Deep learning · causal inference

Cluster DAGs (C-DAGs) provide an abstraction of causal graphs in which nodes represent clusters of variables, and edges encode both cluster-level causal relationships and dependencies arisen from unobserved confounding. C-DAGs define an equivalence class of acyclic causal graphs that agree on cluster-level relationships, enabling causal reasoning at a higher level of abstraction. However, when the chosen clustering induces cycles in the resulting C-DAG, the partition is deemed inadmissible under conventional C-DAG semantics. In this work, we extend the C-DAG framework to support arbitrary variable clusterings by relaxing the partition admissibility constraint, thereby allowing cyclic C-DAG representations. We extend the notions of d-separation and causal calculus to this setting, significantly broadening the scope of causal reasoning across clusters and enabling the application of C-DAGs in previously intractable scenarios. Our calculus is both sound and atomically complete with respect to the do-calculus: all valid interventional queries at the cluster level can be derived using our rules, each corresponding to a primitive do-calculus step.

Data fusion techniques integrate information from heterogeneous data sources to improve learning, generalization, and decision-making across data sciences. In causal inference, these methods leverage rich observational data to improve causal effect estimation, while maintaining the trustworthiness of randomized controlled trials. Existing approaches often relax the strong "no unobserved confounding" assumption by instead assuming exchangeability of counterfactual outcomes across data sources. However, when both assumptions simultaneously fail—a common scenario in practice—current methods cannot identify or estimate causal effects. We address this limitation by proposing a novel partial identification framework that enables researchers to answer key questions such as: *Is the causal effect positive/negative?* and *How severe must assumption violations be to overturn this conclusion?* Our approach introduces interpretable sensitivity parameters that quantify assumption violations and derives corresponding causal effect bounds. We develop doubly robust estimators for these bounds and operationalize breakdown frontier analysis to understand how causal conclusions change as assumption violations increase. We apply our framework to the Project STAR study, which investigates the effect of classroom size on students’ third-grade standardized test performance. Our analysis reveals that the Project STAR results are robust to simultaneous violations of key assumptions, both on average and across various subgroups of interest. This strengthens confidence in the study's conclusions despite potential unmeasured biases in the data.

We study the problem of causal function estimation in the Proxy Causal Learning (PCL) framework, where confounders are not observed but proxies for the confounders are available. Two main approaches have been proposed: outcome bridge-based and treatment bridge-based methods. In this work, we propose two kernel-based doubly robust estimators that combine the strengths of both approaches, and naturally handle continuous and high-dimensional variables. Our identification strategy builds on a recent density ratio-free method for treatment bridge-based PCL; furthermore, in contrast to previous approaches, it does not require indicator functions or kernel smoothing over the treatment variable. These properties make it especially well-suited for continuous or high-dimensional treatments. By using kernel mean embeddings, we propose the first density-ratio free doubly robust estimators for proxy causal learning, which have closed form solutions and strong uniform consistency guarantees. Our estimators outperform existing methods on PCL benchmarks, including a prior doubly robust method that requires both kernel smoothing and density ratio estimation.

Causal effect estimation is critical to a range of scientific disciplines. Existing methods for this task either require interventional data, knowledge about the ground-truth causal graph, or rely on assumptions such as unconfoundedness, restricting their applicability in real-world settings. In the domain of tabular machine learning, Prior-data fitted networks (PFNs) have achieved state-of-the-art predictive performance, having been pre-trained on synthetic causal data to solve tabular prediction problems via in-context learning. To assess whether this can be transferred to the problem of causal effect estimation, we pre-train PFNs on synthetic data drawn from a wide variety of causal structures, including interventions, to predict interventional outcomes given observational data. Through extensive experiments in synthetic and semi-synthetic settings, we show that our approach allows for the accurate estimation of causal effects without knowledge of the underlying causal graph.

In many scientific experiments, the data annotating cost constraints the pace for testing novel hypotheses. Yet, modern machine learning pipelines offer a promising solution—provided their predictions yield correct conclusions. We focus on Prediction-Powered Causal Inferences (PPCI), i.e., estimating the treatment effect in an unlabeled target experiment, relying on training data with the same outcome annotated but potentially different treatment or effect modifiers. We first show that conditional calibration guarantees valid PPCI at population level. Then, we introduce a sufficient representation constraint transferring validity across experiments, which we propose to enforce in practice in Deconfounded Empirical Risk Minimization, our new model-agnostic training objective. We validate our method on synthetic and real-world scientific data, solving impossible problem instances for Empirical Risk Minimization even with standard invariance constraints. In particular, for the first time, we achieve valid causal inference on a scientific experiment with complex recording and no human annotations, fine-tuning a foundational model on our similar annotated experiment.

