Learning Gaussian Graphical Models under Total Positivity via Spectral Graph Sparsification

TL;DR

This paper introduces Spectral-MTP2, a scalable spectral graph sparsification method for learning Gaussian graphical models under total positivity, which produces sparser, more interpretable graphs while maintaining fit quality.

Contribution

The authors propose a novel spectral sparsification approach for Gaussian graphical models under MTP2, preserving positivity and model accuracy with significantly sparser graphs.

Findings

Spectral-MTP2 retains most fit quality of dense models.

It produces substantially sparser and more interpretable graphs.

The method is validated on simulations, equity returns, and gene expression data.

Abstract

Many practical data analysis tasks reduce to learning, from observed samples, how a collection of variables depend on each other. A widely used approach is to fit a Gaussian graphical model, which represents the dependence structure as a graph connecting the variables. In a number of important applications, such as financial returns, gene co-expression, and climate or network analysis, the dependencies tend to be positive: variables move together rather than offset each other. Encoding this positivity through the constraint of multivariate total positivity of order two (MTP2) yields an attractive estimator that produces accurate fits with no tuning required. The resulting graphs are, however, typically much denser than the underlying ground-truth model, which makes them hard to interpret and slow to use in any downstream task that operates on the graph. In this work, we propose a novel highly-scalable approach for learning Gaussian graphical models from data using spectral sparsification; we call it Spectral-MTP2. Spectral graph sparsification is a fundamental method which aims to preserve meaningful properties of a dense graph with a sparser subgraph. We theoretically and empirically investigate and validate our method, and show that learning Gaussian Graphical Models under MTP2 using spectral sparsification preserves MTP2 and approximates well the original model in terms of Kullback-Leibler divergence and Gaussian log-likelihood. In simulations and applications to equity returns and gene expression, we observe that Spectral-MTP2 retains most of the fit quality of the denser MTP2 baseline, while producing substantially sparser and more interpretable graphs.