Causal inference in longitudinal biomedical data remains a central challenge, especially in psychiatry, where symptom heterogeneity and latent confounding frequently undermine classical estimators. Most existing methods for treatment effect estimation presuppose a fixed outcome variable and address confounding through observed covariate adjustment. However, the assumption of unconfoundedness may not hold for a fixed outcome in practice. To address this foundational limitation, we directly optimize the outcome definition to maximize causal identifiability. Our DEBIAS (Durable Effects with Backdoor-Invariant Aggregated Symptoms) algorithm learns non-negative, clinically interpretable weights for outcome aggregation, maximizing durable treatment effects and empirically minimizing both observed and latent confounding by leveraging the time-limited direct effects of prior treatments in psychiatric longitudinal data. The algorithm also furnishes an empirically verifiable test for outcome unconfoundedness. DEBIAS consistently outperforms state-of-the-art methods in recovering causal effects for clinically interpretable composite outcomes across comprehensive experiments in depression and schizophrenia.
Explaining why the species lives at a particular location is important for understanding ecological systems and conserving biodiversity. However, existing ecological workflows are fragmented and often inaccessible to non-specialists. We propose an end-to-end visual-to-causal framework that transforms a species image into interpretable causal insights about its habitat preference. The system integrates species recognition, global occurrence retrieval, pseudo-absence sampling, and climate data extraction. We then discover causal structures among environmental features and estimate their influence on species occurrence using modern causal inference methods. Finally, we generate statistically grounded, human-readable causal explanations from structured templates and large language models. We demonstrate the framework on a bee and a flower species and report early results as part of an ongoing project, showing the potential of the multimodal AI assistant backed up by a recommended ecological modeling practice for describing species habitat in human-understandable language.
Recent advancements in Multimodal Emotion Recognition (MER) face challenges in addressing both modality missing and Out-Of-Distribution (OOD) data simultaneously. Existing methods often rely on specific models or introduce excessive parameters, which limits their practicality. To address these issues, we propose a novel robust MER framework, Causal Inference Distiller (CIDer), and introduce a new task, Random Modality Feature Missing (RMFM), to generalize the definition of modality missing. CIDer integrates two key components: a Model-Specific Self-Distillation (MSSD) module and a Model-Agnostic Causal Inference (MACI) module. MSSD enhances robustness under the RMFM task through a weight-sharing self-distillation approach applied across low-level features, attention maps, and high-level representations. Additionally, a Word-level Self-aligned Attention Module (WSAM) reduces computational complexity, while a Multimodal Composite Transformer (MCT) facilitates efficient multimodal fusion. To tackle OOD challenges, MACI employs a tailored causal graph to mitigate label and language biases using a Multimodal Causal Module (MCM) and fine-grained counterfactual texts. Notably, MACI can independently enhance OOD generalization with minimal additional parameters. Furthermore, we also introduce the new repartitioned MER OOD datasets. Experimental results demonstrate that CIDer achieves robust performance in both RMFM and OOD scenarios, with fewer parameters and faster training compared to state-of-the-art methods. The implementation of this work is publicly accessible at https://github.com/gw-zhong/CIDer.
Inferring causal relationships between variable pairs is crucial for understanding multivariate interactions in complex systems. Knowledge-based causal discovery -- which involves inferring causal relationships by reasoning over the metadata of variables (e.g., names or textual context) -- offers a compelling alternative to traditional methods that rely on observational data. However, existing methods using Large Language Models (LLMs) often produce unstable and inconsistent results, compromising their reliability for causal inference. To address this, we introduce a novel approach that integrates Knowledge Graphs (KGs) with LLMs to enhance knowledge-based causal discovery. Our approach identifies informative metapath-based subgraphs within KGs and further refines the selection of these subgraphs using Learning-to-Rank-based models. The top-ranked subgraphs are then incorporated into zero-shot prompts, improving the effectiveness of LLMs in inferring the causal relationship. Extensive experiments on biomedical and open-domain datasets demonstrate that our method outperforms most baselines by up to 44.4 points in F1 scores, evaluated across diverse LLMs and KGs. Our code and datasets are available on GitHub: https://github.com/susantiyuni/path-to-causality
This paper investigates causal effect identification in latent variable Linear Non-Gaussian Acyclic Models (lvLiNGAM) using higher-order cumulants, addressing two prominent setups that are challenging in the presence of latent confounding: (1) a single proxy variable that may causally influence the treatment and (2) underspecified instrumental variable cases where fewer instruments exist than treatments. We prove that causal effects are identifiable with a single proxy or instrument and provide corresponding estimation methods. Experimental results demonstrate the accuracy and robustness of our approaches compared to existing methods, advancing the theoretical and practical understanding of causal inference in linear systems with latent confounders.
