Circular Arc Length-Based Kernel Matrix For Protein Sequence Classification

Biological sequence analysis is crucial in understanding the sequence structure, function, and evolutionary relationships. In traditional methods, using Euclidean distance metrics is common in measuring the similarity between sequence embeddings. However, they fail to capture sequence space’s inherent curvature and spherical nature. Therefore, we explore the application of spherical geometry and distance metric, circular arc length (CAL) based distance for comparing biological sequence embeddings. Spherical geometry is a non-Euclidean geometry that models the surface of a sphere, accounting for its curvature. By leveraging CAL, we can more accurately measure the pairwise distances between bio-sequence embeddings. In this study, we propose the utilization of CAL for comparing bio-sequence embeddings. We develop a function to compute the CAL distance between two sequence embeddings, enabling researchers to accurately measure the similarity between sequences while considering the underlying spherical geometry. Incorporating spherical geometry enables a more comprehensive understanding of the relationships and similarities between biological sequences, improving various downstream tasks such as classification, clustering, and evolutionary analysis. Our experimental evaluation demonstrates the advantages of using a spherical distance metric over Euclidean metrics for bio-sequence analysis. Our proposed CAL-based approach outperforms the Euclidean geometry-based baselines by depicting a huge performance improvement for the protein subcellular location classification task. In our experiments, accuracy is improved by 52.5% and 60. 3% compared to the PWM2Vec and Autoencoder methods, respectively, corresponding to the DT classifier.