Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification

Abstract

Biological sequence classification is vital in various fields, such as genomics and bioinformatics. The advancement and reduced cost of genomic sequencing have brought the attention of researchers for protein and nucleotide sequence classification. Traditional approaches face limitations in capturing the intricate relationships and hierarchical structures inherent in genomic sequences, while numerous machine-learning models have been proposed to tackle this challenge. In this work, we propose Hist2Vec, a novel kernel-based embedding generation approach for capturing sequence similarities. Hist2Vec combines the concept of histogram-based kernel matrices and Gaussian kernel functions. It constructs histogram-based representations using the unique k-mers present in the sequences. By leveraging the power of Gaussian kernels, Hist2Vec transforms these representations into high-dimensional feature spaces, preserving important sequence information. Hist2Vec aims to address the limitations of existing methods by capturing sequence similarities in a high-dimensional feature space while providing a robust and efficient framework for classification. We employ kernel Principal Component Analysis (PCA) using standard machine-learning algorithms to generate embedding for efficient classification. Experimental evaluations on protein and nucleotide datasets demonstrate the efficacy of Hist2Vec in achieving high classification accuracy compared to state-of-the-art methods. It outperforms state-of-the-art methods by achieving > 76% and > 83% accuracies for DNA and Protein datasets, respectively. Hist2Vec provides a robust framework for biological sequence classification, enabling better classification and promising avenues for further analysis of biological data.