Daily Papers

Spatial confounding poses a significant challenge in scientific studies involving spatial data, where unobserved spatial variables can influence both treatment and outcome, possibly leading to spurious associations. To address this problem, we introduce SpaCE: The Spatial Confounding Environment, the first toolkit to provide realistic benchmark datasets and tools for systematically evaluating causal inference methods designed to alleviate spatial confounding. Each dataset includes training data, true counterfactuals, a spatial graph with coordinates, and smoothness and confounding scores characterizing the effect of a missing spatial confounder. It also includes realistic semi-synthetic outcomes and counterfactuals, generated using state-of-the-art machine learning ensembles, following best practices for causal inference benchmarks. The datasets cover real treatment and covariates from diverse domains, including climate, health and social sciences. SpaCE facilitates an automated end-to-end pipeline, simplifying data loading, experimental setup, and evaluating machine learning and causal inference models. The SpaCE project provides several dozens of datasets of diverse sizes and spatial complexity. It is publicly available as a Python package, encouraging community feedback and contributions.

A prominent challenge of offline reinforcement learning (RL) is the issue of hidden confounding: unobserved variables may influence both the actions taken by the agent and the observed outcomes. Hidden confounding can compromise the validity of any causal conclusion drawn from data and presents a major obstacle to effective offline RL. In the present paper, we tackle the problem of hidden confounding in the nonidentifiable setting. We propose a definition of uncertainty due to hidden confounding bias, termed delphic uncertainty, which uses variation over world models compatible with the observations, and differentiate it from the well-known epistemic and aleatoric uncertainties. We derive a practical method for estimating the three types of uncertainties, and construct a pessimistic offline RL algorithm to account for them. Our method does not assume identifiability of the unobserved confounders, and attempts to reduce the amount of confounding bias. We demonstrate through extensive experiments and ablations the efficacy of our approach on a sepsis management benchmark, as well as on electronic health records. Our results suggest that nonidentifiable hidden confounding bias can be mitigated to improve offline RL solutions in practice.

Fairness for machine learning predictions is widely required in practice for legal, ethical, and societal reasons. Existing work typically focuses on settings without unobserved confounding, even though unobserved confounding can lead to severe violations of causal fairness and, thus, unfair predictions. In this work, we analyze the sensitivity of causal fairness to unobserved confounding. Our contributions are three-fold. First, we derive bounds for causal fairness metrics under different sources of unobserved confounding. This enables practitioners to examine the sensitivity of their machine learning models to unobserved confounding in fairness-critical applications. Second, we propose a novel neural framework for learning fair predictions, which allows us to offer worst-case guarantees of the extent to which causal fairness can be violated due to unobserved confounding. Third, we demonstrate the effectiveness of our framework in a series of experiments, including a real-world case study about predicting prison sentences. To the best of our knowledge, ours is the first work to study causal fairness under unobserved confounding. To this end, our work is of direct practical value as a refutation strategy to ensure the fairness of predictions in high-stakes applications.

State-of-the-art methods for conditional average treatment effect (CATE) estimation make widespread use of representation learning. Here, the idea is to reduce the variance of the low-sample CATE estimation by a (potentially constrained) low-dimensional representation. However, low-dimensional representations can lose information about the observed confounders and thus lead to bias, because of which the validity of representation learning for CATE estimation is typically violated. In this paper, we propose a new, representation-agnostic framework for estimating bounds on the representation-induced confounding bias that comes from dimensionality reduction (or other constraints on the representations) in CATE estimation. First, we establish theoretically under which conditions CATEs are non-identifiable given low-dimensional (constrained) representations. Second, as our remedy, we propose to perform partial identification of CATEs or, equivalently, aim at estimating of lower and upper bounds of the representation-induced confounding bias. We demonstrate the effectiveness of our bounds in a series of experiments. In sum, our framework is of direct relevance in practice where the validity of CATE estimation is of importance.

Counterfactual data augmentation has recently emerged as a method to mitigate confounding biases in the training data for a machine learning model. These biases, such as spurious correlations, arise due to various observed and unobserved confounding variables in the data generation process. In this paper, we formally analyze how confounding biases impact downstream classifiers and present a causal viewpoint to the solutions based on counterfactual data augmentation. We explore how removing confounding biases serves as a means to learn invariant features, ultimately aiding in generalization beyond the observed data distribution. Additionally, we present a straightforward yet powerful algorithm for generating counterfactual images, which effectively mitigates the influence of confounding effects on downstream classifiers. Through experiments on MNIST variants and the CelebA datasets, we demonstrate the effectiveness and practicality of our approach.

