An extended de Bruijn graph for feature engineering over biological sequential data

Abstract

In this study, we introduce a novel de Bruijn graph (dBG) based framework for feature engineering in biological sequential data such as proteins. This framework simplifies feature extraction by dynamically generating high-quality, interpretable features for traditional AI (TAI) algorithms. Our framework accounts for amino acid substitutions by efficiently adjusting the edge weights in the dBG using a secondary trie structure. We extract motifs from the dBG by traversing the heavy edges, and then incorporate alignment algorithms like BLAST and Smith-Waterman to generate features for TAI algorithms. Empirical validation on TIMP (tissue inhibitors of matrix metalloproteinase) data demonstrates significant accuracy improvements over a robust baseline, state-of-the-art (SOTA) PLM models, and those from the popular GLAM2 tool. Furthermore, our framework successfully identified Glycine and Arginine-rich (GAR) motifs with high coverage, highlighting it's potential in general pattern discovery. The software code is accessible at: https://github.com/parichit/TIMP_Classification