arXiv subjects

Shohei Shimizu

Publications and source records attributed to Shohei Shimizu.

At least 19 recordsLinked to original sources

arXiv2026

Beyond Additivity: Causal Discovery in Location-Scale Noise Models with Hidden Variables

We study causal discovery from observational data when some variables are hidden and the data-generating process follows a location-scale noise model (LSNM). Existing methods that handle hidden confounders typically assume additive noise, but in practice, causes often modulate not just the mean but also the variance of their effects. We prove that acyclic directed mixed graphs (ADMGs) satisfying a bow-free condition are identifiable under LSNM with hidden variables, establishing the first identifiability result for causally insufficient models beyond noise additivity. We further provide sufficient conditions for identifying causal direction even when the bow-free assumption is violated. Our two-stage algorithm, LSNM-UV, is sound and complete, and experiments demonstrate improved performance over additive baselines on heteroscedastic data.

stat.ML↗

arXiv2026

Causal Additive Models with Unobserved Causal Paths and Backdoor Paths

Causal additive models provide a tractable yet expressive framework for causal discovery in the presence of hidden variables. When unobserved backdoor or causal paths exist between two variables, their causal relationship is often unidentifiable under existing theories. We establish sufficient conditions under which causal directions can be identified in many such cases. These conditions rely on new characterizations of regression sets to determine independence among regression residuals and conditional independencies among observed variables. Building on these results, we introduce a search algorithm that incorporates these innovations and prove its soundness and completeness. Empirical evaluations demonstrate its competitive performance against state-of-the-art methods.

cs.LG↗

arXiv2026

I-CAM-UV: Integrating Causal Graphs over Non-Identical Variable Sets Using Causal Additive Models with Unobserved Variables

Causal discovery from observational data is a fundamental tool in various fields of science. While existing approaches are typically designed for a single dataset, we often need to handle multiple datasets with non-identical variable sets in practice. One straightforward approach is to estimate a causal graph from each dataset and construct a single causal graph by overlapping. However, this approach identifies limited causal relationships because unobserved variables in each dataset can be confounders, and some variable pairs may be unobserved in any dataset. To address this issue, we leverage Causal Additive Models with Unobserved Variables (CAM-UV) that provide causal graphs having information related to unobserved variables. We show that the ground truth causal graph has structural consistency with the information of CAM-UV on each dataset. As a result, we propose an approach named I-CAM-UV to integrate CAM-UV results by enumerating all consistent causal graphs. We also provide an efficient combinatorial search algorithm and demonstrate the usefulness of I-CAM-UV against existing methods.

cs.LG↗

arXiv2026

Operationalizing Longitudinal Causal Discovery Under Real-World Workflow Constraints

Causal discovery has achieved substantial theoretical progress, yet its deployment in large-scale longitudinal systems remains limited. A key obstacle is that operational data are generated under institutional workflows whose induced partial orders are rarely formalized, enlarging the admissible graph space in ways inconsistent with the recording process. We characterize a workflow-induced constraint class for longitudinal causal discovery that restricts the admissible directed acyclic graph space through protocol-derived structural masks and timeline-aligned indexing. Rather than introducing a new optimization algorithm, we show that explicitly encoding workflow-consistent partial orders reduces structural ambiguity, especially in mixed discrete--continuous panels where within-time orientation is weakly identified. The framework combines workflow-derived admissible-edge constraints, measurement-aligned time indexing and block structure, bootstrap-based uncertainty quantification for lagged total effects, and a dynamic representation supporting intervention queries. In a nationwide annual health screening cohort in Japan with 107,261 individuals and 429,044 person-years, workflow-constrained longitudinal LiNGAM yields temporally consistent within-time substructures and interpretable lagged total effects with explicit uncertainty. Sensitivity analyses using alternative exposure and body-composition definitions preserve the main qualitative patterns. We argue that formalizing workflow-derived constraint classes improves structural interpretability without relying on domain-specific edge specification, providing a reproducible bridge between operational workflows and longitudinal causal discovery under standard identifiability assumptions.

