conformal efficiency of the federated over the single-partner model of 5.5% (with increases up to 9.7%). Subject to distributional conditions, that efficiency increase can be directly interpreted as the expected increase in conformal i.e. high confidence predictions. In conclusion, we present the first evidence that privacy-preserving federated machine learning across massive drug-discovery datasets from ten pharma partners indeed extends the applicability domain of property prediction models.
Complementary figures and details
Complementary figures on several analyses. Details on the hyperparameter search.