Granger causality (GC) [15] is a time series causal discovery framework that uses predictive modeling to identify the underlying causal structure of a time series system. Relying on the assumption that cause precedes effect, GC assesses whether including the lagged information from one time series in the autoregressive model of a second time series enhances its predictions. This improvement indicates a predictive relationship between the time series variables, where one time series provides supplemental information about the future of another time series, thereby signifying the presence of a (Granger) causal relationship. GC requires only observational data, and has been used for time series causal discovery across diverse domains, including climate science [33], political and social sciences [17], econometrics [4], and biological systems studies [13]. The original formulation of GC requires several assumptions to be satisfied for causal identifiability. In regards to the candidate time series system, it is assumed that the time series variables are stationary, and that all variables are observed (absence of latent confounders). GC was initially proposed for bivariate time series systems, but was generalised for the multivariate setting to accommodate the assumption that all relevant variables are included in the analysis [15]. Additional assumptions are made with regard to the types of causal relationships that can be identified within the time series system. GC cannot estimate a causal relationship between time series at an instantaneous time point, relying on the relationship between the lags and predicted values to determine a GC relationship.

To gain insight into complex systems it is a key challenge to infer nonlinear causal directional relations from observational time-series data. Specifically, estimating causal relationships between interacting components in large systems with only short recordings over few temporal observations remains an important, yet unresolved problem. Here, we introduce a large-scale Nonlinear Granger Causality (lsNGC) approach for inferring directional, nonlinear, multivariate causal interactions between system components from short high-dimensional time-series recordings. By modeling interactions with nonlinear state-space transformations from limited observational data, lsNGC identifies casual relations with no explicit a priori assumptions on functional interdependence between component time-series in a computationally efficient manner. Additionally, our method provides a mathematical formulation revealing statistical significance of inferred causal relations. We extensively study the ability of lsNGC to recovering network structure from two-node to thirty-four node chaotic time-series systems. Our results suggest that lsNGC captures meaningful interactions from limited observational data, where it performs favorably when compared to traditionally used methods. Finally, we demonstrate the applicability of lsNGC to estimating causality in large, real-world systems by inferring directional nonlinear, multivariate causal relationships among a large number of relatively short time-series acquired from functional Magnetic Resonance Imaging (fMRI) data of the human brain.