BPP: a platform for automatic biochemical pathway prediction.

Abstract

A biochemical pathway consists of a series of interconnected biochemical reactions to accomplish specific life activities. The participating reactants and resultant products of a pathway, including gene fragments, proteins, and small molecules, coalesce to form a complex reaction network. Biochemical pathways play a critical role in the biochemical domain as they can reveal the flow of biochemical reactions in living organisms, making them essential for understanding life processes. Existing studies of biochemical pathway networks are mainly based on experimentation and pathway database analysis methods, which are plagued by substantial cost constraints. Inspired by the success of representation learning approaches in biomedicine, we develop the biochemical pathway prediction (BPP) platform, which is an automatic BPP platform to identify potential links or attributes within biochemical pathway networks. Our BPP platform incorporates a variety of representation learning models, including the latest hypergraph neural networks technology to model biochemical reactions in pathways. In particular, BPP contains the latest biochemical pathway-based datasets and enables the prediction of potential participants or products of biochemical reactions in biochemical pathways. Additionally, BPP is equipped with an SHAP explainer to explain the predicted results and to calculate the contributions of each participating element. We conduct extensive experiments on our collected biochemical pathway dataset to benchmark the effectiveness of all models available on BPP. Furthermore, our detailed case studies based on the chronological pattern of our dataset demonstrate the effectiveness of our platform. Our BPP web portal, source code and datasets are freely accessible at https://github.com/Glasgow-AI4BioMed/BPP.