Peter Spirtes

Yujia Zheng, Biwei Huang, Wei Chen et al.

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.

Zeyu Tang, Jialu Wang, Yang Liu et al. · stanford

We reveal and address the frequently overlooked yet important issue of disguised procedural unfairness, namely, the potentially inadvertent alterations on the behavior of neutral (i.e., not problematic) aspects of data generating process, and/or the lack of procedural assurance of the greatest benefit of the least advantaged individuals. Inspired by John Rawls's advocacy for pure procedural justice, we view automated decision-making as a microcosm of social institutions, and consider how the data generating process itself can satisfy the requirements of procedural fairness. We propose a framework that decouples the objectionable data generating components from the neutral ones by utilizing reference points and the associated value instantiation rule. Our findings highlight the necessity of preventing disguised procedural unfairness, drawing attention not only to the objectionable data generating components that we aim to mitigate, but also more importantly, to the neutral components that we intend to keep unaffected.

Xinshuai Dong, Ignavier Ng, Biwei Huang et al.

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. Code: https://github.com/dongxinshuai/scm-identify.

Haoyue Dai, Peter Spirtes, Kun Zhang

Causal discovery aims to recover causal structures generating the observational data. Despite its success in certain problems, in many real-world scenarios the observed variables are not the target variables of interest, but the imperfect measures of the target variables. Causal discovery under measurement error aims to recover the causal graph among unobserved target variables from observations made with measurement error. We consider a specific formulation of the problem, where the unobserved target variables follow a linear non-Gaussian acyclic model, and the measurement process follows the random measurement error model. Existing methods on this formulation rely on non-scalable over-complete independent component analysis (OICA). In this work, we propose the Transformed Independent Noise (TIN) condition, which checks for independence between a specific linear transformation of some measured variables and certain other measured variables. By leveraging the non-Gaussianity and higher-order statistics of data, TIN is informative about the graph structure among the unobserved target variables. By utilizing TIN, the ordered group decomposition of the causal model is identifiable. In other words, we could achieve what once required OICA to achieve by only conducting independence tests. Experimental results on both synthetic and real-world data demonstrate the effectiveness and reliability of our method.

Joseph D. Ramsey, Bryan Andrews, Peter Spirtes

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.

Bryan Andrews, Gregory F. Cooper, Thomas S. Richardson et al.

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.

Ignavier Ng, Xinshuai Dong, Haoyue Dai et al.

Identifying latent variables and the causal structure involving them is essential across various scientific fields. While many existing works fall under the category of constraint-based methods (with e.g. conditional independence or rank deficiency tests), they may face empirical challenges such as testing-order dependency, error propagation, and choosing an appropriate significance level. These issues can potentially be mitigated by properly designed score-based methods, such as Greedy Equivalence Search (GES) (Chickering, 2002) in the specific setting without latent variables. Yet, formulating score-based methods with latent variables is highly challenging. In this work, we develop score-based methods that are capable of identifying causal structures containing causally-related latent variables with identifiability guarantees. Specifically, we show that a properly formulated scoring function can achieve score equivalence and consistency for structure learning of latent variable causal models. We further provide a characterization of the degrees of freedom for the marginal over the observed variables under multiple structural assumptions considered in the literature, and accordingly develop both exact and continuous score-based methods. This offers a unified view of several existing constraint-based methods with different structural assumptions. Experimental results validate the effectiveness of the proposed methods.

Haoyue Dai, Yiwen Qiu, Ignavier Ng et al.

Addressing selection bias in latent variable causal discovery is important yet underexplored, largely due to a lack of suitable statistical tools: While various tools beyond basic conditional independencies have been developed to handle latent variables, none have been adapted for selection bias. We make an attempt by studying rank constraints, which, as a generalization to conditional independence constraints, exploits the ranks of covariance submatrices in linear Gaussian models. We show that although selection can significantly complicate the joint distribution, interestingly, the ranks in the biased covariance matrices still preserve meaningful information about both causal structures and selection mechanisms. We provide a graph-theoretic characterization of such rank constraints. Using this tool, we demonstrate that the one-factor model, a classical latent variable model, can be identified under selection bias. Simulations and real-world experiments confirm the effectiveness of using our rank constraints.

Yiwen Qiu, Filip Kovacevic, Shimeng Huang et al.

