A fundamental step in the PC causal discovery algorithm consists of testing for (conditional) independence. When the number of data records is very small, a classical statistical independence test is typically unable to reject the (null) independence hypothesis. In this paper, we are comparing two conflicting pieces of advice in the literature that in case of too few data records recommend (1) assuming dependence and (2) assuming independence. Our results show that assuming independence is a safer strategy in minimizing the structural distance between the causal structure that has generated the data and the discovered structure. We also propose a simple improvement on the PC algorithm that we call blacklisting. We demonstrate that blacklisting can lead to orders of magnitude savings in computation by avoiding unnecessary independence tests
