Non-Gaussian methods and high-pass filters in the estimation of effective connections

We consider several alternative ways of exploiting non-Gaussian distributional features, including some that can in principle identify direct, positive feedback relations (graphically, 2-cycles) and combinations of methods that can identify high dimensional graphs. All of the procedures are implemented in the TETRAD freeware (Ramsey et al., 2013). We show that in most cases the limited accuracy of the several non-Gaussian methods in the Smith et al. (2011) simulations can be attributed to the high-pass Butterworth filter used in that study. Without that filter, or with the filter in the widely used FSL program (Jenkinson et al., 2012), the directional accuracies of several of the non-Gaussian methods are at or near ceiling in many conditions of the Smith et al. simulation. We show that the improvement of an apparently Gaussian method (Patel et al., 2006) when filtering is removed is due to non-Gaussian features of that method introduced by the Smith et al. implementation. We also investigate some conditions in which multi-subject data help with causal structure identification using higher moments, notably with non-stationary time series or with 2-cycles. We illustrate the accuracy of the methods with more complex graphs with and without 2-cycles, and with a 500 node graph; to illustrate applicability and provide a further test we apply the methods to an empirical case for which aspects of the causal structure are known. Finally, we note a number of cautions and issues that remain to be investigated, and some outstanding problems for determining the structure of effective connections from fMRI data.