A Biologically Interpretable Graph Convolutional Network to Link Genetic Risk Pathways and Imaging Phenotypes of Disease

Sayan Ghosal, Qiang Chen, Giulio Pergola, Aaron L Goldman, William Ulrich, Daniel R Weinberger, Archana Venkataraman

Keywords: Imaging-genetics, Hierarchical Graph Convolution, Gene Ontology, Bayesian Feature Selection, Schizophrenia

Abstract: We propose a novel end-to-end framework for whole-brain and whole-genome imaging-genetics. Our genetics network uses hierarchical graph convolution and pooling operations to embed subject-level data onto a low-dimensional latent space. The hierarchical network implicitly tracks the convergence of genetic risk across well-established biological pathways, while an attention mechanism automatically identifies the salient edges of this network at the subject level. In parallel, our imaging network projects multimodal data onto a set of latent embeddings. For interpretability, we implement a Bayesian feature selection strategy to extract the discriminative imaging biomarkers; these feature weights are optimized alongside the other model parameters. We couple the imaging and genetic embeddings with a predictor network, to ensure that the learned representations are linked to phenotype. We evaluate our framework on a schizophrenia dataset that includes two functional MRI paradigms and gene scores derived from Single Nucleotide Polymorphism data. Using repeated 10-fold cross-validation, we show that our imaging-genetics fusion achieves the better classification performance than state-of-the-art baselines. In an exploratory analysis, we further show that the biomarkers identified by our model are reproducible and closely associated with deficits in schizophrenia.

One-sentence Summary: Biologically Informed Imaging-Genetics