Graph Neural Network for Interpreting Task-fMRI Biomarkers

Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11768)


Finding the biomarkers associated with ASD is helpful for understanding the underlying roots of the disorder and can lead to earlier diagnosis and more targeted treatment. A promising approach to identify biomarkers is using Graph Neural Networks (GNNs), which can be used to analyze graph structured data, i.e. brain networks constructed by fMRI. One way to interpret important features is through looking at how the classification probability changes if the features are occluded or replaced. The major limitation of this approach is that replacing values may change the distribution of the data and lead to serious errors. Therefore, we develop a 2-stage pipeline to eliminate the need to replace features for reliable biomarker interpretation. Specifically, we propose an inductive GNN to embed the graphs containing different properties of task-fMRI for identifying ASD and then discover the brain regions/sub-graphs used as evidence for the GNN classifier. We first show GNN can achieve high accuracy in identifying ASD. Next, we calculate the feature importance scores using GNN and compare the interpretation ability with Random Forest. Finally, we run with different atlases and parameters, proving the robustness of the proposed method. The detected biomarkers reveal their association with social behaviors and are consistent with those reported in the literature. We also show the potential of discovering new informative biomarkers. Our pipeline can be generalized to other graph feature importance interpretation problems.


Graph Neural Network Task-fMRI ASD biomarker 



This work was supported by NIH Grant R01 NS035193.


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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Biomedical EngineeringYale UniversityNew HavenUSA
  2. 2.Electrical EngineeringYale UniversityNew HavenUSA
  3. 3.Statistics and Data ScienceYale UniversityNew HavenUSA
  4. 4.Child Study CenterYale School of MedicineNew HavenUSA
  5. 5.Radiology and Biomedical ImagingYale School of MedicineNew HavenUSA

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