stat.ME↗

arXiv2026

Density Ratio-based Causal Discovery from Bivariate Continuous-Discrete Data

We address the problem of inferring the causal direction between a continuous variable $X$ and a discrete variable $Y$ from observational data. For the model $X \to Y$, we adopt the threshold model used in prior work. For the model $Y \to X$, we consider two cases: (1) the conditional distributions of $X$ given different values of $Y$ form a location-shift family, and (2) they are mixtures of generalized normal distributions with independently parameterized components. We establish identifiability of the causal direction through three theoretical results. First, we prove that under $X \to Y$, the density ratio of $X$ conditioned on different values of $Y$ is monotonic. Second, we establish that under $Y \to X$ with non-location-shift conditionals, monotonicity of the density ratio holds only on a set of Lebesgue measure zero in the parameter space. Third, we show that under $X \to Y$, the conditional distributions forming a location-shift family requires a precise coordination between the causal mechanism and input distribution, which is non-generic under the principle of independent mechanisms. Together, these results imply that monotonicity of the density ratio characterizes the direction $X \to Y$, whereas non-monotonicity or location-shift conditionals characterizes $Y \to X$. Based on this, we propose Density Ratio-based Causal Discovery (DRCD), a method that determines causal direction by testing for location-shift conditionals and monotonicity of the estimated density ratio. Experiments on synthetic and real-world datasets demonstrate that DRCD outperforms existing methods.

cs.LG↗

arXiv2025

Integrating Large Language Models in Causal Discovery: A Statistical Causal Approach

In practical statistical causal discovery (SCD), embedding domain expert knowledge as constraints into the algorithm is important for reasonable causal models reflecting the broad knowledge of domain experts, despite the challenges in the systematic acquisition of background knowledge. To overcome these challenges, this paper proposes a novel method for causal inference, in which SCD and knowledge-based causal inference (KBCI) with a large language model (LLM) are synthesized through ``statistical causal prompting (SCP)'' for LLMs and prior knowledge augmentation for SCD. The experiments in this work have revealed that the results of LLM-KBCI and SCD augmented with LLM-KBCI approach the ground truths, more than the SCD result without prior knowledge. These experiments have also revealed that the SCD result can be further improved if the LLM undergoes SCP. Furthermore, with an unpublished real-world dataset, we have demonstrated that the background knowledge provided by the LLM can improve the SCD on this dataset, even if this dataset has never been included in the training data of the LLM. For future practical application of this proposed method across important domains such as healthcare, we also thoroughly discuss the limitations, risks of critical errors, expected improvement of techniques around LLMs, and realistic integration of expert checks of the results into this automatic process, with SCP simulations under various conditions both in successful and failure scenarios. The careful and appropriate application of the proposed approach in this work, with improvement and customization for each domain, can thus address challenges such as dataset biases and limitations, illustrating the potential of LLMs to improve data-driven causal inference across diverse scientific domains. The code used in this work is publicly available at: www.github.com/mas-takayama/LLM-and-SCD

cs.LG↗

arXiv2025

Causal-discovery-based root-cause analysis and its application in time-series prediction error diagnosis

Recent rapid advancements of machine learning have greatly enhanced the accuracy of prediction models, but most models remain "black boxes", making prediction error diagnosis challenging, especially with outliers. This lack of transparency hinders trust and reliability in industrial applications. Heuristic attribution methods, while helpful, often fail to capture true causal relationships, leading to inaccurate error attributions. Various root-cause analysis methods have been developed using Shapley values, yet they typically require predefined causal graphs, limiting their applicability for prediction errors in machine learning models. To address these limitations, we introduce the Causal-Discovery-based Root-Cause Analysis (CD-RCA) method that estimates causal relationships between the prediction error and the explanatory variables, without needing a pre-defined causal graph. By simulating synthetic error data, CD-RCA can identify variable contributions to outliers in prediction errors by Shapley values. Extensive experiments show CD-RCA outperforms current heuristic attribution methods.

stat.ML↗

arXiv2025

Differentiable Causal Discovery of Linear Non-Gaussian Acyclic Models Under Unmeasured Confounding

We propose a novel score-based causal discovery method, named ABIC LiNGAM, which extends the linear non-Gaussian acyclic model (LiNGAM) framework to address the challenges of causal structure estimation in scenarios involving unmeasured confounders. By introducing the assumption that error terms follow a multivariate generalized normal distribution, our method leverages continuous optimization techniques to recover acyclic directed mixed graphs (ADMGs), including causal directions rather than just equivalence classes. We provide theoretical guarantees on the identifiability of causal parameters and demonstrate the effectiveness of our approach through extensive simulations and applications to real-world datasets.

stat.ME↗

arXiv2024

Does Financial Literacy Impact Investment Participation and Retirement Planning in Japan?

