Benchmarking Datasets from Malaria Cytotoxic T-cell Epitopes Using Machine Learning Approach

Abstract

Background: Epitope prediction remains a major challenge in malaria due to the unique parasite biology, in addition to rapidly evolving parasite sequence variation in Plasmodium species. Although several models for epitope prediction exist, they are not useful in Plasmodium specific epitope development. Hence, it was proposed to use machine learning based methods to develop a peptide sequence based epitope predictor specific for malaria.

Methods: Model datasets were developed and performance was tested using various machine learning algorithms. Machine learning classifiers were trained on epitope data using sequence features and comparison of amino acid physicochemical properties was done to yield a valid prediction model.

Results: The findings from the analysis reveal that the model developed using selected classifiers after preprocessing by Waikato Environment for Knowledge Analysis (WEKA) performed better than other methods. The datasets for benchmarks of performance are deposited in the repository https://github.com/githubramaadiga/epitope_dataset .

Conclusion: The study is the first in-silico study on benchmarking Plasmodium cytotoxic T cell epitope datasets using machine learning approach. The peptide based predictors have been used for the first time to classify cytotoxic T cell epitopes in malaria. Algorithms has been evaluated using real datasets from malaria to obtain the model.

Keywords: Benchmarking; Epitopes; Machine learning; Malaria; Plasmodium.