Using Deep Siamese Neural Networks to Speed up Natural Products Research

Nicholas Roberts, Poornav S. Purushothama, Vishal T. Vasudevan, Siddarth Ravichandran, Chen Zhang, William H. Gerwick, Garrison W. Cottrell

Abstract: Natural products (NPs, compounds derived from plants and animals) are an important source of novel disease treatments. A bottleneck in the search for new NPs is structure determination. One method is to use 2D Nuclear Magnetic Resonance (NMR) imaging, which indicates bonds between nuclei in the compound, and hence is the "fingerprint" of the compound. Computing a similarity score between 2D NMR spectra for a novel compound and a compound whose structure is known helps determine the structure of the novel compound. Standard approaches to this problem do not appear to scale to larger databases of compounds. Here we use deep convolutional Siamese networks to map NMR spectra to a cluster space, where similarity is given by the distance in the space. This approach results in an AUC score that is more than four times better than an approach using Latent Dirichlet Allocation.

Keywords: clustering, deep learning, application, chemistry, natural products

TL;DR: We learn a direct mapping from NMR spectra of small molecules to a molecular structure based cluster space.