Geometric Causal Models

arXiv:2607.05153 · stat.ML, cs.LG, q-bio.BM · Submitted 2026-07-06 · Read on arXiv

Eli N. Weinstein, David M. Blei

stat.ML, cs.LG, q-bio.BM

Submitted: 2026-07-06

Code: https://github.com/EWeinstein/GCM

License: http://creativecommons.org/licenses/by-nc-nd/4.0/

The gist: Scientists often seek to draw causal inferences from structured data that is not independently and identically distributed, such as spatial data, network data, or molecular data.

Terminology

Abstract

Scientists often seek to draw causal inferences from structured data that is not independently and identically distributed, such as spatial data, network data, or molecular data. We develop geometric causal models (GCMs), a framework for causal inference from dependent data that exploits underlying symmetries of the data generating process. For example, in spatial data, we consider processes that are symmetric under translations, or in graph data, symmetric under permutations of the nodes. We show how symmetries, formalized with group theory, can enable causal identification and estimation. We deploy ergodic theory for amenable groups to establish identification, and combine geometric deep learning with scalable Bayesian inference for estimation. We recover i.i.d. causal models and do-calculus when the data is a sequence and the symmetry is permutation equivariance, and find novel types of causal models when we use alternate structures and symmetries. As an example, we construct a causal model that satisfies the symmetries of DNA. This GCM enables new estimators for the effects of genetic variation, combining deep functional genomics models to describe outcomes and DNA language models to describe propensities. We illustrate on semisynthetic data.

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