For observational studies, we study the sensitivity of causal inference when treatment assignments may depend on unobserved confounders. We develop a loss minimization approach for estimating bounds on the conditional average treatment effect (CATE) when unobserved confounders have a bounded effect on the odds ratio of treatment selection. Our approach is scalable and allows flexible use of model classes in estimation, including nonparametric and black-box machine learning methods. Based on these bounds for the CATE, we propose a sensitivity analysis for the average treatment effect (ATE). Our semi-parametric estimator extends/bounds the augmented inverse propensity weighted (AIPW) estimator for the ATE under bounded unobserved confounding. By constructing a Neyman orthogonal score, our estimator of the bound for the ATE is a regular root-n estimator so long as the nuisance parameters are estimated at the o_p(n^{-1/4}) rate. We complement our methodology with optimality results showing that our proposed bounds are tight in certain cases. We demonstrate our method on simulated and real data examples, and show accurate coverage of our confidence intervals in practical finite sample regimes with rich covariate information.

Unobserved confounding is common in many applications, making causal inference from observational data challenging. As a remedy, causal sensitivity analysis is an important tool to draw causal conclusions under unobserved confounding with mathematical guarantees. In this paper, we propose NeuralCSA, a neural framework for generalized causal sensitivity analysis. Unlike previous work, our framework is compatible with (i) a large class of sensitivity models, including the marginal sensitivity model, f-sensitivity models, and Rosenbaum's sensitivity model; (ii) different treatment types (i.e., binary and continuous); and (iii) different causal queries, including (conditional) average treatment effects and simultaneous effects on multiple outcomes. The generality of \frameworkname is achieved by learning a latent distribution shift that corresponds to a treatment intervention using two conditional normalizing flows. We provide theoretical guarantees that NeuralCSA is able to infer valid bounds on the causal query of interest and also demonstrate this empirically using both simulated and real-world data.

Causal inference plays a vital role in diverse domains like epidemiology, healthcare, and economics. De-confounding and counterfactual prediction in observational data has emerged as a prominent concern in causal inference research. While existing models tackle observed confounders, the presence of unobserved confounders remains a significant challenge, distorting causal inference and impacting counterfactual outcome accuracy. To address this, we propose a novel variational learning model of unobserved confounders for counterfactual inference (VLUCI), which generates the posterior distribution of unobserved confounders. VLUCI relaxes the unconfoundedness assumption often overlooked by most causal inference methods. By disentangling observed and unobserved confounders, VLUCI constructs a doubly variational inference model to approximate the distribution of unobserved confounders, which are used for inferring more accurate counterfactual outcomes. Extensive experiments on synthetic and semi-synthetic datasets demonstrate VLUCI's superior performance in inferring unobserved confounders. It is compatible with state-of-the-art counterfactual inference models, significantly improving inference accuracy at both group and individual levels. Additionally, VLUCI provides confidence intervals for counterfactual outcomes, aiding decision-making in risk-sensitive domains. We further clarify the considerations when applying VLUCI to cases where unobserved confounders don't strictly conform to our model assumptions using the public IHDP dataset as an example, highlighting the practical advantages of VLUCI.

Direct Preference Optimization (DPO) has become a widely used training method for the instruction fine-tuning of large language models (LLMs). In this work, we explore an under-investigated aspect of DPO - its dependency on the reference model or policy. Such reference policies, typically instantiated as the model to be further fine-tuned, are important since they can impose an upper limit on DPO's effectiveness. Therefore, we address three related research questions in this work. First, we explore the optimal strength of the KL-divergence constraint in DPO, which penalizes deviations from the reference policy, and find that DPO is sensitive to this strength. Next, we examine the necessity of reference policies for instruction fine-tuning by providing both theoretical and empirical comparisons between DPO and related learning objectives, demonstrating DPO's superiority. Additionally, we investigate whether DPO benefits from stronger reference policies, finding that a stronger reference policy can lead to improved performance, but only when it is similar to the model being fine-tuned. Our findings highlight the confounding role of reference policies in DPO and offer insights for best practices, while also identifying open research questions for future studies.

