Nearest Neighbor CCP-Based Molecular Sequence Analysis

Sarwan Ali

doi:10.1109/TCBBIO.2025.3621138

Nearest Neighbor CCP-Based Molecular Sequence Analysis

2025-10-15

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DOI：10.1109/TCBBIO.2025.3621138

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Molecular sequence analysis is crucial for understanding several biological processes, including protein-protein interactions, functional annotation, and disease classification. The large number of sequences and the inherently complicated nature of protein structures make it challenging to analyze such data. Finding patterns and enhancing subsequent research requires the use of dimensionality reduction and feature selection approaches. Recently, a method called Correlated Clustering and Projection (CCP) has been proposed as an effective method for biological sequencing data. The CCP technique remains computationally expensive, despite its effectiveness for sequence visualization. Furthermore, its utility for classifying molecular sequences is still uncertain. To solve these two problems, we present a Nearest-Neighbor Correlated Clustering and Projection (CCP-NN)-based technique for efficiently preprocessing molecular sequence data. To group related molecular sequences and produce representative supersequences, CCP makes use of sequence-to-sequence correlations. As opposed to conventional methods, CCP does not rely on matrix diagonalization, therefore, it can be applied to a range of machine-learning problems. We estimate the density map and compute the correlation using a nearest-neighbor search technique. We perform a molecular sequence classification using CCP and CCP-NN representations to assess the efficacy of our proposed approach. Our findings show that CCP-NN considerably improves classification accuracy and significantly outperforms CCP in computational runtime.

Keywords:

Nucleotides

CCP

spike sequence

dimensionality reduction

Nearest Neighbor CCP-Based Molecular Sequence Analysis

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