TAWFN: A Deep Learning Framework for Protein Function Prediction.

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Abstract

Proteins play pivotal roles in biological systems, and precise prediction of their functions is indispensable for practical applications. Despite the surge in protein sequence data facilitated by high-throughput techniques, unraveling the exact functionalities of proteins still demands considerable time and resources. Currently, numerous methods rely on protein sequences for prediction, while methods targeting protein structures are scarce, often employing Convolutional Neural Networks (CNN) or Graph Convolutional Networks (GCN) individually.To address these challenges, our approach starts from protein structures and proposes a method that combines CNN and GCN into a unified framework called the Two-model Adaptive Weight Fusion Network (TAWFN) for protein function prediction. First, amino acid contact maps and sequences are extracted from the protein structure. Then, the sequence is used to generate one-hot encoded features and deep semantic features. These features, along with the constructed graph, are fed into the Adaptive Graph Convolutional Networks (AGCN) module and the Multilayer Convolutional Neural Network (MCNN) module as needed, resulting in preliminary classification outcomes. Finally, the preliminary classification results are inputted into the adaptive weight computation network, where adaptive weights are calculated to fuse the initial predictions from both networks, yielding the final prediction result. To evaluate the effectiveness of our method, experiments were conducted on the PDBset and AFset datasets. For molecular function, biological process, and cellular component tasks, TAWFN achieved Area Under the Precision-Recall curve (AUPR) values of 0.718, 0.385, and 0.488 respectively, with corresponding Fmax scores of 0.762, 0.628, and 0.693, and Smin scores of 0.326, 0.483, and 0.454. The experimental results demonstrate that TAWFN exhibits promising performance, outperforming existing methods.The TAWFN source code can be found at https://github.com/ss0830/TAWFN.Supplementary data are available at Bioinformatics online.© The Author(s) 2024. Published by Oxford University Press.