Digital Image Processing to Detect Adaptive Evolution

• Published in: Molecular biology and evolution 2024-11, Vol.41 (12)
• Main Authors: Amin, Md Ruhul, Hasan, Mahmudul, DeGiorgio, Michael
• Format: Article
• Language: English
• Subjects: Evolution, Molecular; Haplotypes; Humans; Image Processing, Computer-Assisted - methods; Machine Learning; Methods; Neural Networks, Computer; Selection, Genetic
• ISSN: 0737-4038; 1537-1719; 1537-1719
• DOI: 10.1093/molbev/msae242

In recent years, advances in image processing and machine learning have fueled a paradigm shift in detecting genomic regions under natural selection. Early machine learning techniques employed population-genetic summary statistics as features, which focus on specific genomic patterns expected by adaptive and neutral processes. Though such engineered features are important when training data are limited, the ease at which simulated data can now be generated has led to the recent development of approaches that take in image representations of haplotype alignments and automatically extract important features using convolutional neural networks. Digital image processing methods termed α-molecules are a class of techniques for multiscale representation of objects that can extract a diverse set of features from images. One such α-molecule method, termed wavelet decomposition, lends greater control over high-frequency components of images. Another α-molecule method, termed curvelet decomposition, is an extension of the wavelet concept that considers events occurring along curves within images. We show that application of these α-molecule techniques to extract features from image representations of haplotype alignments yield high true positive rate and accuracy to detect hard and soft selective sweep signatures from genomic data with both linear and nonlinear machine learning classifiers. Moreover, we find that such models are easy to visualize and interpret, with performance rivaling those of contemporary deep learning approaches for detecting sweeps.