Imputing Brain Measurements Across Data Sets via Graph Neural Networks

Yixin Wang; Wei Peng; Susan F Tapert; Qingyu Zhao; Kilian M Pohl

doi:10.1007/978-3-031-46005-0_15

Imputing Brain Measurements Across Data Sets via Graph Neural Networks

Predict Intell Med. 2023:14277:172-183. doi: 10.1007/978-3-031-46005-0_15.

Authors

Yixin Wang¹, Wei Peng², Susan F Tapert³, Qingyu Zhao², Kilian M Pohl^{2

4}

Affiliations

¹ Department of Bioengineering, Stanford University, Stanford, CA, USA.
² Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
³ Department of Psychiatry, University of California, San Diego, CA, USA.
⁴ Center for Biomedical Sciences, SRI International, Menlo Park, CA, USA.

Abstract

Publicly available data sets of structural MRIs might not contain specific measurements of brain Regions of Interests (ROIs) that are important for training machine learning models. For example, the curvature scores computed by Freesurfer are not released by the Adolescent Brain Cognitive Development (ABCD) Study. One can address this issue by simply reapplying Freesurfer to the data set. However, this approach is generally computationally and labor intensive (e.g., requiring quality control). An alternative is to impute the missing measurements via a deep learning approach. However, the state-of-the-art is designed to estimate randomly missing values rather than entire measurements. We therefore propose to re-frame the imputation problem as a prediction task on another (public) data set that contains the missing measurements and shares some ROI measurements with the data sets of interest. A deep learning model is then trained to predict the missing measurements from the shared ones and afterwards is applied to the other data sets. Our proposed algorithm models the dependencies between ROI measurements via a graph neural network (GNN) and accounts for demographic differences in brain measurements (e.g. sex) by feeding the graph encoding into a parallel architecture. The architecture simultaneously optimizes a graph decoder to impute values and a classifier in predicting demographic factors. We test the approach, called Demographic Aware Graph-based Imputation (DAGI), on imputing those missing Freesurfer measurements of ABCD (N=3760; minimum age 12 years) by training the predictor on those publicly released by the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA, N=540). 5-fold cross-validation on NCANDA reveals that the imputed scores are more accurate than those generated by linear regressors and deep learning models. Adding them also to a classifier trained in identifying sex results in higher accuracy than only using those Freesurfer scores provided by ABCD.

Keywords: Brain measurements; Feature imputation; Graph representation learning.

Abstract

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