By employing causal discovery method, the Fast Causal Inference (FCI) model to analyze data from the 2022 "Financial Literacy Survey," we explore the causal relationships between financial literacy and financial activities, specifically investment participation and retirement planning. Our findings indicate that increasing financial literacy may not directly boost engagement in financial investments or retirement planning in Japan, which underscores the necessity for alternative strategies to motivate financial activities among Japanese households. This research offers valuable insights for policymakers focused on improving financial well-being by advancing the use of causal discovery algorithms in understanding financial behaviors.

econ.GN↗

arXiv2024

Counterfactual Explanations of Black-box Machine Learning Models using Causal Discovery with Applications to Credit Rating

Explainable artificial intelligence (XAI) has helped elucidate the internal mechanisms of machine learning algorithms, bolstering their reliability by demonstrating the basis of their predictions. Several XAI models consider causal relationships to explain models by examining the input-output relationships of prediction models and the dependencies between features. The majority of these models have been based their explanations on counterfactual probabilities, assuming that the causal graph is known. However, this assumption complicates the application of such models to real data, given that the causal relationships between features are unknown in most cases. Thus, this study proposed a novel XAI framework that relaxed the constraint that the causal graph is known. This framework leveraged counterfactual probabilities and additional prior information on causal structure, facilitating the integration of a causal graph estimated through causal discovery methods and a black-box classification model. Furthermore, explanatory scores were estimated based on counterfactual probabilities. Numerical experiments conducted employing artificial data confirmed the possibility of estimating the explanatory score more accurately than in the absence of a causal graph. Finally, as an application to real data, we constructed a classification model of credit ratings assigned by Shiga Bank, Shiga prefecture, Japan. We demonstrated the effectiveness of the proposed method in cases where the causal graph is unknown.

cs.LG↗

arXiv2024

Use of Prior Knowledge to Discover Causal Additive Models with Unobserved Variables and its Application to Time Series Data

This paper proposes two methods for causal additive models with unobserved variables (CAM-UV). CAM-UV assumes that the causal functions take the form of generalized additive models and that latent confounders are present. First, we propose a method that leverages prior knowledge for efficient causal discovery. Then, we propose an extension of this method for inferring causality in time series data. The original CAM-UV algorithm differs from other existing causal function models in that it does not seek the causal order between observed variables, but rather aims to identify the causes for each observed variable. Therefore, the first proposed method in this paper utilizes prior knowledge, such as understanding that certain variables cannot be causes of specific others. Moreover, by incorporating the prior knowledge that causes precedes their effects in time, we extend the first algorithm to the second method for causal discovery in time series data. We validate the first proposed method by using simulated data to demonstrate that the accuracy of causal discovery increases as more prior knowledge is accumulated. Additionally, we test the second proposed method by comparing it with existing time series causal discovery methods, using both simulated data and real-world data.

cs.LG↗

arXiv2023

Scalable Counterfactual Distribution Estimation in Multivariate Causal Models

We consider the problem of estimating the counterfactual joint distribution of multiple quantities of interests (e.g., outcomes) in a multivariate causal model extended from the classical difference-in-difference design. Existing methods for this task either ignore the correlation structures among dimensions of the multivariate outcome by considering univariate causal models on each dimension separately and hence produce incorrect counterfactual distributions, or poorly scale even for moderate-size datasets when directly dealing with such multivariate causal model. We propose a method that alleviates both issues simultaneously by leveraging a robust latent one-dimensional subspace of the original high-dimension space and exploiting the efficient estimation from the univariate causal model on such space. Since the construction of the one-dimensional subspace uses information from all the dimensions, our method can capture the correlation structures and produce good estimates of the counterfactual distribution. We demonstrate the advantages of our approach over existing methods on both synthetic and real-world data.

stat.ML↗

arXiv2023

Linkages among the Foreign Exchange, Stock, and Bond Markets in Japan and the United States

