Federated learning of molecular properties with graph neural networks in a heterogeneous setting

Chemistry research has both high material and computational costs to conduct experiments. Intuitions are interested in differing classes of molecules, creating heterogeneous data that cannot be easily joined by conventional methods. This work introduces federated heterogeneous molecular learning. Federated learning allows end users to build a global model collaboratively while keeping their training data isolated. We first simulate a heterogeneous federated-learning benchmark (FedChem) by jointly performing scaffold splitting and latent Dirichlet allocation on existing datasets. Our results on FedChem show that significant learning challenges arise when working with heterogeneous molecules across clients. We then propose a method to alleviate the problem: Federated Learning by Instance reweighTing (FLIT(+)). FLIT(+) can align local training across clients. Experiments conducted on FedChem validate the advantages of this method. This work should enable a new type of collaboration for improving artificial intelligence (AI) in chemistry that mitigates concerns about sharing valuable chemical data.