Selection bias is pervasive in observational studies. For example, large scale biobanks data can exhibit ``healthy volunteer bias'' when respondents are healthier and of higher socio-economic status than the population they are meant to represent. Recovering causal effects from such sub-population is an important problem in causal inference, as estimating average treatment effects (ATE) from selected populations can result in a severely biased estimate of the ATE from the whole population. In this paper, we investigate the identifiability of the ATE under selection bias. We provide necessary and sufficient conditions for ATE identifiability, leveraging weak assumptions on probability classes to characterize propensity score and selection probability. Compared to previous works, our results extend existing graphical identifiability criteria and offer a more comprehensive understanding of causal effect identification with strictly weaker conditions in the presence of selection bias.

Ignavier Ng, Shaoan Xie, Xinshuai Dong et al.

Causal representation learning aims to recover the latent causal variables and their causal relations, typically represented by directed acyclic graphs (DAGs), from low-level observations such as image pixels. A prevailing line of research exploits multiple environments, which assume how data distributions change, including single-node interventions, coupled interventions, or hard interventions, or parametric constraints on the mixing function or the latent causal model, such as linearity. Despite the novelty and elegance of the results, they are often violated in real problems. Accordingly, we formalize a set of desiderata for causal representation learning that applies to a broader class of environments, referred to as general environments. Interestingly, we show that one can fully recover the latent DAG and identify the latent variables up to minor indeterminacies under a nonparametric mixing function and nonlinear latent causal models, such as additive (Gaussian) noise models or heteroscedastic noise models, by properly leveraging sufficient change conditions on the causal mechanisms up to third-order derivatives. These represent, to our knowledge, the first results to fully recover the latent DAG from general environments under nonparametric mixing. Notably, our results match or improve upon many existing works, but require less restrictive assumptions about changing environments.

Xinshuai Dong, Biwei Huang, Ignavier Ng et al.

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.

Jingling Li, Zeyu Tang, Xiaoyu Liu et al. · stanford

Large language models (LLMs), despite their remarkable capabilities, are susceptible to generating biased and discriminatory responses. As LLMs increasingly influence high-stakes decision-making (e.g., hiring and healthcare), mitigating these biases becomes critical. In this work, we propose a causality-guided debiasing framework to tackle social biases, aiming to reduce the objectionable dependence between LLMs' decisions and the social information in the input. Our framework introduces a novel perspective to identify how social information can affect an LLM's decision through different causal pathways. Leveraging these causal insights, we outline principled prompting strategies that regulate these pathways through selection mechanisms. This framework not only unifies existing prompting-based debiasing techniques, but also opens up new directions for reducing bias by encouraging the model to prioritize fact-based reasoning over reliance on biased social cues. We validate our framework through extensive experiments on real-world datasets across multiple domains, demonstrating its effectiveness in debiasing LLM decisions, even with only black-box access to the model.

Haoyue Dai, Ignavier Ng, Gongxu Luo et al.

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.

Haoyue Dai, Ignavier Ng, Jianle Sun et al. · stanford

We address the common yet often-overlooked selection bias in interventional studies, where subjects are selectively enrolled into experiments. For instance, participants in a drug trial are usually patients of the relevant disease; A/B tests on mobile applications target existing users only, and gene perturbation studies typically focus on specific cell types, such as cancer cells. Ignoring this bias leads to incorrect causal discovery results. Even when recognized, the existing paradigm for interventional causal discovery still fails to address it. This is because subtle differences in when and where interventions happen can lead to significantly different statistical patterns. We capture this dynamic by introducing a graphical model that explicitly accounts for both the observed world (where interventions are applied) and the counterfactual world (where selection occurs while interventions have not been applied). We characterize the Markov property of the model, and propose a provably sound algorithm to identify causal relations as well as selection mechanisms up to the equivalence class, from data with soft interventions and unknown targets. Through synthetic and real-world experiments, we demonstrate that our algorithm effectively identifies true causal relations despite the presence of selection bias.

Zeyu Tang, Zhenhao Chen, Xiangchen Song et al. · stanford

The autoregressive decoding for text generation in large language models (LLMs), while widely used, is inherently suboptimal due to the lack of a built-in mechanism to perform refinement and/or correction of the generated content. In this paper, we consider optimality in terms of the joint probability over the generated response, when jointly considering all tokens at the same time. We theoretically characterize the potential deviation of the autoregressively generated response from its globally optimal counterpart that is of the same length. Our analysis suggests that we need to be cautious when noticeable uncertainty arises during text generation, which may signal the sub-optimality of the generation history. To address the pitfall of autoregressive decoding for text generation, we propose an approach that incorporates a sliding reflection window and a pausing criterion, such that refinement and generation can be carried out interchangeably as the decoding proceeds. Our selective refinement framework strikes a balance between efficiency and optimality, and our extensive experimental results demonstrate the effectiveness of our approach.

