A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data.
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.


CONCLUSIONS
We demonstrated that our approach is a promising method to assess the associations between CFS and SNPs.
Huang
Lung-Cheng
LC
Department of Psychiatry, National Taiwan University Hospital Yun-Lin Branch, Taiwan. psychidr@gmail.com
Hsu
Sen-Yen
SY
Lin
Eugene
E
D000465:Algorithms; D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods*; D003663:Decision Trees; D015673:Fatigue Syndrome, Chronic / Q000145:classification / Q000235:genetics; D020022:Genetic Predisposition to Disease; D023281:Genomics / Q000145:classification / Q000379:methods; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity