Bootstrap aggregation and confidence measures to improve time series causal discovery

Causal discovery methods have demonstrated the ability to identify the time series graphs representing the causal temporal dependency structure of dynamical systems. However, they do not include a measure of the confidence of the estimated links. Here, we introduce a novel bootstrap aggregation (bagging) and confidence measure method that is combined with time series causal discovery. This new method allows measuring confidence for the links of the time series graphs calculated by causal discovery methods. This is done by bootstrapping the original times series data set while preserving temporal dependencies. Next to confidence measures, aggregating the bootstrapped graphs by majority voting yields a final aggregated output graph. In this work, we combine our approach with the state-of-the-art conditional-independence-based algorithm PCMCI+. With extensive numerical experiments we empirically demonstrate that, in addition to providing confidence measures for links, Bagged-PCMCI+ improves the precision and recall of its base algorithm PCMCI+. Specifically, Bagged-PCMCI+ has a higher detection power regarding adjacencies and a higher precision in orienting contemporaneous edges while at the same time showing a lower rate of false positives. These performance improvements are especially pronounced in the more challenging settings (short time sample size, large number of variables, high autocorrelation). Our bootstrap approach can also be combined with other time series causal discovery algorithms and can be of considerable use in many real-world applications, especially when confidence measures for the links are desired.