TensorVAE: A Direct Generative Model for Molecular Conformation Generation driven by Novel Feature Engineering

Hongyang Yu, Hongjiang Yu

Keywords: generative model, feature engineering, molecular conformation generation

Abstract: Efficient generation of 3D conformations of a molecule from its 2D graph is a key challenge in in-silico drug discovery. Deep learning (DL) based generative modelling has recently become a potent tool to tackling this challenge. However, many existing DL-based methods are either indirect-leveraging inter-atomic distances or direct-but requiring complex feature transformation or numerous sampling steps to generate conformations. In this work, we propose a simple model abbreviated TensorVAE capable of generating conformations directly from a 2D molecular graph in a single step. The main novelty of the proposed method is focused on feature engineering. We develop a novel encoding and feature extraction mechanism relying solely on standard convolution operation to generate token-like feature vector for each atom. These feature vectors are then transformed through standard transformer encoders under a conditional Variational Auto Encoder framework for learning to generate conformations directly. We show through experiments on two benchmark datasets that with intuitive and sensible feature engineering, a relatively simple and standard model can provide promising generative capability rivalling recent state-of-the-art models employing more sophisticated and specialized generative architecture.

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