This paper concerns, more specifically, the inconsistency of separating sets used to remove dispensable edges, iteratively, based on conditional independence tests.

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.

The design of Priv-PC follows a novel paradigm called sieve-and-examine which uses a small amount of privacy budget to filter out "insignificant" queries, and leverages the remaining budget to obtain highly accurate answers for the "significant" queries.

We propose GaussDetect-LiNGAM, a novel approach for bivariate causal discovery that eliminates the need for explicit Gaussianity tests by leveraging a fundamental equivalence between noise Gaussianity and residual independence in the reverse regression. Under the standard LiNGAM assumptions of linearity, acyclicity, and exogeneity, we prove that the Gaussianity of the forward-model noise is equivalent to the independence between the regressor and residual in the reverse model. This theoretical insight allows us to replace fragile and sample-sensitive Gaussianity tests with robust kernel-based independence tests. Experimental results validate the equivalence and demonstrate that GaussDetect-LiNGAM maintains high consistency across diverse noise types and sample sizes, while reducing the number of tests per decision (TPD). Our method enhances both the efficiency and practical applicability of causal inference, making LiNGAM more accessible and reliable in real-world scenarios.

For testing two vector random variables for independence, we propose testing whether the distance of one vector from an arbitrary center point is independent from the distance of the other vector from another arbitrary center point by a univariate test. We prove that under minimal assumptions, it is enough to have a consistent univariate independence test on the distances, to guarantee that the power to detect dependence between the random vectors increases to one with sample size. If the univariate test is distribution-free, the multivariate test will also be distribution-free.

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.

We first present a topological sorting algorithm that leverages ancestral relationships in linear structural causal models to establish a compact top-down hierarchical ordering, encoding more causal information than linear orderings produced by existing methods.