Nearest neighbor (NN) methods have re-emerged as competitive tools for matrix completion, offering strong empirical performance and recent theoretical guarantees, including entry-wise error bounds, confidence intervals, and minimax optimality. Despite their simplicity, recent work has shown that NN approaches are robust to a range of missingness patterns and effective across diverse applications. This paper introduces N$^2$, a unified Python package and testbed that consolidates a broad class of NN-based methods through a modular, extensible interface. Built for both researchers and practitioners, N$^2$ supports rapid experimentation and benchmarking. Using this framework, we introduce a new NN variant that achieves state-of-the-art results in several settings. We also release a benchmark suite of real-world datasets, from healthcare and recommender systems to causal inference and LLM evaluation, designed to stress-test matrix completion methods beyond synthetic scenarios. Our experiments demonstrate that while classical methods excel on idealized data, NN-based techniques consistently outperform them in real-world settings.
Biomedical researchers increasingly rely on large-scale structured databases for complex analytical tasks. However, current text-to-SQL systems often struggle to map qualitative scientific questions into executable SQL, particularly when implicit domain reasoning is required. We introduce BiomedSQL, the first benchmark explicitly designed to evaluate scientific reasoning in text-to-SQL generation over a real-world biomedical knowledge base. BiomedSQL comprises 68,000 question/SQL query/answer triples grounded in a harmonized BigQuery knowledge base that integrates gene-disease associations, causal inference from omics data, and drug approval records. Each question requires models to infer domain-specific criteria, such as genome-wide significance thresholds, effect directionality, or trial phase filtering, rather than rely on syntactic translation alone. We evaluate a range of open- and closed-source LLMs across prompting strategies and interaction paradigms. Our results reveal a substantial performance gap: GPT-o3-mini achieves 59.0% execution accuracy, while our custom multi-step agent, BMSQL, reaches 62.6%, both well below the expert baseline of 90.0%. BiomedSQL provides a new foundation for advancing text-to-SQL systems capable of supporting scientific discovery through robust reasoning over structured biomedical knowledge bases. Our dataset is publicly available at https://huggingface.co/datasets/NIH-CARD/BiomedSQL, and our code is open-source at https://github.com/NIH-CARD/biomedsql.
We introduce DeCaFlow, a deconfounding causal generative model. Training once per dataset using just observational data and the underlying causal graph, DeCaFlow enables accurate causal inference on continuous variables under the presence of hidden confounders. Specifically, we extend previous results on causal estimation under hidden confounding to show that a single instance of DeCaFlow provides correct estimates for all causal queries identifiable with do-calculus, leveraging proxy variables to adjust for the causal effects when do-calculus alone is insufficient. Moreover, we show that counterfactual queries are identifiable as long as their interventional counterparts are identifiable, and thus are also correctly estimated by DeCaFlow. Our empirical results on diverse settings (including the Ecoli70 dataset, with 3 independent hidden confounders, tens of observed variables and hundreds of causal queries) show that DeCaFlow outperforms existing approaches, while demonstrating its out-of-the-box applicability to any given causal graph. An implementation can be found in https://github.com/aalmodovares/DeCaFlow
In this paper, we focus on the out-of-distribution (OOD) generalization of self-supervised learning (SSL). By analyzing the mini-batch construction during the SSL training phase, we first give one plausible explanation for SSL having OOD generalization. Then, from the perspective of data generation and causal inference, we analyze and conclude that SSL learns spurious correlations during the training process, which leads to a reduction in OOD generalization. To address this issue, we propose a post-intervention distribution (PID) grounded in the Structural Causal Model. PID offers a scenario where the spurious variable and label variable is mutually independent. Besides, we demonstrate that if each mini-batch during SSL training satisfies PID, the resulting SSL model can achieve optimal worst-case OOD performance. This motivates us to develop a batch sampling strategy that enforces PID constraints through the learning of a latent variable model. Through theoretical analysis, we demonstrate the identifiability of the latent variable model and validate the effectiveness of the proposed sampling strategy. Experiments conducted on various downstream OOD tasks demonstrate the effectiveness of the proposed sampling strategy.