While economic theory explains the linkages among the financial markets of different countries, empirical studies mainly verify the linkages through Granger causality, without considering latent variables or instantaneous effects. Their findings are inconsistent regarding the existence of causal linkages among financial markets, which might be attributed to differences in the focused markets, data periods, and methods applied. Our study adopts causal discovery methods including VAR-LiNGAM and LPCMCI with domain knowledge to explore the linkages among financial markets in Japan and the United States (US) for the post Covid-19 pandemic period under divergent monetary policy directions. The VAR-LiNGAM results reveal that the previous day's US market influences the following day's Japanese market for both stocks and bonds, and the bond markets of the previous day impact the following day's foreign exchange (FX) market directly and the following day's Japanese stock market indirectly. The LPCMCI results indicate the existence of potential latent confounders. Our results demonstrate that VAR-LiNGAM uniquely identifies the directed acyclic graph (DAG), and thus provides informative insight into the causal relationship when the assumptions are considered valid. Our study contributes to a better understanding of the linkages among financial markets in the analyzed data period by supporting the existence of linkages between Japan and the US for the same financial markets and among FX, stock, and bond markets, thus highlighting the importance of leveraging causal discovery methods in the financial domain.

q-fin.ST↗

arXiv2023

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.

cs.LG↗

arXiv2022

Causal Discovery with Multi-Domain LiNGAM for Latent Factors

Discovering causal structures among latent factors from observed data is a particularly challenging problem. Despite some efforts for this problem, existing methods focus on the single-domain data only. In this paper, we propose Multi-Domain Linear Non-Gaussian Acyclic Models for Latent Factors (MD-LiNA), where the causal structure among latent factors of interest is shared for all domains, and we provide its identification results. The model enriches the causal representation for multi-domain data. We propose an integrated two-phase algorithm to estimate the model. In particular, we first locate the latent factors and estimate the factor loading matrix. Then to uncover the causal structure among shared latent factors of interest, we derive a score function based on the characterization of independence relations between external influences and the dependence relations between multi-domain latent factors and latent factors of interest. We show that the proposed method provides locally consistent estimators. Experimental results on both synthetic and real-world data demonstrate the efficacy and robustness of our approach.

cs.LG↗

arXiv2021

Discovery of Causal Additive Models in the Presence of Unobserved Variables

Causal discovery from data affected by unobserved variables is an important but difficult problem to solve. The effects that unobserved variables have on the relationships between observed variables are more complex in nonlinear cases than in linear cases. In this study, we focus on causal additive models in the presence of unobserved variables. Causal additive models exhibit structural equations that are additive in the variables and error terms. We take into account the presence of not only unobserved common causes but also unobserved intermediate variables. Our theoretical results show that, when the causal relationships are nonlinear and there are unobserved variables, it is not possible to identify all the causal relationships between observed variables through regression and independence tests. However, our theoretical results also show that it is possible to avoid incorrect inferences. We propose a method to identify all the causal relationships that are theoretically possible to identify without being biased by unobserved variables. The empirical results using artificial data and simulated functional magnetic resonance imaging (fMRI) data show that our method effectively infers causal structures in the presence of unobserved variables.

cs.LG↗

arXiv2020

Causal discovery of linear non-Gaussian acyclic models in the presence of latent confounders

Causal discovery from data affected by latent confounders is an important and difficult challenge. Causal functional model-based approaches have not been used to present variables whose relationships are affected by latent confounders, while some constraint-based methods can present them. This paper proposes a causal functional model-based method called repetitive causal discovery (RCD) to discover the causal structure of observed variables affected by latent confounders. RCD repeats inferring the causal directions between a small number of observed variables and determines whether the relationships are affected by latent confounders. RCD finally produces a causal graph where a bi-directed arrow indicates the pair of variables that have the same latent confounders, and a directed arrow indicates the causal direction of a pair of variables that are not affected by the same latent confounder. The results of experimental validation using simulated data and real-world data confirmed that RCD is effective in identifying latent confounders and causal directions between observed variables.

cs.LG↗

arXiv2019

Analysis of cause-effect inference by comparing regression errors

We address the problem of inferring the causal direction between two variables by comparing the least-squares errors of the predictions in both possible directions. Under the assumption of an independence between the function relating cause and effect, the conditional noise distribution, and the distribution of the cause, we show that the errors are smaller in causal direction if both variables are equally scaled and the causal relation is close to deterministic. Based on this, we provide an easily applicable algorithm that only requires a regression in both possible causal directions and a comparison of the errors. The performance of the algorithm is compared with various related causal inference methods in different artificial and real-world data sets.

cs.AI↗