We study the problem of automatically discovering Granger causal relations from observational multivariate time-series data. Vector autoregressive (VAR) models have been time-tested for this problem, including Bayesian variants and more recent developments using deep neural networks. Most existing VAR methods for Granger causality use sparsity-inducing penalties/priors or post-hoc thresholds to interpret their coefficients as Granger causal graphs. Instead, we propose a new Bayesian VAR model with a hierarchical graph prior over binary Granger causal graphs, separately from the VAR coefficients. We develop an efficient algorithm to infer the posterior over binary Granger causal graphs. Our method provides better uncertainty quantification, has less hyperparameters, and achieves better performance than competing approaches, especially on sparse multivariate time-series data.

Modern health care systems are conducting continuous, automated surveillance of the electronic medical record (EMR) to identify adverse events with increasing frequency; however, many events such as sepsis do not have elucidated prodromes (i.e., event chains) that can be used to identify and intercept the adverse event early in its course. Clinically relevant and interpretable results require a framework that can (i) infer temporal interactions across multiple patient features found in EMR data (e.g., Labs, vital signs, etc.) and (ii) identify patterns that precede and are specific to an impending adverse event (e.g., sepsis). In this work, we propose a linear multivariate Hawkes process model, coupled with ReLU link function, to recover a Granger Causal (GC) graph with both exciting and inhibiting effects. We develop a scalable two-phase gradient-based method to obtain a maximum surrogate-likelihood estimator, which is shown to be effective via extensive numerical simulation. Our method is subsequently extended to a data set of patients admitted to Grady hospital system in Atlanta, GA, USA, where the estimated GC graph identifies several highly interpretable GC chains that precede sepsis. The code is available at \url{https://github.com/SongWei-GT/two-phase-MHP}.