Understanding the Limitations of Deep Models for Molecular property prediction: Insights and Solutions

Molecular Property Prediction (MPP) is a crucial task in the AI-driven Drug Discovery (AIDD) pipeline, which has recently gained considerable attention thanks to advancements in deep learning. However, recent research has revealed that deep models struggle to beat traditional non-deep ones on MPP. In this study, we benchmark 12 representative models (3 non-deep models and 9 deep models) on 15 molecule datasets. Through the most comprehensive study to date, we make the following key observations: \textbf{(\romannumeral 1)} Deep models are generally unable to outperform non-deep ones; \textbf{(\romannumeral 2)} The failure of deep models on MPP cannot be solely attributed to the small size of molecular datasets; \textbf{(\romannumeral 3)} In particular, some traditional models including XGB and RF that use molecular fingerprints as inputs tend to perform better than other competitors. Furthermore, we conduct extensive empirical investigations into the unique patterns of molecule data and inductive biases of various models underlying these phenomena. These findings stimulate us to develop a simple-yet-effective feature mapping method for molecule data prior to feeding them into deep models. Empirically, deep models equipped with this mapping method can beat non-deep ones in most MoleculeNet datasets. Notably, the effectiveness is further corroborated by extensive experiments on cutting-edge dataset related to COVID-19 and activity cliff datasets.