Curvature-enhanced graph convolutional network for biomolecular interaction prediction

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL(2024)

Cited 0|Views9
No score
Abstract
Geometric deep learning has demonstrated a great potential in non-Euclidean data analysis. The incorporation of geometric insights into learning architecture is vital to its success. Here we propose a curvature-enhanced graph convolutional network (CGCN) for biomolecular interaction prediction. Our CGCN employs Ollivier-Ricci curvature (ORC) to characterize network local geometric properties and enhance the learning capability of GCNs. More specifically, ORCs are evaluated based on the local topology from node neighborhoods, and further incorporated into the weight function for the feature aggregation in message-passing procedure. Our CGCN model is extensively validated on fourteen real -world bimolecular interaction networks and analyzed in details using a series of well-designed simulated data. It has been found that our CGCN can achieve the state -of -the -art results. It outperforms all existing models, as far as we know, in thirteen out of the fourteen real -world datasets and ranks as the second in the rest one. The results from the simulated data show that our CGCN model is superior to the traditional GCN models regardless of the positive-to-negative-curvature ratios, network densities, and network sizes (when larger than 500).
More
Translated text
Key words
Ollivier-Ricci curvature,Graph convolutional network,Biomolecular interaction
AI Read Science
Must-Reading Tree
Example
Generate MRT to find the research sequence of this paper
Chat Paper
Summary is being generated by the instructions you defined