Donghuo Zeng, Roberto Legaspi, Yuewen Sun et al.

Tailoring persuasive conversations to users leads to more effective persuasion. However, existing dialogue systems often struggle to adapt to dynamically evolving user states. This paper presents a novel method that leverages causal discovery and counterfactual reasoning for optimizing system persuasion capability and outcomes. We employ the Greedy Relaxation of the Sparsest Permutation (GRaSP) algorithm to identify causal relationships between user and system utterance strategies, treating user strategies as states and system strategies as actions. GRaSP identifies user strategies as causal factors influencing system responses, which inform Bidirectional Conditional Generative Adversarial Networks (BiCoGAN) in generating counterfactual utterances for the system. Subsequently, we use the Dueling Double Deep Q-Network (D3QN) model to utilize counterfactual data to determine the best policy for selecting system utterances. Our experiments with the PersuasionForGood dataset show measurable improvements in persuasion outcomes using our approach over baseline methods. The observed increase in cumulative rewards and Q-values highlights the effectiveness of causal discovery in enhancing counterfactual reasoning and optimizing reinforcement learning policies for online dialogue systems.

Donghuo Zeng, Roberto S. Legaspi, Yuewen Sun et al.

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.

Haoyue Dai, Immanuel Albrecht, Peter Spirtes et al.

Causal discovery with latent variables is a fundamental task. Yet most existing methods rely on strong structural assumptions, such as enforcing specific indicator patterns for latents or restricting how they can interact with others. We argue that a core obstacle to a general, structural-assumption-free approach is the lack of an equivalence characterization: without knowing what can be identified, one generally cannot design methods for how to identify it. In this work, we aim to close this gap for linear non-Gaussian models. We establish the graphical criterion for when two graphs with arbitrary latent structure and cycles are distributionally equivalent, that is, they induce the same observed distribution set. Key to our approach is a new tool, edge rank constraints, which fills a missing piece in the toolbox for latent-variable causal discovery in even broader settings. We further provide a procedure to traverse the whole equivalence class and develop an algorithm to recover models from data up to such equivalence. To our knowledge, this is the first equivalence characterization with latent variables in any parametric setting without structural assumptions, and hence the first structural-assumption-free discovery method. Code and an interactive demo are available at https://equiv.cc.

Joseph Ramsey, Bryan Andrews, Peter Spirtes

Learning graphical conditional independence structures from nonlinear, continuous or mixed data is a central challenge in machine learning and the sciences, and many existing methods struggle to scale to thousands of samples or hundreds of variables. We introduce two basis-expansion tools for scalable causal discovery. First, the Basis Function BIC (BF-BIC) score uses truncated additive expansions to approximate nonlinear dependencies. BF-BIC is theoretically consistent under additive models and extends to post-nonlinear (PNL) models via an invertible reparameterization. It remains robust under moderate interactions and supports mixed data through a degenerate-Gaussian embedding for discrete variables. In simulations with fully nonlinear neural causal models (NCMs), BF-BIC outperforms kernel- and constraint-based methods (e.g., KCI, RFCI) in both accuracy and runtime. Second, the Basis Function Likelihood Ratio Test (BF-LRT) provides an approximate conditional independence test that is substantially faster than kernel tests while retaining competitive accuracy. Extensive simulations and a real-data application to Canadian wildfire risk show that, when integrated into hybrid searches, BF-based methods enable interpretable and scalable causal discovery. Implementations are available in Python, R, and Java.

Joseph Ramsey, Bryan Andrews, Peter Spirtes

Learning causal structure from observational data is especially challenging when latent variables or selection bias are present. The Fast Causal Inference (FCI) algorithm addresses this setting but performs exhaustive conditional independence tests across many subsets, often leading to spurious independences, missing or extra edges, and unreliable orientations. We present a family of score-guided mixed-strategy causal search algorithms that extend this framework. First, we introduce BOSS-FCI and GRaSP-FCI, variants of GFCI (Greedy Fast Causal Inference) that substitute BOSS (Best Order Score Search) or GRaSP (Greedy Relaxations of Sparsest Permutation) for FGES (Fast Greedy Equivalence Search), preserving correctness while trading off scalability and conservativeness. Second, we develop FCI Targeted-Testing (FCIT), a novel hybrid method that replaces exhaustive testing with targeted, score-informed tests guided by BOSS. FCIT guarantees well-formed PAGs and achieves higher precision and efficiency across sample sizes. Finally, we propose a lightweight heuristic, LV-Dumb (Latent Variable "Dumb"), which returns the PAG of the BOSS DAG (Directed Acyclic Graph). Though not strictly sound for latent confounding, LV-Dumb often matches FCIT's accuracy while running substantially faster. Simulations and real-data analyses show that BOSS-FCI and GRaSP-FCI provide robust baselines, FCIT yields the best balance of precision and reliability, and LV-Dumb offers a fast, near-equivalent alternative. Together, these methods demonstrate that targeted and score-guided strategies can dramatically improve the efficiency and correctness of latent-variable causal discovery.

