Convolutional Networks on Graphs for Learning Molecular Fingerprints

Part of Advances in Neural Information Processing Systems 28 (NIPS 2015)

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David K. Duvenaud, Dougal Maclaurin, Jorge Iparraguirre, Rafael Bombarell, Timothy Hirzel, Alan Aspuru-Guzik, Ryan P. Adams


We introduce a convolutional neural network that operates directly on graphs.These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape.The architecture we present generalizes standard molecular feature extraction methods based on circular fingerprints.We show that these data-driven features are more interpretable, and have better predictive performance on a variety of tasks.