For future human-autonomous vehicle (AV) interactions to be effective and smooth, human-aware systems that analyze and align human needs with automation decisions are essential. Achieving this requires systems that account for human cognitive states. We present a novel computational model in the form of a Dynamic Bayesian Network (DBN) that infers the cognitive states of both AV users and other road users, integrating this information into the AV's decision-making process. Specifically, our model captures the well-being of both an AV user and an interacting road user as cognitive states alongside trust. Our DBN models infer beliefs over the AV user's evolving well-being, trust, and intention states, as well as the possible well-being of other road users, based on observed interaction experiences. Using data collected from an interaction study, we refine the model parameters and empirically assess its performance. Finally, we extend our model into a causal inference model (CIM) framework for AV decision-making, enabling the AV to enhance user well-being and trust while balancing these factors with its own operational costs and the well-being of interacting road users. Our evaluation demonstrates the model's effectiveness in accurately predicting user's states and guiding informed, human-centered AV decisions.
Causal world models are systems that can answer counterfactual questions about an environment of interest, i.e. predict how it would have evolved if an arbitrary subset of events had been realized differently. It requires understanding the underlying causes behind chains of events and conducting causal inference for arbitrary unseen distributions. So far, this task eludes foundation models, notably large language models (LLMs), which do not have demonstrated causal reasoning capabilities beyond the memorization of existing causal relationships. Furthermore, evaluating counterfactuals in real-world applications is challenging since only the factual world is observed, limiting evaluation to synthetic datasets. We address these problems by explicitly extracting and modeling causal relationships and propose the Causal Cartographer framework. First, we introduce a graph retrieval-augmented generation agent tasked to retrieve causal relationships from data. This approach allows us to construct a large network of real-world causal relationships that can serve as a repository of causal knowledge and build real-world counterfactuals. In addition, we create a counterfactual reasoning agent constrained by causal relationships to perform reliable step-by-step causal inference. We show that our approach can extract causal knowledge and improve the robustness of LLMs for causal reasoning tasks while reducing inference costs and spurious correlations.
Large Language Models (LLMs) demonstrate strong reasoning and task planning capabilities but remain fundamentally limited in physical interaction modeling. Existing approaches integrate perception via Vision-Language Models (VLMs) or adaptive decision-making through Reinforcement Learning (RL), but they fail to capture dynamic object interactions or require task-specific training, limiting their real-world applicability. We introduce APEX (Anticipatory Physics-Enhanced Execution), a framework that equips LLMs with physics-driven foresight for real-time task planning. APEX constructs structured graphs to identify and model the most relevant dynamic interactions in the environment, providing LLMs with explicit physical state updates. Simultaneously, APEX provides low-latency forward simulations of physically feasible actions, allowing LLMs to select optimal strategies based on predictive outcomes rather than static observations. We evaluate APEX on three benchmarks designed to assess perception, prediction, and decision-making: (1) Physics Reasoning Benchmark, testing causal inference and object motion prediction; (2) Tetris, evaluating whether physics-informed prediction enhances decision-making performance in long-horizon planning tasks; (3) Dynamic Obstacle Avoidance, assessing the immediate integration of perception and action feasibility analysis. APEX significantly outperforms standard LLMs and VLM-based models, demonstrating the necessity of explicit physics reasoning for bridging the gap between language-based intelligence and real-world task execution. The source code and experiment setup are publicly available at https://github.com/hwj20/APEX_EXP .