Xinshuai Dong, Ignavier Ng, Boyang Sun et al.

Recent advances have shown that statistical tests for the rank of cross-covariance matrices play an important role in causal discovery. These rank tests include partial correlation tests as special cases and provide further graphical information about latent variables. Existing rank tests typically assume that all the continuous variables can be perfectly measured, and yet, in practice many variables can only be measured after discretization. For example, in psychometric studies, the continuous level of certain personality dimensions of a person can only be measured after being discretized into order-preserving options such as disagree, neutral, and agree. Motivated by this, we propose Mixed data Permutation-based Rank Test (MPRT), which properly controls the statistical errors even when some or all variables are discretized. Theoretically, we establish the exchangeability and estimate the asymptotic null distribution by permutations; as a consequence, MPRT can effectively control the Type I error in the presence of discretization while previous methods cannot. Empirically, our method is validated by extensive experiments on synthetic data and real-world data to demonstrate its effectiveness as well as applicability in causal discovery.

Xinshuai Dong, Ignavier Ng, Haoyue Dai et al.

Identifying the structure of a partially observed causal system is essential to various scientific fields. Recent advances have focused on constraint-based causal discovery to solve this problem, and yet in practice these methods often face challenges related to multiple testing and error propagation. These issues could be mitigated by a score-based method and thus it has raised great attention whether there exists a score-based greedy search method that can handle the partially observed scenario. In this work, we propose the first score-based greedy search method for the identification of structure involving latent variables with identifiability guarantees. Specifically, we propose Generalized N Factor Model and establish the global consistency: the true structure including latent variables can be identified up to the Markov equivalence class by using score. We then design Latent variable Greedy Equivalence Search (LGES), a greedy search algorithm for this class of model with well-defined operators, which search very efficiently over the graph space to find the optimal structure. Our experiments on both synthetic and real-life data validate the effectiveness of our method (code will be publicly available).

Loka Li, Wong Yu Kang, Minghao Fu et al.

Understanding human behavior traits is central to applications in human-computer interaction, computational social science, and personalized AI systems. Such understanding often requires integrating multiple modalities to capture nuanced patterns and relationships. However, existing resources rarely provide datasets that combine behavioral descriptors with complementary modalities such as facial attributes and biographical information. To address this gap, we present PersonaX, a curated collection of multimodal datasets designed to enable comprehensive analysis of public traits across modalities. PersonaX consists of (1) CelebPersona, featuring 9444 public figures from diverse occupations, and (2) AthlePersona, covering 4181 professional athletes across 7 major sports leagues. Each dataset includes behavioral trait assessments inferred by three high-performing large language models, alongside facial imagery and structured biographical features. We analyze PersonaX at two complementary levels. First, we abstract high-level trait scores from text descriptions and apply five statistical independence tests to examine their relationships with other modalities. Second, we introduce a novel causal representation learning (CRL) framework tailored to multimodal and multi-measurement data, providing theoretical identifiability guarantees. Experiments on both synthetic and real-world data demonstrate the effectiveness of our approach. By unifying structured and unstructured analysis, PersonaX establishes a foundation for studying LLM-inferred behavioral traits in conjunction with visual and biographical attributes, advancing multimodal trait analysis and causal reasoning.

Zeyu Tang, Alex John London, Atoosa Kasirzadeh et al. · stanford

Social determinants are variables that, while not directly pertaining to any specific individual, capture key aspects of contexts and environments that have direct causal influences on certain attributes of an individual. Previous algorithmic fairness literature has primarily focused on sensitive attributes, often overlooking the role of social determinants. Our paper addresses this gap by introducing formal and quantitative rigor into a space that has been shaped largely by qualitative proposals regarding the use of social determinants. To demonstrate theoretical perspectives and practical applicability, we examine a concrete setting of college admissions, using region as a proxy for social determinants. Our approach leverages a region-based analysis with Gamma distribution parameterization to model how social determinants impact individual outcomes. Despite its simplicity, our method quantitatively recovers findings that resonate with nuanced insights in previous qualitative debates, that are often missed by existing algorithmic fairness approaches. Our findings suggest that mitigation strategies centering solely around sensitive attributes may introduce new structural injustice when addressing existing discrimination. Considering both sensitive attributes and social determinants facilitates a more comprehensive explication of benefits and burdens experienced by individuals from diverse demographic backgrounds as well as contextual environments, which is essential for understanding and achieving fairness effectively and transparently.

