A Comparison of Classification Methods for Predicting Chronic Fatigue Syndrome Based on Genetic Data

Overview

Journal J Transl Med

Publisher Biomed Central

Specialties Biomedical Engineering
General Medicine

Date 2009 Sep 24

PMID 19772600

Citations 34

Authors

Lung-Cheng Huang

Sen-Yen Hsu

Eugene Lin

Affiliations

Soon will be listed here.

Abstract

Background: In the studies of genomics, it is essential to select a small number of genes that are more significant than the others for the association studies of disease susceptibility. In this work, our goal was to compare computational tools with and without feature selection for predicting chronic fatigue syndrome (CFS) using genetic factors such as single nucleotide polymorphisms (SNPs).

Methods: We employed the dataset that was original to the previous study by the CDC Chronic Fatigue Syndrome Research Group. To uncover relationships between CFS and SNPs, we applied three classification algorithms including naive Bayes, the support vector machine algorithm, and the C4.5 decision tree algorithm. Furthermore, we utilized feature selection methods to identify a subset of influential SNPs. One was the hybrid feature selection approach combining the chi-squared and information-gain methods. The other was the wrapper-based feature selection method.

Results: The naive Bayes model with the wrapper-based approach performed maximally among predictive models to infer the disease susceptibility dealing with the complex relationship between CFS and SNPs.

Conclusion: We demonstrated that our approach is a promising method to assess the associations between CFS and SNPs.

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