Motivation: Externalizing behaviors in children, such as aggression, hyperactivity, and defiance, are influenced by complex interplays between genetic predispositions and environmental factors, particularly parental behaviors. Unraveling these intricate causal relationships can benefit from the use of robust data-driven methods. Methods: We developed a method called Hillclimb-Causal Inference, a causal discovery approach that integrates the Hill Climb Search algorithm with a customized Linear Gaussian Bayesian Information Criterion (BIC). This method was applied to data from the Adolescent Brain Cognitive Development (ABCD) Study, which included parental behavior assessments, children's genotypes, and externalizing behavior measures. We performed dimensionality reduction to address multicollinearity among parental behaviors and assessed children's genetic risk for externalizing disorders using polygenic risk scores (PRS), which were computed based on GWAS summary statistics from independent cohorts. Once the causal pathways were identified, we employed structural equation modeling (SEM) to quantify the relationships within the model. Results: We identified prominent causal pathways linking parental behaviors to children's externalizing outcomes. Parental alcohol misuse and broader behavioral issues exhibited notably stronger direct effects (0.33 and 0.20, respectively) compared to children's polygenic risk scores (0.07). Moreover, when considering both direct and indirect paths, parental substance misuse (alcohol, drug, and tobacco) collectively resulted in a total effect exceeding 1.1 on externalizing behaviors. Bootstrap and sensitivity analyses further validated the robustness of these findings.
Interpretable insights from predictive models remain critical in bio-statistics, particularly when assessing causality, where classical statistical and machine learning methods often provide inherent clarity. While Neural Networks (NNs) offer powerful capabilities for modeling complex biological data, their traditional "black-box" nature presents challenges for validation and trust in high-stakes health applications. Recent advances in Mechanistic Interpretability (MI) aim to decipher the internal computations learned by these networks. This work investigates the application of MI techniques to NNs within the context of causal inference for bio-statistics. We demonstrate that MI tools can be leveraged to: (1) probe and validate the internal representations learned by NNs, such as those estimating nuisance functions in frameworks like Targeted Minimum Loss-based Estimation (TMLE); (2) discover and visualize the distinct computational pathways employed by the network to process different types of inputs, potentially revealing how confounders and treatments are handled; and (3) provide methodologies for comparing the learned mechanisms and extracted insights across statistical, machine learning, and NN models, fostering a deeper understanding of their respective strengths and weaknesses for causal bio-statistical analysis.
The growing integration of robots in shared environments -- such as warehouses, shopping centres, and hospitals -- demands a deep understanding of the underlying dynamics and human behaviours, including how, when, and where individuals engage in various activities and interactions. This knowledge goes beyond simple correlation studies and requires a more comprehensive causal analysis. By leveraging causal inference to model cause-and-effect relationships, we can better anticipate critical environmental factors and enable autonomous robots to plan and execute tasks more effectively. To this end, we propose a novel causality-based decision-making framework that reasons over a learned causal model to predict battery usage and human obstructions, understanding how these factors could influence robot task execution. Such reasoning framework assists the robot in deciding when and how to complete a given task. To achieve this, we developed also PeopleFlow, a new Gazebo-based simulator designed to model context-sensitive human-robot spatial interactions in shared workspaces. PeopleFlow features realistic human and robot trajectories influenced by contextual factors such as time, environment layout, and robot state, and can simulate a large number of agents. While the simulator is general-purpose, in this paper we focus on a warehouse-like environment as a case study, where we conduct an extensive evaluation benchmarking our causal approach against a non-causal baseline. Our findings demonstrate the efficacy of the proposed solutions, highlighting how causal reasoning enables autonomous robots to operate more efficiently and safely in dynamic environments shared with humans.
