CFD: Learning Generalized Molecular Representation via Concept-Enhanced  Feedback Disentanglement
Aming WU Cheng Deng
To accelerate biochemical research, e.g., drug and protein discovery, molecular representation learning (MRL) has attracted much attention. However, most existing methods follow the closed-set assumption that training and testing data share identical distribution, which limits their generalization abilities in out-of-distribution (OOD) cases. In this paper, we explore designing a new disentangled mechanism for learning generalized molecular representation that exhibits robustness against distribution shifts. And an approach of Concept-Enhanced Feedback Disentanglement (CFD) is proposed, whose goal is to exploit the feedback mechanism to learn distribution-agnostic representation. Specifically, we first propose two dedicated variational encoders to separately decompose distribution-agnostic and spurious features. Then, a set of molecule-aware concepts are tapped to focus on invariant substructure characteristics. By fusing these concepts into the disentangled distribution-agnostic features, the generalization ability of the learned molecular representation could be further enhanced. Next, we execute iteratively the disentangled operations based on a feedback received from the previous output. Finally, based on the outputs of multiple feedback iterations, we construct a self-supervised objective to promote the variational encoders to possess the disentangled capability. In the experiments, our method is verified on multiple real-world molecular datasets. The significant performance gains over state-of-the-art baselines demonstrate that our method can effectively disentangle generalized molecular representation in the presence of various distribution shifts. The source code will be released at https://github.com/AmingWu/MoleculeCFD.
Molecular Representation, Generalization, Feedback Disentanglement, Concepts