A hybrid machine learning method for fusing fMRI and genetic data: Combining both improves classification of schizophrenia

Honghui Yang, Jingyu Liu, Jing Sui, Godfrey Pearlson, Vince D. Calhoun

Research output: Contribution to journalArticlepeer-review

125 Scopus citations


We demonstrate a hybrid machine learning method to classify schizophrenia patients and healthy controls, using functional magnetic resonance imaging (fMRI) and single nucleotide polymorphism (SNP) data. The method consists of four stages: (1) SNPs with the most discriminating information between the healthy controls and schizophrenia patients are selected to construct a support vector machine ensemble (SNP-SVME). (2) Voxels in the fMRI map contributing to classification are selected to build another SVME (Voxel-SVME). (3) Components of fMRI activation obtained with independent component analysis (ICA) are used to construct a single SVM classifier (ICA-SVMC). (4) The above three models are combined into a single module using a majority voting approach to make a final decision (Combined SNP-fMRI). The method was evaluated by a fully validated leave-one-out method using 40 subjects (20 patients and 20 controls). The classification accuracy was: 0.74 for SNP-SVME, 0.82 for Voxel-SVME, 0.83 for ICA-SVMC, and 0.87 for Combined SNP-fMRI. Experimental results show that better classification accuracy was achieved by combining genetic and fMRI data than using either alone, indicating that genetic and brain function representing different, but partially complementary aspects, of schizophrenia etiopathology. This study suggests an effective way to reassess biological classification of individuals with schizophrenia, which is also potentially useful for identifying diagnostically important markers for the disorder.

Original languageEnglish (US)
JournalFrontiers in Human Neuroscience
StatePublished - 2010
Externally publishedYes


  • Feature selection
  • Functional magnetic resonance imaging
  • Gene
  • Machine learning
  • Schizophrenia
  • Single nucleotide polymorphisms
  • Support vector machine ensemble

ASJC Scopus subject areas

  • Neuropsychology and Physiological Psychology
  • Neurology
  • Psychiatry and Mental health
  • Biological Psychiatry
  • Behavioral Neuroscience


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