Choosing DAG Models Using Markov and Minimal Edge Count in the Absence of Ground Truth

We give a novel nonparametric pointwise consistent statistical test (the Markov Checker) of the Markov condition for directed acyclic graph (DAG) or completed partially directed acyclic graph (CPDAG) models given a dataset. We also introduce the Cross-Algorithm Frugality Search (CAFS) for rejecting DAG models that either do not pass the Markov Checker test or that are not edge minimal. Edge minimality has been used previously by Raskutti and Uhler as a nonparametric simplicity criterion, though CAFS readily generalizes to other simplicity conditions. Reference to the ground truth is not necessary for CAFS, so it is useful for finding causal structure learning algorithms and tuning parameter settings that output causal models that are approximately true from a given data set. We provide a software tool for this analysis that is suitable for even quite large or dense models, provided a suitably fast pointwise consistent test of conditional independence is available. In addition, we show in simulation that the CAFS procedure can pick approximately correct models without knowing the ground truth.

On the Parameter Identifiability of Partially Observed Linear Causal Models

Linear causal models are important tools for modeling causal dependencies and yet in practice, only a subset of the variables can be observed. In this paper, we examine the parameter identifiability of these models by investigating whether the edge coefficients can be recovered given the causal structure and partially observed data. Our setting is more general than that of prior research - we allow all variables, including both observed and latent ones, to be flexibly related, and we consider the coefficients of all edges, whereas most existing works focus only on the edges between observed variables. Theoretically, we identify three types of indeterminacy for the parameters in partially observed linear causal models. We then provide graphical conditions that are sufficient for all parameters to be identifiable and show that some of them are provably necessary. Methodologically, we propose a novel likelihood-based parameter estimation method that addresses the variance indeterminacy of latent variables in a specific way and can asymptotically recover the underlying parameters up to trivial indeterminacy. Empirical studies on both synthetic and real-world datasets validate our identifiability theory and the effectiveness of the proposed method in the finite-sample regime.

Counterfactual Reasoning Using Predicted Latent Personality Dimensions for Optimizing Persuasion Outcome

Customizing persuasive conversations related to the outcome of interest for specific users achieves better persuasion results. However, existing persuasive conversation systems rely on persuasive strategies and encounter challenges in dynamically adjusting dialogues to suit the evolving states of individual users during interactions. This limitation restricts the system's ability to deliver flexible or dynamic conversations and achieve suboptimal persuasion outcomes. In this paper, we present a novel approach that tracks a user's latent personality dimensions (LPDs) during ongoing persuasion conversation and generates tailored counterfactual utterances based on these LPDs to optimize the overall persuasion outcome. In particular, our proposed method leverages a Bi-directional Generative Adversarial Network (BiCoGAN) in tandem with a Dialogue-based Personality Prediction Regression (DPPR) model to generate counterfactual data. This enables the system to formulate alternative persuasive utterances that are more suited to the user. Subsequently, we utilize the D3QN model to learn policies for optimized selection of system utterances on counterfactual data. Experimental results we obtained from using the PersuasionForGood dataset demonstrate the superiority of our approach over the existing method, BiCoGAN. The cumulative rewards and Q-values produced by our method surpass ground truth benchmarks, showcasing the efficacy of employing counterfactual reasoning and LPDs to optimize reinforcement learning policy in online interactions.

Gene Regulatory Network Inference in the Presence of Dropouts: a Causal View

Gene regulatory network inference (GRNI) is a challenging problem, particularly owing to the presence of zeros in single-cell RNA sequencing data: some are biological zeros representing no gene expression, while some others are technical zeros arising from the sequencing procedure (aka dropouts), which may bias GRNI by distorting the joint distribution of the measured gene expressions. Existing approaches typically handle dropout error via imputation, which may introduce spurious relations as the true joint distribution is generally unidentifiable. To tackle this issue, we introduce a causal graphical model to characterize the dropout mechanism, namely, Causal Dropout Model. We provide a simple yet effective theoretical result: interestingly, the conditional independence (CI) relations in the data with dropouts, after deleting the samples with zero values (regardless if technical or not) for the conditioned variables, are asymptotically identical to the CI relations in the original data without dropouts. This particular test-wise deletion procedure, in which we perform CI tests on the samples without zeros for the conditioned variables, can be seamlessly integrated with existing structure learning approaches including constraint-based and greedy score-based methods, thus giving rise to a principled framework for GRNI in the presence of dropouts. We further show that the causal dropout model can be validated from data, and many existing statistical models to handle dropouts fit into our model as specific parametric instances. Empirical evaluation on synthetic, curated, and real-world experimental transcriptomic data comprehensively demonstrate the efficacy of our method.

Steering LLMs Towards Unbiased Responses: A Causality-Guided Debiasing Framework

Large language models (LLMs) can easily generate biased and discriminative responses. As LLMs tap into consequential decision-making (e.g., hiring and healthcare), it is of crucial importance to develop strategies to mitigate these biases. This paper focuses on social bias, tackling the association between demographic information and LLM outputs. We propose a causality-guided debiasing framework that utilizes causal understandings of (1) the data-generating process of the training corpus fed to LLMs, and (2) the internal reasoning process of LLM inference, to guide the design of prompts for debiasing LLM outputs through selection mechanisms. Our framework unifies existing de-biasing prompting approaches such as inhibitive instructions and in-context contrastive examples, and sheds light on new ways of debiasing by encouraging bias-free reasoning. Our strong empirical performance on real-world datasets demonstrates that our framework provides principled guidelines on debiasing LLM outputs even with only the black-box access.

