We consider the problem of non-parametric Conditional Independence testing (CI testing) for continuous random variables. Given i.i.d samples from the joint distribution $f(x,y,z)$ of continuous random vectors $X,Y$ and $Z,$ we determine whether $X \independent Y \vert Z$. We approach this by converting the conditional independence test into a classification problem. This allows us to harness very powerful classifiers like gradient-boosted trees and deep neural networks. These models can handle complex probability distributions and allow us to perform significantly better compared to the prior state of the art, for high-dimensional CI testing. The main technical challenge in the classification problem is the need for samples from the conditional product distribution $f^{CI}(x,y,z) = f(x|z)f(y|z)f(z)$ -- the joint distribution if and only if $X \independent Y \vert Z.$ -- when given access only to i.i.d.

Conditional independence (CI) is central to causal inference, feature selection, and graphical modeling, yet it is untestable in many settings without additional assumptions. Existing CI tests often rely on restrictive structural conditions, limiting their validity on real-world data. Kernel methods using the partial covariance operator offer a more principled approach but suffer from limited adaptivity, slow convergence, and poor scalability. In this work, we explore whether representation learning can help address these limitations. Specifically, we focus on representations derived from the singular value decomposition of the partial covariance operator and use them to construct a simple test statistic, reminiscent of the Hilbert-Schmidt Independence Criterion (HSIC). We also introduce a practical bi-level contrastive algorithm to learn these representations. Our theory links representation learning error to test performance and establishes asymptotic validity and power guarantees. Preliminary experiments suggest that this approach offers a practical and statistically grounded path toward scalable CI testing, bridging kernel-based theory with modern representation learning.

We consider the problem of non-parametric Conditional Independence testing (CI testing) for continuous random variables. Given i.i.d samples from the joint distribution $f(x,y,z)$ of continuous random vectors $X,Y$ and $Z,$ we determine whether $X \independent Y \vert Z$. We approach this by converting the conditional independence test into a classification problem. This allows us to harness very powerful classifiers like gradient-boosted trees and deep neural networks. These models can handle complex probability distributions and allow us to perform significantly better compared to the prior state of the art, for high-dimensional CI testing. The main technical challenge in the classification problem is the need for samples from the conditional product distribution $f^{CI}(x,y,z) = f(x|z)f(y|z)f(z)$ -- the joint distribution if and only if $X \independent Y \vert Z.$ -- when given access only to i.i.d.

We consider the problem of non-parametric Conditional Independence testing (CI testing) for continuous random variables. Given i.i.d samples from the joint distribution

We establish a fundamental connection between optimal structure learning and optimal conditional independence testing by showing that the minimax optimal rate for structure learning problems is determined by the minimax rate for conditional independence testing in these problems. This is accomplished by establishing a general reduction between these two problems in the case of poly-forests, and demonstrated by deriving optimal rates for several examples, including Bernoulli, Gaussian and nonparametric models. Furthermore, we show that the optimal algorithm in these settings is a suitable modification of the PC algorithm. This theoretical finding provides a unified framework for analyzing the statistical complexity of structure learning through the lens of minimax testing.

Determining conditional independence (CI) relationships between random variables is a fundamental yet challenging task in machine learning and statistics, especially in high-dimensional settings. Existing generative model-based CI testing methods, such as those utilizing generative adversarial networks (GANs), often struggle with undesirable modeling of conditional distributions and training instability, resulting in subpar performance. To address these issues, we propose a novel CI testing method via score-based generative modeling, which achieves precise Type I error control and strong testing power. Concretely, we first employ a sliced conditional score matching scheme to accurately estimate conditional score and use Langevin dynamics conditional sampling to generate null hypothesis samples, ensuring precise Type I error control. Then, we incorporate a goodness-of-fit stage into the method to verify generated samples and enhance interpretability in practice. We theoretically establish the error bound of conditional distributions modeled by score-based generative models and prove the validity of our CI tests. Extensive experiments on both synthetic and real-world datasets show that our method significantly outperforms existing state-of-the-art methods, providing a promising way to revitalize generative model-based CI testing.

Testing for the conditional independence structure in data is a fundamental and critical task in statistics and machine learning, which finds natural applications in causal discovery-a highly relevant problem to many scientific disciplines. Existing methods seek to design explicit test statistics that quantify the degree of conditional dependence, which is highly challenging yet cannot capture nor utilize prior knowledge in a data-driven manner. In this study, an entirely new approach is introduced, where we instead propose to amortize conditional independence testing and devise ACID ( Amortized C onditional In D ependence test)- a novel transformer-based neural network architecture that learns to test for conditional independence . ACID can be trained on synthetic data in a supervised learning fashion, and the learned model can then be applied to any dataset of similar natures or adapted to new domains by fine-tuning with a negligible computational cost. Our extensive empirical evaluations on both synthetic and real data reveal that ACID consistently achieves state-of-the-art performance against existing baselines under multiple metrics, and is able to generalize robustly to unseen sample sizes, dimensionalities, as well as non-linearities with a remarkably low inference time.

We consider the problem of non-parametric Conditional Independence testing (CI testing) for continuous random variables. Given i.i.d samples from the joint distribution f(x, y, z) of continuous random vectors X, Y and Z, we determine whether X? Y |Z. We approach this by converting the conditional independence test into a classification problem. This allows us to harness very powerful classifiers like gradient-boosted trees and deep neural networks. These models can handle complex probability distributions and allow us to perform significantly better compared to the prior state of the art, for high-dimensional CI testing.

We consider the problem of non-parametric Conditional Independence testing (CI testing) for continuous random variables. Given i.i.d samples from the joint distribution $f(x,y,z)$ of continuous random vectors $X,Y$ and $Z,$ we determine whether $X \independent Y \vert Z$. We approach this by converting the conditional independence test into a classification problem. This allows us to harness very powerful classifiers like gradient-boosted trees and deep neural networks. These models can handle complex probability distributions and allow us to perform significantly better compared to the prior state of the art, for high-dimensional CI testing.

Markov blanket feature selection, while theoretically optimal, generally is challenging to implement. This is due to the shortcomings of existing approaches to conditional independence (CI) testing, which tend to struggle either with the curse of dimensionality or computational complexity. We propose a novel two-step approach which facilitates Markov blanket feature selection in high dimensions. First, neural networks are used to map features to low-dimensional representations. In the second step, CI testing is performed by applying the k-NN conditional mutual information estimator to the learned feature maps. The mappings are designed to ensure that mapped samples both preserve information and share similar information about the target variable if and only if they are close in Euclidean distance. We show that these properties boost the performance of the k-NN estimator in the second step. The performance of the proposed method is evaluated on synthetic, as well as real data pertaining to datacenter hard disk drive failures.