Donghuo Zeng, Roberto Legaspi, Yuewen Sun et al.

We hypothesize that optimal system responses emerge from adaptive strategies grounded in causal and counterfactual knowledge. Counterfactual inference allows us to create hypothetical scenarios to examine the effects of alternative system responses. We enhance this process through causal discovery, which identifies the strategies informed by the underlying causal structure that govern system behaviors. Moreover, we consider the psychological constructs and unobservable noises that might be influencing user-system interactions as latent factors. We show that these factors can be effectively estimated. We employ causal discovery to identify strategy-level causal relationships among user and system utterances, guiding the generation of personalized counterfactual dialogues. We model the user utterance strategies as causal factors, enabling system strategies to be treated as counterfactual actions. Furthermore, we optimize policies for selecting system responses based on counterfactual data. Our results using a real-world dataset on social good demonstrate significant improvements in persuasive system outcomes, with increased cumulative rewards validating the efficacy of causal discovery in guiding personalized counterfactual inference and optimizing dialogue policies for a persuasive dialogue system.

Anne Helby Petersen, Joseph Ramsey, Claus Thorn Ekstrøm et al.

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.

Shuyan Wang, Peter Spirtes

Kalisch and Bühlmann (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.

Naji Shajarisales, Peter Spirtes, Kun Zhang

In binary classification, Learning from Positive and Unlabeled data (LePU) is semi-supervised learning but with labeled elements from only one class. Most of the research on LePU relies on some form of independence between the selection process of annotated examples and the features of the annotated class, known as the Selected Completely At Random (SCAR) assumption. Yet the annotation process is an important part of the data collection, and in many cases it naturally depends on certain features of the data (e.g., the intensity of an image and the size of the object to be detected in the image). Without any constraints on the model for the annotation process, classification results in the LePU problem will be highly non-unique. So proper, flexible constraints are needed. In this work we incorporate more flexible and realistic models for the annotation process than SCAR, and more importantly, offer a solution for the challenging LePU problem. On the theory side, we establish the identifiability of the properties of the annotation process and the classification function, in light of the considered constraints on the data-generating process. We also propose an inference algorithm to learn the parameters of the model, with successful experimental results on both simulated and real data. We also propose a novel real-world dataset forLePU, as a benchmark dataset for future studies.

Kun Zhang, Mingming Gong, Joseph Ramsey et al.

Measurement error in the observed values of the variables can greatly change the output of various causal discovery methods. This problem has received much attention in multiple fields, but it is not clear to what extent the causal model for the measurement-error-free variables can be identified in the presence of measurement error with unknown variance. In this paper, we study precise sufficient identifiability conditions for the measurement-error-free causal model and show what information of the causal model can be recovered from observed data. In particular, we present two different sets of identifiability conditions, based on the second-order statistics and higher-order statistics of the data, respectively. The former was inspired by the relationship between the generating model of the measurement-error-contaminated data and the factor analysis model, and the latter makes use of the identifiability result of the over-complete independent component analysis problem.

Andrew J Sedgewick, Joseph D. Ramsey, Peter Spirtes et al.

Graphical causal models are an important tool for knowledge discovery because they can represent both the causal relations between variables and the multivariate probability distributions over the data. Once learned, causal graphs can be used for classification, feature selection and hypothesis generation, while revealing the underlying causal network structure and thus allowing for arbitrary likelihood queries over the data. However, current algorithms for learning sparse directed graphs are generally designed to handle only one type of data (continuous-only or discrete-only), which limits their applicability to a large class of multi-modal biological datasets that include mixed type variables. To address this issue, we developed new methods that modify and combine existing methods for finding undirected graphs with methods for finding directed graphs. These hybrid methods are not only faster, but also perform better than the directed graph estimation methods alone for a variety of parameter settings and data set sizes. Here, we describe a new conditional independence test for learning directed graphs over mixed data types and we compare performances of different graph learning strategies on synthetic data.

Peter Grunwald, Peter Spirtes

This is the Proceedings of the Twenty-Sixth Conference on Uncertainty in Artificial Intelligence, which was held on Catalina Island, CA, July 8 - 11 2010.