Are You Doing Better Than Random Guessing? A Call for Using Negative Controls When Evaluating Causal Discovery Algorithms

Anne Helby Petersen

Keywords: causal discovery, negative controls, evaluation study, benchmarking, structure learning

Abstract: New proposals for causal discovery algorithms are typically evaluated using simulations and a few selected real data examples with known data generating mechanisms. However, there does not exist a general guideline for how such evaluation studies should be designed, and therefore, comparing results across different studies can be difficult. In this article, we propose to use negative controls as a common evaluation baseline by posing the question: Are we doing better than random guessing? For the task of graph skeleton estimation, we derive exact distributional results under random guessing for the expected behavior of a range of typical causal discovery evaluation metrics, including precision and recall. We show that these metrics can achieve very favorable values under random guessing in certain scenarios, and hence warn against using them without also reporting negative control results, i.e., performance under random guessing. We also propose an exact test of overall skeleton fit, and showcase its use on a real data application. Finally, we propose a general pipeline for using negative controls beyond the skeleton estimation task, and apply it both in a simulated example and a real data application.

Code Link: https://github.com/annennenne/negcontrol-disco

Readers: auai.org/UAI/2025/Conference, auai.org/UAI/2025/Conference/Area_Chairs, auai.org/UAI/2025/Conference/Reviewers, auai.org/UAI/2025/Conference/Submission302/Authors, auai.org/UAI/2025/Conference/Submission302/Reproducibility_Reviewers

Submission Number: 302