Systematic evaluation of machine learning methods for identifying human–pathogen protein–protein interactions

Abstract In recent years, high-throughput experimental techniques have significantly enhanced the accuracy and coverage of protein–protein interaction identification, including human–pathogen protein–protein interactions (HP-PPIs). Despite this progress, experimental methods are, in general, expensive in terms of both time and labour costs, especially considering that there are enormous amounts of potential protein-interacting partners. Developing computational methods to predict interactions between human and bacteria pathogen has thus become critical and meaningful, in both facilitating the detection of interactions and mining incomplete interaction maps. In this paper, we present a systematic evaluation of machine learning-based computational methods for human–bacterium protein–protein interactions (HB-PPIs). We first reviewed a vast number of publicly available databases of HP-PPIs and then critically evaluate the availability of these databases. Benefitting from its well-structured nature, we subsequently preprocess the data and identified six bacterium pathogens that could be used to study bacterium subjects in which a human was the host. Additionally, we thoroughly reviewed the literature on ‘host–pathogen interactions’ whereby existing models were summarized that we used to jointly study the impact of different feature representation algorithms and evaluate the performance of existing machine learning computational models. Owing to the abundance of sequence information and the limited scale of other protein-related information, we adopted the primary protocol from the literature and dedicated our analysis to a comprehensive assessment of sequence information and machine learning models. A systematic evaluation of machine learning models and a wide range of feature representation algorithms based on sequence information are presented as a comparison survey towards the prediction performance evaluation of HB-PPIs.