An evaluation of different classification algorithms for protein sequence-based reverse vaccinology prediction

• Published in: PloS one Vol. 14; no. 12; p. e0226256
• Main Authors: Heinson, Ashley I., Ewing, Rob M., Holloway, John W., Woelk, Christopher H., Niranjan, Mahesan
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 13.12.2019; Public Library of Science (PLoS)
• Subjects: Algorithms; Amino acid sequence; Amino acids; Analysis; Antibiotics; Antigens; Antigens, Bacterial - immunology; Artificial intelligence; Bacteria; Bacterial Proteins - immunology; Bacterial Vaccines - immunology; Bioinformatics; Biology; Biology and Life Sciences; Classification; Computational Biology - methods; Computer and Information Sciences; Humans; Immunology; Learning algorithms; Machine Learning; Medical research; Medicine and Health Sciences; Novels; Peptides; Physical Sciences; Predictions; Proteins; Research and Analysis Methods; Vaccines; Vaccinology; United Kingdom > UK
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0226256

Previous work has shown that proteins that have the potential to be vaccine candidates can be predicted from features derived from their amino acid sequences. In this work, we make an empirical comparison across various machine learning classifiers on this sequence-based inference problem. Using systematic cross validation on a dataset of 200 known vaccine candidates and 200 negative examples, with a set of 525 features derived from the AA sequences and feature selection applied through a greedy backward elimination approach, we show that simple classification algorithms often perform as well as more complex support vector kernel machines. The work also includes a novel cross validation applied across bacterial species, i.e. the validation proteins all come from a specific species of bacterium not represented in the training set. We termed this type of validation Leave One Bacteria Out Validation (LOBOV).