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1. Identification of Nonlinear Latent Hierarchical Models

   Kong Lingjing, Huang Biwei (July 2023, arXivorg)

   Identifying latent variables and causal structures from observational data is essential to many real-world applications involving biological data, medical data, and unstructured data such as images and languages. However, this task can be highly challenging, especially when observed variables are generated by causally related latent variables and the relationships are nonlinear. In this work, we investigate the identification problem for nonlinear latent hierarchical causal models in which observed variables are generated by a set of causally related latent variables, and some latent variables may not have observed children. We show that the identifiability of both causal structure and latent variables can be achieved under mild assumptions: on causal structures, we allow for the existence of multiple paths between any pair of variables in the graph, which relaxes latent tree assumptions in prior work; on structural functions, we do not make parametric assumptions, thus permitting general nonlinearity and multi-dimensional continuous variables. Specifically, we first develop a basic identification criterion in the form of novel identifiability guarantees for an elementary latent variable model. Leveraging this criterion, we show that both causal structures and latent variables of the hierarchical model can be identified asymptotically by explicitly constructing an estimation procedure. To the best of our knowledge, our work is the first to establish identifiability guarantees for both causal structures and latent variables in nonlinear latent hierarchical models. 

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2. Identification of Nonlinear Latent Hierarchical Models

   Kong, Lingjing; Huang, Biwei; Xie, Feng; Xing, Eric; Chi, Yuejie; Zhang, Kun (December 2023, Advances in neural information processing systems)

   Identifying latent variables and causal structures from observational data is essential to many real-world applications involving biological data, medical data, and unstructured data such as images and languages. However, this task can be highly challenging, especially when observed variables are generated by causally related latent variables and the relationships are nonlinear. In this work, we investigate the identification problem for nonlinear latent hierarchical causal models in which observed variables are generated by a set of causally related latent variables, and some latent variables may not have observed children. We show that the identifiability of causal structures and latent variables (up to invertible transformations) can be achieved under mild assumptions: on causal structures, we allow for multiple paths between any pair of variables in the graph, which relaxes latent tree assumptions in prior work; on structural functions, we permit general nonlinearity and multi-dimensional continuous variables, alleviating existing work's parametric assumptions. Specifically, we first develop an identification criterion in the form of novel identifiability guarantees for an elementary latent variable model. Leveraging this criterion, we show that both causal structures and latent variables of the hierarchical model can be identified asymptotically by explicitly constructing an estimation procedure. To the best of our knowledge, our work is the first to establish identifiability guarantees for both causal structures and latent variables in nonlinear latent hierarchical models. 

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3. Triad Constraints for Learning Causal Structure of Latent Variables

   Ruichu Cai, Feng Xie (December 2019, Advances in neural information processing systems)

   Learning causal structure from observational data has attracted much attention,and it is notoriously challenging to find the underlying structure in the presenceof confounders (hidden direct common causes of two variables). In this paper,by properly leveraging the non-Gaussianity of the data, we propose to estimatethe structure over latent variables with the so-called Triad constraints: we design a form of "pseudo-residual" from three variables, and show that when causal relations are linear and noise terms are non-Gaussian, the causal direction between the latent variables for the three observed variables is identifiable by checking a certain kind of independence relationship. In other words, the Triad constraints help us to locate latent confounders and determine the causal direction between them. This goes far beyond the Tetrad constraints and reveals more information about the underlying structure from non-Gaussian data. Finally, based on the Triad constraints, we develop a two-step algorithm to learn the causal structure corresponding to measurement models. Experimental results on both synthetic and real data demonstrate the effectiveness and reliability of our method. 

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4. Causal Inference with Latent Variables: Recent Advances and Future Prospectives

   https://doi.org/10.1145/3637528.3671450  

   Zhu, Yaochen; He, Yinhan; Ma, Jing; Hu, Mengxuan; Li, Sheng; Li, Jundong (August 2024, Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining)

   Causality lays the foundation for the trajectory of our world. Causal inference (CI), which aims to infer intrinsic causal relations among variables of interest, has emerged as a crucial research topic. Nevertheless, the lack of observation of important variables (e.g., confounders, mediators, exogenous variables, etc.) severely compromises the reliability of CI methods. The issue may arise from the inherent difficulty in measuring the variables. Additionally, in observational studies where variables are passively recorded, certain covariates might be inadvertently omitted by the experimenter. Depending on the type of unobserved variables and the specific CI task, various consequences can be incurred if these latent variables are carelessly handled, such as biased estimation of causal effects, incomplete understanding of causal mechanisms, lack of individual-level causal consideration, etc. In this survey, we provide a comprehensive review of recent developments in CI with latent variables. We start by discussing traditional CI techniques when variables of interest are assumed to be fully observed. Afterward, under the taxonomy of circumvention and inference-based methods, we provide an in-depth discussion of various CI strategies to handle latent variables, covering the tasks of causal effect estimation, mediation analysis, counterfactual reasoning, and causal discovery. Furthermore, we generalize the discussion to graph data where interference among units may exist. Finally, we offer fresh aspects for further advancement of CI with latent variables, especially new opportunities in the era of large language models (LLMs). 

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5. Differentiable Cyclic Causal Discovery Under Unmeasured Confounders

   Sethuraman, Muralikrishnna G; Fekri, Faramarz (December 2025, 39th Conference on Neural Information Processing Systems (NeurIPS 2025))

   Understanding causal relationships between variables is fundamental across scientific disciplines. Most causal discovery algorithms rely on two key assump- tions: (i) all variables are observed, and (ii) the underlying causal graph is acyclic. While these assumptions simplify theoretical analysis, they are often violated in real-world systems, such as biological networks. Existing methods that account for confounders either assume linearity or struggle with scalability. To address these limitations, we propose DCCD-CONF, a novel framework for differentiable learning of nonlinear cyclic causal graphs in the presence of unmeasured confounders using interventional data. Our approach alternates between optimizing the graph structure and estimating the confounder distribution by maximizing the log-likelihood of the data. Through experiments on synthetic data and real-world gene perturbation datasets, we show that DCCD-CONF outperforms state-of-the-art methods in both causal graph recovery and confounder identification. Additionally, we provide consistency guarantees for our framework, reinforcing its theoretical soundness. 

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