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A Demographic-Conditioned Variational Autoencoder for Removal of Confounds from fMRI Data
  • +7
  • Anton Orlichenko,
  • Gang Qu,
  • Ziyu Zhou,
  • Anqi Liu,
  • Hong-Wen Deng,
  • Zhengming Ding,
  • Julia M Stephen,
  • Tony W Wilson,
  • Vince D Calhoun,
  • Yu-Ping Wang
Anton Orlichenko

Corresponding Author:[email protected]

Author Profile
Gang Qu
Ziyu Zhou
Anqi Liu
Hong-Wen Deng
Zhengming Ding
Julia M Stephen
Tony W Wilson
Vince D Calhoun
Yu-Ping Wang


Objective: fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always clear that all demographic confounds, such as age, sex, and race, have been removed from fMRI data. Additionally, many fMRI datasets are restricted to authorized researchers, making dissemination of these valuable data sources challenging. Methods: We create a variational autoencoder (VAE)-based model, DemoVAE, to decorrelate fMRI features from demographics and generate high-quality synthetic fMRI data based on user-supplied demographics. We train and validate our model using two large, widely used datasets, the Philadelphia Neurodevelopmental Cohort (PNC) and Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP). Results: We find that DemoVAE recapitulates group differences in fMRI data while capturing the full breadth of individual variations. Significantly, we also find that most clinical and computerized battery fields that are correlated with fMRI data are not correlated with DemoVAE latents. An exception are several fields related to schizophrenia medication and symptom severity. Conclusion: Our model generates fMRI data that captures the full distribution of FC better than traditional VAE or GAN models. We also find that most prediction using fMRI data is dependent on correlation with, and prediction of, demographics. Significance: Our DemoVAE model allows for generation of high quality synthetic data conditioned on subject demographics as well as the removal of the confounding effects of demographics. We identify that FC-based prediction tasks are highly influenced by demographic confounds.
11 May 2024Submitted to TechRxiv
17 May 2024Published in TechRxiv