MM-Deacon: Multimodal molecular domain embedding analysis via contrastive learning

Abstract

AbstractMolecular representation learning plays an essential role in cheminformatics. Recently, language model-based approaches have been popular as an alternative to traditional expert-designed features to encode molecules. However, these approaches only utilize a single modality for representing molecules. Driven by the fact that a given molecule can be described through different modalities such as Simplified Molecular Line Entry System (SMILES), The International Union of Pure and Applied Chemistry (IUPAC), and The IUPAC International Chemical Identifier (InChI), we propose a multimodal molecular embedding generation approach called MM-Deacon (multimodal molecular domain embedding analysis via contrastive learning). MM-Deacon is trained using SMILES and IUPAC molecule representations as two different modalities. First, SMILES and IUPAC strings are encoded by using two different transformer-based language models independently, then the contrastive loss is utilized to bring these encoded representations from different modalities closer to each other if they belong to the same molecule, and to push embeddings farther from each other if they belong to different molecules. We evaluate the robustness of our molecule embeddings on molecule clustering, cross-modal molecule search, drug similarity assessment and drug-drug interaction tasks.