Efficient Approximate Kernel Based Spike Sequence Classification

TL;DR

This paper introduces improved approximate kernel methods for classifying coronavirus spike protein sequences, leveraging domain knowledge and efficient preprocessing to enhance predictive accuracy over existing approaches.

Contribution

It proposes novel enhancements to approximate kernel algorithms using minimizers and information gain tailored for coronavirus sequence classification.

Findings

Improved classification accuracy on coronavirus datasets

Enhanced kernel performance over baseline and state-of-the-art methods

Effective use of domain knowledge and preprocessing techniques

Abstract

Machine learning (ML) models, such as SVM, for tasks like classification and clustering of sequences, require a definition of distance/similarity between pairs of sequences. Several methods have been proposed to compute the similarity between sequences, such as the exact approach that counts the number of matches between $k$-mers (sub-sequences of length $k$) and an approximate approach that estimates pairwise similarity scores. Although exact methods yield better classification performance, they pose high computational costs, limiting their applicability to a small number of sequences. The approximate algorithms are proven to be more scalable and perform comparably to (sometimes better than) the exact methods -- they are designed in a "general" way to deal with different types of sequences (e.g., music, protein, etc.). Although general applicability is a desired property of an algorithm, it is not the case in all scenarios. For example, in the current COVID-19 (coronavirus) pandemic, there is a need for an approach that can deal specifically with the coronavirus. To this end, we propose a series of ways to improve the performance of the approximate kernel (using minimizers and information gain) in order to enhance its predictive performance pm coronavirus sequences. More specifically, we improve the quality of the approximate kernel using domain knowledge (computed using information gain) and efficient preprocessing (using minimizers computation) to classify coronavirus spike protein sequences corresponding to different variants (e.g., Alpha, Beta, Gamma). We report results using different classification and clustering algorithms and evaluate their performance using multiple evaluation metrics. Using two datasets, we show that our proposed method helps improve the kernel's performance compared to the baseline and state-of-the-art approaches in the healthcare domain.