Towards Physically Reliable Molecular Representation Learning

Seunghoon Yi, Youngwoo Cho, Jinhwan Sul, Seung Woo Ko, Soo Kyung Kim, Jaegul Choo, Hongkee Yoon, Joonseok Lee

Keywords: molecular, representation learning, physics-driven modeling, masked atomic modeling

TL;DR: We propose a physics-driven molecular representation learning method powered by self-supervised masked atomic modeling, and novel evaluation schemes to ensure reliability of the model in various ways.

Abstract: Estimating the energetic properties of molecular systems is a critical task in material design. Machine learning has shown remarkable promise on this task over classical force-fields, but a fully data-driven approach suffers from limited labeled data; not just the amount of available data lacks, but the distribution of labeled examples is highly skewed to stable states. In this work, we propose a molecular representation learning method that extrapolates well beyond the training distribution, powered by physics-driven parameter estimation from classical energy equations and self-supervised learning inspired from masked language modeling. To ensure reliability of the proposed model, we introduce a series of novel evaluation schemes in multifaceted ways, beyond the energy or force accuracy that has been dominantly used. From extensive experiments, we demonstrate that the proposed method is effective in discovering molecular structures, outperforming other baselines. Furthermore, we extrapolate it to the chemical reaction pathways beyond stable states, taking a step towards physically reliable molecular representation learning.