Augmenting Molecular Images with Vector Representations as a Featurization Technique for Drug Classification

TL;DR

This paper introduces a novel molecular featurization technique combining images with binary vector representations, leading to improved drug classification performance and faster convergence.

Contribution

It proposes augmenting molecular images with Morgan fingerprints and MACCS keys, enhancing feature richness for deep learning models in drug classification.

Findings

Achieved state-of-the-art AUC ROC on HIV dataset

Model converged faster and required less computational power

Outperformed previous molecular featurization methods

Abstract

One of the key steps in building deep learning systems for drug classification and generation is the choice of featurization for the molecules. Previous featurization methods have included molecular images, binary strings, graphs, and SMILES strings. This paper proposes the creation of molecular images captioned with binary vectors that encode information not contained in or easily understood from a molecular image alone. Specifically, we use Morgan fingerprints, which encode higher level structural information, and MACCS keys, which encode yes or no questions about a molecules properties and structure. We tested our method on the HIV dataset published by the Pande lab, which consists of 41,127 molecules labeled by if they inhibit the HIV virus. Our final model achieved a state of the art AUC ROC on the HIV dataset, outperforming all other methods. Moreover, the model converged significantly faster than most other methods, requiring dramatically less computational power than unaugmented images.