Graph Memory Networks for Molecular Activity Prediction
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Molecular activity prediction is critical in drug design. Machine learning techniques such as kernel methods and random forests have been successful for this task. These models require fixed-size feature vectors as input while the molecules are variable in size and structure. As a result, fixed-sized fingerprint representation is poor in handling substructures for large molecules. Here we approach the problem through deep neural networks as they are flexible in modeling structured data such as grids, sequences and graphs. We propose Graph Memory Network (GraphMem), a memory-augmented neural network to model the graph structure in molecules. GraphMem consists of a recurrent controller coupled with an external memory whose cells dynamically interact and change through a multi-hop reasoning process. The dynamic interactions enable an iterative refinement of the representation of molecular graphs with multiple bond types. We demonstrate the effectiveness of the proposed model on 10 BioAssay activity tests.
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