Making Multi-Axis Models Robust to Multiplicative Noise: How, and Why?

In this paper we develop a graph-learning algorithm, MED-MAGMA, to fit multi-axis (Kronecker-sum-structured) models corrupted by multiplicative noise. This type of noise is natural in many application domains, such as that of single-cell RNA sequencing, in which it naturally captures technical biases of RNA sequencing platforms. Our work is evaluated against prior work on each and every public dataset in the Single Cell Expression Atlas under a certain size, demonstrating that our methodology learns networks with better local and global structure. MED-MAGMA is made available as a Python package (MED-MAGMA).

Graphical Modelling without Independence Assumptions for Uncentered Data

The independence assumption is a useful tool to increase the tractability of one's modelling framework. However, this assumption does not match reality; failing to take dependencies into account can cause models to fail dramatically. The field of multi-axis graphical modelling (also called multi-way modelling, Kronecker-separable modelling) has seen growth over the past decade, but these models require that the data have zero mean. In the multi-axis case, inference is typically done in the single sample scenario, making mean inference impossible. In this paper, we demonstrate how the zero-mean assumption can cause egregious modelling errors, as well as propose a relaxation to the zero-mean assumption that allows the avoidance of such errors. Specifically, we propose the "Kronecker-sum-structured mean" assumption, which leads to models with nonconvex-but-unimodal log-likelihoods that can be solved efficiently with coordinate descent.

Making Multi-Axis Gaussian Graphical Models Scalable to Millions of Samples and Features

Gaussian graphical models can be used to extract conditional dependencies between the features of the dataset. This is often done by making an independence assumption about the samples, but this assumption is rarely satisfied in reality. However, state-of-the-art approaches that avoid this assumption are not scalable, with $O(n^3)$ runtime and $O(n^2)$ space complexity. In this paper, we introduce a method that has $O(n^2)$ runtime and $O(n)$ space complexity, without assuming independence. We validate our model on both synthetic and real-world datasets, showing that our method's accuracy is comparable to that of prior work We demonstrate that our approach can be used on unprecedentedly large datasets, such as a real-world 1,000,000-cell scRNA-seq dataset; this was impossible with previous approaches. Our method maintains the flexibility of prior work, such as the ability to handle multi-modal tensor-variate datasets and the ability to work with data of arbitrary marginal distributions. An additional advantage of our method is that, unlike prior work, our hyperparameters are easily interpretable.

antGLasso: An Efficient Tensor Graphical Lasso Algorithm

The class of bigraphical lasso algorithms (and, more broadly, 'tensor'-graphical lasso algorithms) has been used to estimate dependency structures within matrix and tensor data. However, all current methods to do so take prohibitively long on modestly sized datasets. We present a novel tensor-graphical lasso algorithm that analytically estimates the dependency structure, unlike its iterative predecessors. This provides a speedup of multiple orders of magnitude, allowing this class of algorithms to be used on large, real-world datasets.