K-Nearest Robust Active Learning on Big Data and Application in Epitope Prediction

Abstract

B-cells that induce antigen-specific immune responses in vivo produce large numbers of antigen-specific antibodies by recognizing subregions (epitopes) of antigenic proteins, in which they can inhibit the function of antigen protein. Epitope region prediction facilitates the design and development of vaccines that induce the production of antigen-specific antibodies. There are many diseases which are difficult to treat without vaccines. And the COVID-19 has destroyed many people’s lives. Therefore, making vaccines to COVID-19 is very important. Making vaccines needs a large number of experiments to get labeled targets. However, obtaining tremendous labeled data from experiments is a challenge for humans. Big data analysis has proposed some solutions to deal with this challenge. Big data technology has developed very fast and has been applied in many areas. In the bioinformatics area, big data analysis solves a large number of problems, particularly in the area of active learning. Active learning is a method of building more predictive models with less labeled data. Active learning establishes models with less data by asking the oracle (human) for the most valuable samples to train models. Hence, active learning’s application in making vaccines is meaningful that the scientists do not need to do tremendous experiments. This paper proposed a more robust active learning method based on uncertainty sampling and K-nearest density and applies it to the vaccine manufacture. This paper evaluates the new algorithm with accuracy and robustness. In order to evaluate the robustness of active learners, a new robustness index is designed in this paper. And this paper compares the new algorithm with a pool-based active learning algorithm, density-weighted active learning algorithm, and traditional machine learning algorithm. Finally, the new algorithm is applied to epitope prediction of B-cell data, which is significant to making vaccines.