Convergent Cross Mapping (CCM) is a powerful method for detecting causality in coupled nonlinear dynamical systems, providing a model-free approach to capture dynamic causal interactions. Partial Cross Mapping (PCM) was introduced as an extension of CCM to address indirect causality in three-variable systems by comparing cross-mapping quality between direct cause-effect mapping and indirect mapping through an intermediate conditioning variable. However, PCM remains limited to univariate delay embeddings in its cross-mapping processes. In this work, we extend PCM to the multivariate setting, introducing multiPCM, which leverages multivariate embeddings to more effectively distinguish indirect causal relationships. We further propose a multivariate cross-mapping framework (MXMap) for causal discovery in dynamical systems. This two-phase framework combines (1) pairwise CCM tests to establish an initial causal graph and (2) multiPCM to refine the graph by pruning indirect causal connections. Through experiments on simulated data and the ERA5 Reanalysis weather dataset, we demonstrate the effectiveness of MXMap. Additionally, MXMap is compared against several baseline methods, showing advantages in accuracy and causal graph refinement.

We consider causal discovery from time series using conditional independence (CI) based network learning algorithms such as the PC algorithm. The PC algorithm is divided into a skeleton phase where adjacencies are determined based on efficiently selected CI tests and subsequent phases where links are oriented utilizing the Markov and Faithfulness assumptions. Here we show that autocorrelation makes the PC algorithm much less reliable with very low adjacency and orientation detection rates and inflated false positives. We propose a new algorithm, called PCMCI$^+$ that extends the PCMCI method from [Runge et al., 2019b] to also include discovery of contemporaneous links. It separates the skeleton phase for lagged and contemporaneous conditioning sets and modifies the conditioning sets for the individual CI tests. We show that this algorithm now benefits from increasing autocorrelation and yields much more adjacency detection power and especially more orientation recall for contemporaneous links while controlling false positives and having much shorter runtimes. Numerical experiments indicate that the algorithm can be of considerable use in many application scenarios for dozens of variables and large time delays.