PCA based dimensionality reduction of MRI images for training support vector machine to aid diagnosis of bipolar disorder

Abstract: This study aims to investigate how dimensionality reduction of neuroimaging data prior to training support vector machines (SVMs) affects the classification accuracy of bipolar disorder. This study uses principal component analysis (PCA) for dimensionality reduction. An open source data set of 19 bipolar and 31 control structural magnetic resonance imaging (sMRI) samples was used, part of the UCLA Consortium for Neuropsychiatric Phenomics LA5c Study funded by the NIH Roadmap Initiative aiming to foster breakthroughs in the development of novel treatments for neuropsychiatric disorders. The images underwent smoothing, feature extraction and PCA before they were used as input to train SVMs. 3-fold cross-validation was used to tune a number of hyperparameters for linear, radial, and polynomial kernels. Experiments were done to investigate the performance of SVM models trained using 1 to 29 principal components (PCs). Several PC sets reached 100% accuracy in the final evaluation, with the minimal set being the first two principal components. Accumulated variance explained by the PCs used did not have a correlation with the performance of the model. The choice of kernel and hyperparameters is of utmost importance as the performance obtained can vary greatly. The results support previous studies that SVM can be useful in aiding the diagnosis of bipolar disorder, and that the use of PCA as a dimensionality reduction method in combination with SVM may be appropriate for the classification of neuroimaging data for illnesses not limited to bipolar disorder. Due to the limitation of a small sample size, the results call for future research using larger collaborative data sets to validate the accuracies obtained.