Bulletin of Electrical Engineering and Informatics
Vol 15, No 1: February 2026

Improving genomic classification via Pearson-based SNP selection: a comparison of k-NN, SVM, and random forest

Prihanto Ngesti Basuki (Satya Wacana Christian University)
Sri Yulianto Joko Prasetyo (Satya Wacana Christian University)
Adi Setiawan (Satya Wacana Christian University)



Article Info

Publish Date
01 Feb 2026

Abstract

Accurate genomic classification is vital for precision health and population studies, yet high-dimensional single-nucleotide polymorphism (SNP) data (pn) amplify noise, redundancy, and overfitting. This study evaluates a simple, model-independent Pearson-based selection that ranks SNPs by feature–label correlation, and assesses k-nearest neighbors (k-NN), linear support vector machine (SVM), and random forest (RF) under leakage-free stratified Monte Carlo cross-validation (MCCV). Performance increases monotonically with |r|: the strongest tiers reach ?99–100% accuracy; SVM leads in mid tiers (RF second), while k-NN is competitive mainly at the extremes. A matched-dimensionality PCA-120 baseline (TRAIN-only) attains parity for SVM/RF and trails slightly for k-NN at the 10% test size. With 120-SNP panels, prediction medians are ?0.30 ms (SVM), 1.81–1.83 ms (k-NN), and 34–35 ms (RF), supporting CPU-only deployment. A consensus panel combining correlation evidence with principal component analysis (PCA) selection frequency yields interpretable Top-20/Top-120 subsets and |r|-based operating thresholds. Overall, Pearson-based selection provides a transparent, reproducible baseline for small-sample SNP classification, offering accuracy competitive with PCA at lower computational complexity and straightforward extensions to broader cohorts and multi-omics integration.

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Journal Info

Abbrev

EEI

Publisher

Subject

Electrical & Electronics Engineering

Description

Bulletin of Electrical Engineering and Informatics (Buletin Teknik Elektro dan Informatika) ISSN: 2089-3191, e-ISSN: 2302-9285 is open to submission from scholars and experts in the wide areas of electrical, electronics, instrumentation, control, telecommunication and computer engineering from the ...