In this paper, we introduce knowledge image generation as a new task, alongside the Massive Multi-Discipline Multi-Tier Knowledge-Image Generation Benchmark (MMMG) to probe the reasoning capability of image generation models. Knowledge images have been central to human civilization and to the mechanisms of human learning -- a fact underscored by dual-coding theory and the picture-superiority effect. Generating such images is challenging, demanding multimodal reasoning that fuses world knowledge with pixel-level grounding into clear explanatory visuals. To enable comprehensive evaluation, MMMG offers 4,456 expert-validated (knowledge) image-prompt pairs spanning 10 disciplines, 6 educational levels, and diverse knowledge formats such as charts, diagrams, and mind maps. To eliminate confounding complexity during evaluation, we adopt a unified Knowledge Graph (KG) representation. Each KG explicitly delineates a target image's core entities and their dependencies. We further introduce MMMG-Score to evaluate generated knowledge images. This metric combines factual fidelity, measured by graph-edit distance between KGs, with visual clarity assessment. Comprehensive evaluations of 16 state-of-the-art text-to-image generation models expose serious reasoning deficits -- low entity fidelity, weak relations, and clutter -- with GPT-4o achieving an MMMG-Score of only 50.20, underscoring the benchmark's difficulty. To spur further progress, we release FLUX-Reason (MMMG-Score of 34.45), an effective and open baseline that combines a reasoning LLM with diffusion models and is trained on 16,000 curated knowledge image-prompt pairs.

Recent advances in deep learning have driven rapid progress in time series forecasting, yet many state-of-the-art models continue to struggle with robust performance in real-world applications, even when they achieve strong results on standard benchmark datasets. This persistent gap can be attributed to the black-box nature of deep learning architectures and the inherent limitations of current evaluation frameworks, which frequently lack the capacity to provide clear, quantitative insights into the specific strengths and weaknesses of different models, thereby complicating the selection of appropriate models for particular forecasting scenarios. To address these issues, we propose a synthetic data-driven evaluation paradigm, SynTSBench, that systematically assesses fundamental modeling capabilities of time series forecasting models through programmable feature configuration. Our framework isolates confounding factors and establishes an interpretable evaluation system with three core analytical dimensions: (1) temporal feature decomposition and capability mapping, which enables systematic evaluation of model capacities to learn specific pattern types; (2) robustness analysis under data irregularities, which quantifies noise tolerance thresholds and anomaly recovery capabilities; and (3) theoretical optimum benchmarking, which establishes performance boundaries for each pattern type-enabling direct comparison between model predictions and mathematical optima. Our experiments show that current deep learning models do not universally approach optimal baselines across all types of temporal features.The code is available at https://github.com/TanQitai/SynTSBench

In this work, we present a systematic and comprehensive empirical evaluation of state-of-the-art reranking methods, encompassing large language model (LLM)-based, lightweight contextual, and zero-shot approaches, with respect to their performance in information retrieval tasks. We evaluate in total 22 methods, including 40 variants (depending on used LLM) across several established benchmarks, including TREC DL19, DL20, and BEIR, as well as a novel dataset designed to test queries unseen by pretrained models. Our primary goal is to determine, through controlled and fair comparisons, whether a performance disparity exists between LLM-based rerankers and their lightweight counterparts, particularly on novel queries, and to elucidate the underlying causes of any observed differences. To disentangle confounding factors, we analyze the effects of training data overlap, model architecture, and computational efficiency on reranking performance. Our findings indicate that while LLM-based rerankers demonstrate superior performance on familiar queries, their generalization ability to novel queries varies, with lightweight models offering comparable efficiency. We further identify that the novelty of queries significantly impacts reranking effectiveness, highlighting limitations in existing approaches. https://github.com/DataScienceUIBK/llm-reranking-generalization-study

Addressing fairness in artificial intelligence (AI), particularly in medical AI, is crucial for ensuring equitable healthcare outcomes. Recent efforts to enhance fairness have introduced new methodologies and datasets in medical AI. However, the fairness issue under the setting of domain transfer is almost unexplored, while it is common that clinics rely on different imaging technologies (e.g., different retinal imaging modalities) for patient diagnosis. This paper presents FairDomain, a pioneering systemic study into algorithmic fairness under domain shifts, employing state-of-the-art domain adaptation (DA) and generalization (DG) algorithms for both medical segmentation and classification tasks to understand how biases are transferred between different domains. We also introduce a novel plug-and-play fair identity attention (FIA) module that adapts to various DA and DG algorithms to improve fairness by using self-attention to adjust feature importance based on demographic attributes. Additionally, we curate the first fairness-focused dataset with two paired imaging modalities for the same patient cohort on medical segmentation and classification tasks, to rigorously assess fairness in domain-shift scenarios. Excluding the confounding impact of demographic distribution variation between source and target domains will allow clearer quantification of the performance of domain transfer models. Our extensive evaluations reveal that the proposed FIA significantly enhances both model performance accounted for fairness across all domain shift settings (i.e., DA and DG) with respect to different demographics, which outperforms existing methods on both segmentation and classification. The code and data can be accessed at https://ophai.hms.harvard.edu/datasets/harvard-fairdomain20k.

