Efficient Latent Variable Causal Discovery: Combining Score Search and Targeted Testing

Abstract

Learning causal structure from observational data is especially challenging when latent variables or selection bias are present. The Fast Causal Inference (FCI) algorithm addresses this setting but performs exhaustive conditional independence tests across many subsets, often leading to spurious independences, missing or extra edges, and unreliable orientations. We present a family of score-guided mixed-strategy causal search algorithms that extend this framework. First, we introduce BOSS-FCI and GRaSP-FCI, variants of GFCI (Greedy Fast Causal Inference) that substitute BOSS (Best Order Score Search) or GRaSP (Greedy Relaxations of Sparsest Permutation) for FGES (Fast Greedy Equivalence Search), preserving correctness while trading off scalability and conservativeness. Second, we develop FCI Targeted-Testing (FCIT), a novel hybrid method that replaces exhaustive testing with targeted, score-informed tests guided by BOSS. FCIT guarantees well-formed PAGs and achieves higher precision and efficiency across sample sizes. Finally, we propose a lightweight heuristic, LV-Dumb (Latent Variable "Dumb"), which returns the PAG of the BOSS DAG (Directed Acyclic Graph). Though not strictly sound for latent confounding, LV-Dumb often matches FCIT's accuracy while running substantially faster. Simulations and real-data analyses show that BOSS-FCI and GRaSP-FCI provide robust baselines, FCIT yields the best balance of precision and reliability, and LV-Dumb offers a fast, near-equivalent alternative. Together, these methods demonstrate that targeted and score-guided strategies can dramatically improve the efficiency and correctness of latent-variable causal discovery.