Then, we study the performance of regression-based CI tests under misspecified inductive biases.

The inference of causal relationships is a problem of fundamental interest in science. In all fields ofresearch, experiments are systematically performed with the goal ofelucidating the underlying causal dynamics ofsystems.

Constraint-based causal discovery methods require a large number of conditional independence (CI) tests, which severely limits their practical applicability due to high computational complexity. Therefore, it is crucial to design an algorithm that accelerates each individual test. To this end, we propose the Flow Matching-based Conditional Independence Test (FMCIT). The proposed test leverages the high computational efficiency of flow matching and requires the model to be trained only once throughout the entire causal discovery procedure, substantially accelerating causal discovery. According to numerical experiments, FMCIT effectively controls type-I error and maintains high testing power under the alternative hypothesis, even in the presence of high-dimensional conditioning sets. In addition, we further integrate FMCIT into a two-stage guided PC skeleton learning framework, termed GPC-FMCIT, which combines fast screening with guided, budgeted refinement using FMCIT. This design yields explicit bounds on the number of CI queries while maintaining high statistical power. Experiments on synthetic and real-world causal discovery tasks demonstrate favorable accuracy-efficiency trade-offs over existing CI testing methods and PC variants.

Forpredictivemodels toprovidereliable guidance indecision making processes, they are often required to be accurate and robust to distribution shifts. Shortcut learning-where a model relies on spurious correlations or shortcuts to predict thetargetlabel-undermines therobustnessproperty,leadingtomodelswithpoor out-of-distribution accuracy despite good in-distribution performance.

Just as the majority of machine learning methods, existing work focuses on studying $\textit{independent and identically distributed}$ data. However, it is known that even with infinite $i.i.d.\$ data, constraint-based methods can only identify causal structures up to broad Markov equivalence classes, posing a fundamental limitation for causal discovery. In this work, we observe that exchangeable data contains richer conditional independence structure than $i.i.d.\$ data, and show how the richer structure can be leveraged for causal discovery. We first present causal de Finetti theorems, which state that exchangeable distributions with certain non-trivial conditional independences can always be represented as $\textit{independent causal mechanism (ICM)}$ generative processes. We then present our main identifiability theorem, which shows that given data from an ICM generative process, its unique causal structure can be identified through performing conditional independence tests. We finally develop a causal discovery algorithm and demonstrate its applicability to inferring causal relationships from multi-environment data.

Neural Information Processing Systems http://nips.cc/

Causal discovery algorithms often perform poorly with limited samples. While integrating expert knowledge (including from LLMs) as constraints promises to improve performance, guarantees for existing methods require perfect predictions or uncertainty estimates, making them unreliable for practical use. We propose the Guess2Graph (G2G) framework, which uses expert guesses to guide the sequence of statistical tests rather than replacing them. This maintains statistical consistency while enabling performance improvements. We develop two instantiations of G2G: PC-Guess, which augments the PC algorithm, and gPC-Guess, a learning-augmented variant designed to better leverage high-quality expert input. Theoretically, both preserve correctness regardless of expert error, with gPC-Guess provably outperforming its non-augmented counterpart in finite samples when experts are "better than random."

Causal discovery from observational data is fundamental to scientific fields like biology, where controlled experiments are often impractical. However, existing methods, including constraint-based (e.g., PC, causalMGM) and score-based approaches (e.g., NOTEARS), face significant limitations. These include an inability to resolve causal direction, restrictions to linear associations, sensitivity to violations of the faithfulness assumption, and inefficiency in searching vast hypothesis spaces. While large language models (LLMs) offer powerful reasoning capabilities, their application is hindered by a fundamental discrepancy: they are designed for text, while most causal data is tabular. To address these challenges, we introduce CALM, a novel causal analysis language model specifically designed for tabular data in complex systems. CALM leverages a Mamba-based architecture to classify causal patterns from pairwise variable relationships. It integrates a comprehensive suite of evidence, including local causal scores, conditional independence tests, and relational attributes, to capture a wide spectrum of linear, nonlinear, and conditional causal mechanisms. Trained on a diverse corpus of synthetic data (from linear, mixed, and nonlinear models) and 10 real-world biological datasets with rigorously validated causal relationships, our model ensures robustness and generalizability. Empirical evaluation demonstrates that CALM significantly outperforms existing methods in both simulation studies, achieving over 91% accuracy, and in a real-world application identifying causal factors in Hepatitis C virus progression. This work represents a significant step towards accurate and generalizable causal discovery by successfully adapting the pattern recognition capabilities of language models to the intricacies of tabular data.

Then, we study the performance of regression-based CI tests under misspecified inductive biases.