GEASS: Neural causal feature selection for high-dimensional biological data

Mingze Dong, Yuval Kluger

Keywords: Granger causality, feature selection, neural networks, single-cell genomics, spatial transcriptomics

TL;DR: We propose a new method (GEASS) to identify causally interacting features for high-dimensional spatial/temporal structured data, and apply it to several biological data to infer causal regulatory patterns.

Abstract: Identifying nonlinear causal relationships in high-dimensional biological data is an important task. However, current neural network based causality detection approaches for such data suffer from poor interpretability and cannot scale well to the high dimensional regime. Here we present GEASS (Granger fEAture Selection of Spatiotemporal data), which identifies sparse Granger causality mechanisms of high dimensional spatiotemporal data by a single neural network. GEASS maximizes sparsity-regularized modified transfer entropy with a theoretical guarantee of recovering features with spatial/temporal Granger causal relationships. The sparsity regularization is achieved by a novel combinatorial stochastic gate layer to select sparse non-overlapping feature subsets. We demonstrate the efficacy of GEASS in several synthetic datasets and real biological data from single-cell RNA sequencing and spatial transcriptomics.

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