Unified Molecular Modeling via Modality Blending

Self-supervised molecular representation learning is critical for molecule-based tasks such as AI-assisted drug discovery. Recent studies consider leveraging both 2D and 3D information for representation learning, with straightforward alignment strategies that treat each modality separately. In this...

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Bibliographic Details
Published in:arXiv.org 2023-07
Main Authors: Yu, Qiying, Zhang, Yudi, Ni, Yuyan, Feng, Shikun, Lan, Yanyan, Zhou, Hao, Liu, Jingjing
Format: Article
Language:English
Subjects:
Representations
Self-supervised learning
Online Access:Get full text
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Summary:Self-supervised molecular representation learning is critical for molecule-based tasks such as AI-assisted drug discovery. Recent studies consider leveraging both 2D and 3D information for representation learning, with straightforward alignment strategies that treat each modality separately. In this work, we introduce a novel "blend-then-predict" self-supervised learning method (MoleBLEND), which blends atom relations from different modalities into one unified relation matrix for encoding, then recovers modality-specific information for both 2D and 3D structures. By treating atom relationships as anchors, seemingly dissimilar 2D and 3D manifolds are aligned and integrated at fine-grained relation-level organically. Extensive experiments show that MoleBLEND achieves state-of-the-art performance across major 2D/3D benchmarks. We further provide theoretical insights from the perspective of mutual-information maximization, demonstrating that our method unifies contrastive, generative (inter-modal prediction) and mask-then-predict (intra-modal prediction) objectives into a single cohesive blend-then-predict framework.
ISSN:2331-8422