Markovianity-Based Conditioning Depth Diagnostics for Hidden Confounding in Observational Datasets

Abstract

Reliable causal discovery in time series depends on whether the conditioning set adequately represents the system state. If relevant history or unobserved processes are omitted, residual dependence can appear as direct causal links. We study this failure mode on promnient constraint-based causal discovery methods through a simple premise: how much does the inferred graph change as conditioning depth increases? When the observed process is described approximately by a finite-order Markovian representation, inferred graphs should stabilize once sufficient past observations are observed. Hidden confounding and other hidden-memory mechanisms should remain sensitive to depth when the observed state is incomplete. We formalise this behavior with graph instability statistics computed over the conditioning-depth grid. The empirical study covers synthetic systems with known ground truth and calcium imaging recordings with unknown causal structure. In simulations, both Markovian and non-Markovian systems relatively upheld our premise. With known ground truth, we evaluate recovery using confusion matrix metrics; while in real data without ground truth, we use descriptive graph instability summaries. Across synthetic Markovian and hidden memory systems, c-GC variants give the clearest separation, while PCMCI variants show weaker compatible trends. In real data, inferred connectivity drops sharply with conditioning depths and then levels off. This method, however, does not recover latent graphs, nor does it clearly separate latent confounding from lag-order misspecification, non-stationarity, measurement error. Its contribution is more modest and practical: and explicit model-checking tool for deciding when causal claims are stable and when they should be treated caustiosly.