Observational studies require adjustment for confounding factors that are correlated with both the treatment and outcome. In the setting where the observed variables are tabular quantities such as average income in a neighborhood, tools have been developed for addressing such confounding. However, in many parts of the developing world, features about local communities may be scarce. In this context, satellite imagery can play an important role, serving as a proxy for the confounding variables otherwise unobserved. In this paper, we study confounder adjustment in this non-tabular setting, where patterns or objects found in satellite images contribute to the confounder bias. Using the evaluation of anti-poverty aid programs in Africa as our running example, we formalize the challenge of performing causal adjustment with such unstructured data -- what conditions are sufficient to identify causal effects, how to perform estimation, and how to quantify the ways in which certain aspects of the unstructured image object are most predictive of the treatment decision. Via simulation, we also explore the sensitivity of satellite image-based observational inference to image resolution and to misspecification of the image-associated confounder. Finally, we apply these tools in estimating the effect of anti-poverty interventions in African communities from satellite imagery.

Does RL teach LLMs genuinely new skills, or does it merely activate existing ones? This question lies at the core of ongoing debates about the role of RL in LLM post-training. On one side, strong empirical results can be achieved with RL even without preceding supervised finetuning; on the other, critics argue that RL contributes little beyond reweighting existing reasoning strategies. This work provides concrete evidence that LLMs can acquire genuinely new skills during RL by composing existing ones, mirroring one of the central mechanisms by which humans acquire new cognitive skills. To mitigate data contamination and other confounding factors, and to allow precise control over task complexity, we develop a synthetic framework for our investigation. Specifically, we define a skill as the ability to infer the output of a string transformation function f(x) given x. When an LLM has already learned f and g prior to RL, our experiments reveal that RL enables it to learn unseen compositions of them h(x)=g(f(x)). Further, this compositional ability generalizes to more difficult problems such as compositions of >2 functions unseen during RL training. Surprisingly, our experiments show that compositional skill acquired on a source task transfers to a different target task. This transfer happens even without compositional training on the target, requiring only prior knowledge of the target's atomic skills. Our qualitative analysis shows that RL fundamentally changes the reasoning behaviors of the models. In contrast, next-token training with the same data yields none of these findings. Our systematic experiments provide fresh insights into LLM learning, suggesting the value of first building base models with basic skills, then using RL to incentivize advanced, generalizable skills for complex problems.

The technique of data augmentation (DA) is often used in machine learning for regularization purposes to better generalize under i.i.d. settings. In this work, we present a unifying framework with topics in causal inference to make a case for the use of DA beyond just the i.i.d. setting, but for generalization across interventions as well. Specifically, we argue that when the outcome generating mechanism is invariant to our choice of DA, then such augmentations can effectively be thought of as interventions on the treatment generating mechanism itself. This can potentially help to reduce bias in causal effect estimation arising from hidden confounders. In the presence of such unobserved confounding we typically make use of instrumental variables (IVs) -- sources of treatment randomization that are conditionally independent of the outcome. However, IVs may not be as readily available as DA for many applications, which is the main motivation behind this work. By appropriately regularizing IV based estimators, we introduce the concept of IV-like (IVL) regression for mitigating confounding bias and improving predictive performance across interventions even when certain IV properties are relaxed. Finally, we cast parameterized DA as an IVL regression problem and show that when used in composition can simulate a worst-case application of such DA, further improving performance on causal estimation and generalization tasks beyond what simple DA may offer. This is shown both theoretically for the population case and via simulation experiments for the finite sample case using a simple linear example. We also present real data experiments to support our case.