In-context learning (ICL), a nonparametric learning method based on the knowledge of demonstration sets, has become a de facto standard for large language models (LLMs). The primary goal of ICL is to select valuable demonstration sets to enhance the performance of LLMs. Traditional ICL methods choose demonstration sets that share similar features with a given query. However, we have found that the performance of these traditional ICL approaches is limited on out-of-distribution (OOD) datasets, where the demonstration set and the query originate from different distributions. To ensure robust performance in OOD datasets, it is essential to learn causal representations that remain invariant between the source and target datasets. Inspired by causal representation learning, we propose causal-aware in-context learning (CCL). CCL captures the causal representations of a given dataset and selects demonstration sets that share similar causal features with the query. To achieve this, CCL employs a novel VAE-based causal representation learning technique. We demonstrate that CCL improves the OOD generalization performance of LLMs both theoretically and empirically. Code is available at: \url{https://github.com/MLAI-Yonsei/causal-context-learning}

Data integration approaches are increasingly used to enhance the efficiency and generalizability of studies. However, a key limitation of these methods is the assumption that outcome measures are identical across datasets -- an assumption that often does not hold in practice. Consider the following opioid use disorder (OUD) studies: the XBOT trial and the POAT study, both evaluating the effect of medications for OUD on withdrawal symptom severity (not the primary outcome of either trial). While XBOT measures withdrawal severity using the subjective opiate withdrawal scale, POAT uses the clinical opiate withdrawal scale. We analyze this realistic yet challenging setting where outcome measures differ across studies and where neither study records both types of outcomes. Our paper studies whether and when integrating studies with disparate outcome measures leads to efficiency gains. We introduce three sets of assumptions -- with varying degrees of strength -- linking both outcome measures. Our theoretical and empirical results highlight a cautionary tale: integration can improve asymptotic efficiency only under the strongest assumption linking the outcomes. However, misspecification of this assumption leads to bias. In contrast, a milder assumption may yield finite-sample efficiency gains, yet these benefits diminish as sample size increases. We illustrate these trade-offs via a case study integrating the XBOT and POAT datasets to estimate the comparative effect of two medications for opioid use disorder on withdrawal symptoms. By systematically varying the assumptions linking the SOW and COW scales, we show potential efficiency gains and the risks of bias. Our findings emphasize the need for careful assumption selection when fusing datasets with differing outcome measures, offering guidance for researchers navigating this common challenge in modern data integration.

In decision-making processes, an intelligent agent with causal knowledge can optimize action spaces to avoid unnecessary exploration. A *structural causal bandit* framework provides guidance on how to prune actions that are unable to maximize reward by leveraging prior knowledge of the underlying causal structure among actions. A key assumption of this framework is that the agent has access to a fully-specified causal diagram representing the target system. In this paper, we extend the structural causal bandits to scenarios where the agent leverages a Markov equivalence class. In such cases, the causal structure is provided to the agent in the form of a *partial ancestral graph* (PAG). We propose a generalized framework for identifying potentially optimal actions within this graph structure, thereby broadening the applicability of structural causal bandits.

Causal mediation analysis is crucial for deconstructing complex mechanisms of action. However, in current mediation analysis, complex structures derived from causal discovery lack direct interpretation of mediation pathways, while traditional mediation analysis and effect estimation are limited by the reliance on pre-specified pathways, leading to a disconnection between structure discovery and causal mechanism understanding. Therefore, a unified framework integrating structure discovery, pathway identification, and effect estimation systematically quantifies mediation pathways under structural uncertainty, enabling automated identification and inference of mediation pathways. To this end, we propose Structure-Informed Guided Mediation Analysis (SIGMA), which guides automated mediation pathway identification through probabilistic causal structure discovery and uncertainty quantification, enabling end-to-end propagation of structural uncertainty from structure learning to effect estimation. Specifically, SIGMA employs differentiable Flow-Structural Equation Models to learn structural posteriors, generating diverse Directed Acyclic Graphs (DAGs) to quantify structural uncertainty. Based on these DAGs, we introduce the Path Stability Score to evaluate the marginal probability of pathways, identifying high-confidence mediation paths. For identified mediation pathways, we integrate Efficient Influence Functions with Bayesian model averaging to fuse within-structure estimation uncertainty and between-structure effect variation, propagating uncertainty to the final effect estimates. In synthetic data experiments, SIGMA achieves state-of-the-art performance in pathway identification accuracy and effect quantification precision under structures uncertainty, concurrent multiple pathways, and nonlinear scenarios. In real-world applications using Human Phenotype Project data, SIGMA identifies mediation effects of sleep quality on cardiovascular health through inflammatory and metabolic pathways, uncovering previously unspecified multiple mediation paths.