ImageDDI: Image-enhanced Molecular Motif Sequence Representation for Drug-Drug Interaction Prediction

TL;DR

ImageDDI introduces an innovative approach combining molecular motif sequences and visual information from images to improve drug-drug interaction prediction accuracy, surpassing existing methods.

Contribution

The paper presents a novel image-enhanced molecular motif sequence framework that integrates local and global drug structures using transformer encoders and adaptive feature fusion.

Findings

Outperforms state-of-the-art DDI prediction methods

Effective integration of 2D and 3D molecular images

Demonstrates robustness across multiple datasets

Abstract

To mitigate the potential adverse health effects of simultaneous multi-drug use, including unexpected side effects and interactions, accurately identifying and predicting drug-drug interactions (DDIs) is considered a crucial task in the field of deep learning. Although existing methods have demonstrated promising performance, they suffer from the bottleneck of limited functional motif-based representation learning, as DDIs are fundamentally caused by motif interactions rather than the overall drug structures. In this paper, we propose an Image-enhanced molecular motif sequence representation framework for \textbf{DDI} prediction, called ImageDDI, which represents a pair of drugs from both global and local structures. Specifically, ImageDDI tokenizes molecules into functional motifs. To effectively represent a drug pair, their motifs are combined into a single sequence and embedded using a transformer-based encoder, starting from the local structure representation. By leveraging the associations between drug pairs, ImageDDI further enhances the spatial representation of molecules using global molecular image information (e.g. texture, shadow, color, and planar spatial relationships). To integrate molecular visual information into functional motif sequence, ImageDDI employs Adaptive Feature Fusion, enhancing the generalization of ImageDDI by dynamically adapting the fusion process of feature representations. Experimental results on widely used datasets demonstrate that ImageDDI outperforms state-of-the-art methods. Moreover, extensive experiments show that ImageDDI achieved competitive performance in both 2D and 3D image-enhanced scenarios compared to other models.