Making multi-axis Gaussian graphical models scalable to millions of cells

Networks underlie the generation and interpretation of many biological datasets: gene networks shed light on the regulatory structure of the genome, and cell networks can capture structure of the tumor micro-environment. However, most methods that learn such networks make the faulty "independence assumption"; to learn the gene network, they assume that no cell network exists. "Multi-axis" methods, which do not make this assumption, fail to scale beyond a few thousand cells or genes. This limits their applicability to only the smallest datasets.

We develop a multi-axis method, which learns conditional dependency networks, capable of processing million-cell datasets within minutes. This was previously impossible, and unlocks the use of such methods on modern scRNA-seq datasets, as well as more complex datasets. We apply the method to a new scRNA-seq dataset for neuronal cell development, and compare the result to an existing state of the art method, hdWGCNA. We demonstrate that the new method yields gene networks that have a more focused biological interpretation and that the simultaneously learned cell network has advantages over a conventional kNN-based clustering. Further, our method yields novel biological insights by identifying long non-coding RNAs that potentially have a role in neuronal development.

Our methodology is available as a Python package GmGM on PyPI (https://pypi.org/project/GmGM/0.5.3/). The code for all experiments performed in this article is available on GitHub (https://github.com/BaileyAndrew/GmGM-Bioinformatics) and Zenodo (10.5281/zenodo.20384566).