In graphical causal model, causal discovery aims to construct a causal graph based on numerical data and domain knowledge in plain text. However, the evaluation of causal discovery methods remains a challenge in the area as the progress of domain researches often makes benchmark causal graphs contain mis-aligned knowledge. This problem especially affects the evaluation of large language model (LLM) based causal discovery methods as they are sensitive to the new discoveries in the literature. This work is the first to systematically study the quality of benchmark causal graphs. Specifically, we design a pipeline that automatically retrieves relevant research papers from scientific databases, and prompts LLMs to check the consistency between the benchmark causal graphs and domain research papers. We evaluate 11 popular real-world benchmarks, for which our pipeline in total proceeds 38,081 domain papers. Our results show that popular benchmarks vary significantly in their consistency with domain research, with clear implications for causal discovery research.
Causal discovery is a cornerstone of scientific reasoning, yet whether large language models can perform it reliably remains an open question. Recent benchmarks show that even fine-tuned models plateau on simple causal graphs and degrade as complexity grows, but why they fail has not been established. We prove the failure is fundamental: supervised fine-tuning, direct preference optimization, and in-context learning all produce predictors that cannot distinguish between causal graphs generating similar observational data, and any attempt to do so requires the model's internal representations to grow unboundedly, violating the very conditions under which these methods work. We formalize this as a kernel obstruction theorem, establishing that the limitation is intrinsic to the learning paradigm, \emph{not any particular model or dataset}. We propose Agentic Causal Bayesian Optimization (A-CBO), wherein a frozen language model serves as an interventional oracle answering targeted queries about intervention effects, while an external Bayesian loop concentrates beliefs over candidate graphs in logarithmically many rounds. Because the decision operates outside the space where the obstruction applies, A-CBO provably converges while the underlying model remains unchanged. On Corr2Cause, A-CBO matches fine-tuned baselines without any training. On Extended Corr2Cause, a new benchmark scaling to 24 variables with 18K test samples, A-CBO significantly outperforms both fine-tuning and preference optimization, with the advantage growing
Causal discovery from observational data remains challenging due to the fundamental limitations of purely statistical methods, such as statistical distinguishability within equivalence classes and sensitivity to finite sample sizes. While large language models (LLMs) offer a promising source of domain knowledge to complement statistical inference, existing LLM-augmented methods are vulnerable to LLM errors and incur high token costs. Moreover, reliance on a single data-centric algorithm can make results sensitive to algorithm-specific biases. To address these limitations, we propose CauTion, a framework that reliably integrates LLM domain knowledge into an ensemble of statistical causal discovery algorithms through consensus filtering and LLM reliability estimation. CauTion proceeds in three stages. First, an algorithm ensemble utilizes a consensus voting to resolve up to 96% of edges on which algorithms agree, achieving near-perfect accuracy on the filtered consensus edges. Second, a trust-calibrated arbitration mechanism estimates the relative reliability of the LLM and the algorithms via an annotation-free trust calibration procedure, which is then utilized to govern a trust-weighted voting process that restricts LLM arbitration exclusively to edges with unreliable algorithmic evidence. Third, a cycle repair step is applied to guarantee the final causal graph is validly acyclic. Experiments on six datasets demonstrate that CauTion consistently outperforms both data-centric and LLM-augmented baselines, with larger gains on larger graphs and strong robustness to LLM errors. Code is available at https://github.com/OpenCausaLab/CauTion.
Causal discovery aims to uncover causal structures from data and is fundamental to scientific reasoning and intervention-based decision making. Its evaluation relies heavily on structural causal models (SCMs), which specify a causal graph together with the mechanisms that generate data, yet existing studies differ substantially in graph families, mechanisms, and evaluation protocols. The emergence of causal discovery foundation models (CDFMs) further complicates evaluation: performance may reflect not only causal discovery ability, but also overlap between pretraining environments and test SCMs, making results on fixed synthetic benchmarks difficult to interpret. We introduce CausalArena, a unified and evolvable benchmark for causal discovery under a common protocol. Synthetic SCMs supply controlled breadth over structures and mechanisms; semantic operational SCMs provide human-auditable, semantically grounded environments beyond standard synthetic generators; and formula-grounded SCMs test discovery under explicit scientific mechanisms. Public real-world datasets provide an additional external-validity check. Experiments across classical, neural, and pretrained methods reveal substantial ranking shifts across SCM families and protocols, showing that strong performance in one benchmark regime does not reliably transfer to others. These results highlight benchmark diversity and pretraining--evaluation overlap as central challenges for evaluating causal discovery in the foundation model era.