Enhancing the Feature Representation of Protein Sequence Descriptors in Protein-Protein Interaction Prediction.

Abstract

In recent years, computational methods such as machine learning and deep learning have been increasingly used to solve various bioinformatics problems related to protein sequence data, such as predicting protein interaction, protein function, subcellular location, and so on. The first crucial step in applying these methods is how to represent a protein sequence as an input feature vector, as the feature vector quality significantly impacts the performance of those methods. A range of protein sequence descriptors has been proposed to enhance the quality of protein sequence representation. Existing descriptors extract information that can be obtained from sequences, such as composition, distribution, spatial correlation between amino acids, and so on. However, improvements can still be made in spatial correlation to capture better sequence similarity, which is valuable for Protein-Protein Interaction (PPI) prediction tasks. In this study, our aim is to develop new descriptors based on six well-known sequence descriptors to improve the ability to represent protein sequences. We evaluate the performance of the new descriptors on various PPI datasets. The results demonstrate that the proposed descriptors outperform their original versions in terms of PPI prediction performance. This work also introduces ProtSeqDesc (protein sequence descriptors), a flexible Python package that includes 51 types of feature vectors, covering all proposed descriptors. The software package is aimed at meeting the demand for the application of computational methods in bioinformatics.