Researchers and practitioners often wish to measure treatment effects in settings where units interact via markets and recommendation systems. In these settings, units are affected by certain shared states, like prices, algorithmic recommendations or social signals. We formalize this structure, calling it shared-state interference, and argue that our formulation captures many relevant applied settings. Our key modeling assumption is that individuals' potential outcomes are independent conditional on the shared state. We then prove an extension of a double machine learning (DML) theorem providing conditions for achieving efficient inference under shared-state interference. We also instantiate our general theorem in several models of interest where it is possible to efficiently estimate the average direct effect (ADE) or global average treatment effect (GATE).
Predicting future events stands as one of the ultimate aspirations of artificial intelligence. Recent advances in large language model (LLM)-based systems have shown remarkable potential in forecasting future events, thereby garnering significant interest in the research community. Currently, several benchmarks have been established to evaluate the forecasting capabilities by formalizing the event prediction as a retrieval-augmented generation (RAG) and reasoning task. In these benchmarks, each prediction question is answered with relevant retrieved news articles. However, because there is no consideration on whether the questions can be supported by valid or sufficient supporting rationales, some of the questions in these benchmarks may be inherently noninferable. To address this issue, we introduce a new benchmark, PROPHET, which comprises inferable forecasting questions paired with relevant news for retrieval. To ensure the inferability of the benchmark, we propose Causal Intervened Likelihood (CIL), a statistical measure that assesses inferability through causal inference. In constructing this benchmark, we first collected recent trend forecasting questions and then filtered the data using CIL, resulting in an inferable benchmark for event prediction. Through extensive experiments, we first demonstrate the validity of CIL and in-depth investigations into event prediction with the aid of CIL. Subsequently, we evaluate several representative prediction systems on PROPHET, drawing valuable insights for future directions.
The partitioning of data for estimation and calibration critically impacts the performance of propensity score based estimators like inverse probability weighting (IPW) and double/debiased machine learning (DML) frameworks. We extend recent advances in calibration techniques for propensity score estimation, improving the robustness of propensity scores in challenging settings such as limited overlap, small sample sizes, or unbalanced data. Our contributions are twofold: First, we provide a theoretical analysis of the properties of calibrated estimators in the context of DML. To this end, we refine existing calibration frameworks for propensity score models, with a particular emphasis on the role of sample-splitting schemes in ensuring valid causal inference. Second, through extensive simulations, we show that calibration reduces variance of inverse-based propensity score estimators while also mitigating bias in IPW, even in small-sample regimes. Notably, calibration improves stability for flexible learners (e.g., gradient boosting) while preserving the doubly robust properties of DML. A key insight is that, even when methods perform well without calibration, incorporating a calibration step does not degrade performance, provided that an appropriate sample-splitting approach is chosen.
Practical and ethical constraints often require the use of observational data for causal inference, particularly in medicine and social sciences. Yet, observational datasets are prone to confounding, potentially compromising the validity of causal conclusions. While it is possible to correct for biases if the underlying causal graph is known, this is rarely a feasible ask in practical scenarios. A common strategy is to adjust for all available covariates, yet this approach can yield biased treatment effect estimates, especially when post-treatment or unobserved variables are present. We propose RAMEN, an algorithm that produces unbiased treatment effect estimates by leveraging the heterogeneity of multiple data sources without the need to know or learn the underlying causal graph. Notably, RAMEN achieves doubly robust identification: it can identify the treatment effect whenever the causal parents of the treatment or those of the outcome are observed, and the node whose parents are observed satisfies an invariance assumption. Empirical evaluations on synthetic and real-world datasets show that our approach outperforms existing methods.
Variable selection poses a significant challenge in causal modeling, particularly within the social sciences, where constructs often rely on inter-related factors such as age, socioeconomic status, gender, and race. Indeed, it has been argued that such attributes must be modeled as macro-level abstractions of lower-level manipulable features, in order to preserve the modularity assumption essential to causal inference. This paper accordingly extends the theoretical framework of Causal Feature Learning (CFL). Empirically, we apply the CFL algorithm to diverse social science datasets, evaluating how CFL-derived macrostates compare with traditional microstates in downstream modeling tasks.