A Versatile Causal Discovery Framework to Allow Causally-Related Hidden Variables

Most existing causal discovery methods rely on the assumption of no latent confounders, limiting their applicability in solving real-life problems. In this paper, we introduce a novel, versatile framework for causal discovery that accommodates the presence of causally-related hidden variables almost everywhere in the causal network (for instance, they can be effects of observed variables), based on rank information of covariance matrix over observed variables. We start by investigating the efficacy of rank in comparison to conditional independence and, theoretically, establish necessary and sufficient conditions for the identifiability of certain latent structural patterns. Furthermore, we develop a Rank-based Latent Causal Discovery algorithm, RLCD, that can efficiently locate hidden variables, determine their cardinalities, and discover the entire causal structure over both measured and hidden ones. We also show that, under certain graphical conditions, RLCD correctly identifies the Markov Equivalence Class of the whole latent causal graph asymptotically. Experimental results on both synthetic and real-world personality data sets demonstrate the efficacy of the proposed approach in finite-sample cases.

Causal-learn: Causal Discovery in Python

Causal discovery aims at revealing causal relations from observational data, which is a fundamental task in science and engineering. We describe $\textit{causal-learn}$, an open-source Python library for causal discovery. This library focuses on bringing a comprehensive collection of causal discovery methods to both practitioners and researchers. It provides easy-to-use APIs for non-specialists, modular building blocks for developers, detailed documentation for learners, and comprehensive methods for all. Different from previous packages in R or Java, $\textit{causal-learn}$ is fully developed in Python, which could be more in tune with the recent preference shift in programming languages within related communities. The library is available at https://github.com/py-why/causal-learn.

The m-connecting imset and factorization for ADMG models

Directed acyclic graph (DAG) models have become widely studied and applied in statistics and machine learning -- indeed, their simplicity facilitates efficient procedures for learning and inference. Unfortunately, these models are not closed under marginalization, making them poorly equipped to handle systems with latent confounding. Acyclic directed mixed graph (ADMG) models characterize margins of DAG models, making them far better suited to handle such systems. However, ADMG models have not seen wide-spread use due to their complexity and a shortage of statistical tools for their analysis. In this paper, we introduce the m-connecting imset which provides an alternative representation for the independence models induced by ADMGs. Furthermore, we define the m-connecting factorization criterion for ADMG models, characterized by a single equation, and prove its equivalence to the global Markov property. The m-connecting imset and factorization criterion provide two new statistical tools for learning and inference with ADMG models. We demonstrate the usefulness of these tools by formulating and evaluating a consistent scoring criterion with a closed form solution.

Causal discovery for observational sciences using supervised machine learning

Causal inference can estimate causal effects, but unless data are collected experimentally, statistical analyses must rely on pre-specified causal models. Causal discovery algorithms are empirical methods for constructing such causal models from data. Several asymptotically correct methods already exist, but they generally struggle on smaller samples. Moreover, most methods focus on very sparse causal models, which may not always be a realistic representation of real-life data generating mechanisms. Finally, while causal relationships suggested by the methods often hold true, their claims about causal non-relatedness have high error rates. This non-conservative error tradeoff is not ideal for observational sciences, where the resulting model is directly used to inform causal inference: A causal model with many missing causal relations entails too strong assumptions and may lead to biased effect estimates. We propose a new causal discovery method that addresses these three shortcomings: Supervised learning discovery (SLdisco). SLdisco uses supervised machine learning to obtain a mapping from observational data to equivalence classes of causal models. We evaluate SLdisco in a large simulation study based on Gaussian data and we consider several choices of model size and sample size. We find that SLdisco is more conservative, only moderately less informative and less sensitive towards sample size than existing procedures. We furthermore provide a real epidemiological data application. We use random subsampling to investigate real data performance on small samples and again find that SLdisco is less sensitive towards sample size and hence seems to better utilize the information available in small datasets.

A Uniformly Consistent Estimator of non-Gaussian Causal Effects Under the k-Triangle-Faithfulness Assumption

Kalisch and B\"{u}hlmann (2007) showed that for linear Gaussian models, under the Causal Markov Assumption, the Strong Causal Faithfulness Assumption, and the assumption of causal sufficiency, the PC algorithm is a uniformly consistent estimator of the Markov Equivalence Class of the true causal DAG for linear Gaussian models; it follows from this that for the identifiable causal effects in the Markov Equivalence Class, there are uniformly consistent estimators of causal effects as well. The $k$-Triangle-Faithfulness Assumption is a strictly weaker assumption that avoids some implausible implications of the Strong Causal Faithfulness Assumption and also allows for uniformly consistent estimates of Markov Equivalence Classes (in a weakened sense), and of identifiable causal effects. However, both of these assumptions are restricted to linear Gaussian models. We propose the Generalized $k$-Triangle Faithfulness, which can be applied to any smooth distribution. In addition, under the Generalized $k$-Triangle Faithfulness Assumption, we describe the Edge Estimation Algorithm that provides uniformly consistent estimates of causal effects in some cases (and otherwise outputs "can't tell"), and the \textit{Very Conservative }$SGS$ Algorithm that (in a slightly weaker sense) is a uniformly consistent estimator of the Markov equivalence class of the true DAG.