New feature extraction from phylogenetic profiles improved the performance of pathogen-host interactions.

Journal: Frontiers in cellular and infection microbiology
Published Date: Aug 2, 2022

Abstract

MOTIVATION: The understanding of pathogen-host interactions (PHIs) is essential and challenging research because this potentially provides the mechanism of molecular interactions between different organisms. The experimental exploration of PHI is time-consuming and labor-intensive, and computational approaches are playing a crucial role in discovering new unknown PHIs between different organisms. Although it has been proposed that most machine learning (ML)-based methods predict PHI, these methods are all based on the structure-based information extracted from the sequence for prediction. The selection of feature values is critical to improving the performance of predicting PHI using ML.

Authors

  • Yang Fang
    Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
  • Yi Yang
    Department of Orthopedics, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
  • Chengcheng Liu
    State Key Laboratory of Oral Diseases, Department of Periodontics, National Clinical Research Center for Oral Diseases, West China School & Hospital of Stomatology, Sichuan University, Chengdu, China.

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