Large Language Models (LLMs) have shown impressive performance in natural language tasks, but their outputs can exhibit undesirable attributes or biases. Existing methods for steering LLMs toward desired attributes often assume unbiased representations and rely solely on steering prompts. However, the representations learned from pre-training can introduce semantic biases that influence the steering process, leading to suboptimal results. We propose LLMGuardrail, a novel framework that incorporates causal analysis and adversarial learning to obtain unbiased steering representations in LLMs. LLMGuardrail systematically identifies and blocks the confounding effects of biases, enabling the extraction of unbiased steering representations. Additionally, it includes an explainable component that provides insights into the alignment between the generated output and the desired direction. Experiments demonstrate LLMGuardrail's effectiveness in steering LLMs toward desired attributes while mitigating biases. Our work contributes to the development of safe and reliable LLMs that align with desired attributes.

Medical image classification is a critical problem for healthcare, with the potential to alleviate the workload of doctors and facilitate diagnoses of patients. However, two challenges arise when deploying deep learning models to real-world healthcare applications. First, neural models tend to learn spurious correlations instead of desired features, which could fall short when generalizing to new domains (e.g., patients with different ages). Second, these black-box models lack interpretability. When making diagnostic predictions, it is important to understand why a model makes a decision for trustworthy and safety considerations. In this paper, to address these two limitations, we propose a new paradigm to build robust and interpretable medical image classifiers with natural language concepts. Specifically, we first query clinical concepts from GPT-4, then transform latent image features into explicit concepts with a vision-language model. We systematically evaluate our method on eight medical image classification datasets to verify its effectiveness. On challenging datasets with strong confounding factors, our method can mitigate spurious correlations thus substantially outperform standard visual encoders and other baselines. Finally, we show how classification with a small number of concepts brings a level of interpretability for understanding model decisions through case studies in real medical data.

Human-factor analysis typically employs correlation analysis and significance testing to identify relationships between variables. However, these descriptive ('what-is') methods, while effective for identifying associations, are often insufficient for answering causal ('what-if') questions. Their application in such contexts often overlooks confounding and colliding variables, potentially leading to bias and suboptimal or incorrect decisions. We advocate for explicitly distinguishing descriptive from interventional questions in human-factor analysis, and applying causal inference frameworks specifically to these problems to prevent methodological mismatches. This approach disentangles complex variable relationships and enables counterfactual reasoning. Using post-occupancy evaluation (POE) data from the Center for the Built Environment's (CBE) Occupant Survey as a demonstration case, we show how causal discovery reveals intervention hierarchies and directional relationships that traditional associational analysis misses. The systematic distinction between causally associated and independent variables, combined with intervention prioritization capabilities, offers broad applicability to complex human-centric systems, for example, in building science or ergonomics, where understanding intervention effects is critical for optimization and decision-making.

This paper studies the challenging problem of estimating causal effects from observational data, in the presence of unobserved confounders. The two-stage least square (TSLS) method and its variants with a standard instrumental variable (IV) are commonly used to eliminate confounding bias, including the bias caused by unobserved confounders, but they rely on the linearity assumption. Besides, the strict condition of unconfounded instruments posed on a standard IV is too strong to be practical. To address these challenging and practical problems of the standard IV method (linearity assumption and the strict condition), in this paper, we use a conditional IV (CIV) to relax the unconfounded instrument condition of standard IV and propose a non-linear CIV regression with Confounding Balancing Representation Learning, CBRL.CIV, for jointly eliminating the confounding bias from unobserved confounders and balancing the observed confounders, without the linearity assumption. We theoretically demonstrate the soundness of CBRL.CIV. Extensive experiments on synthetic and two real-world datasets show the competitive performance of CBRL.CIV against state-of-the-art IV-based estimators and superiority in dealing with the non-linear situation.

Genome-wide association study (GWAS) tests single nucleotide polymorphism (SNP) markers across the genome to localize the underlying causal variant of a trait. Because causal variants are seldom observed directly, a surrogate model based on genotyped markers are widely considered. Although many methods estimating the parameters of the surrogate model have been proposed, the connection between the surrogate model and the true causal model is yet investigated. In this work, we establish the connection between the surrogate model and the true causal model. The connection shows that population structure is accounted in GWAS by modelling the variant of interest and not the trait. Such observation explains how environmental confounding can be partially corrected using genetic covariates and why the previously claimed connection between PC correction and linear mixed models is incorrect.

Deep neural networks have demonstrated promising performance on image recognition tasks. However, they may heavily rely on confounding factors, using irrelevant artifacts or bias within the dataset as the cue to improve performance. When a model performs decision-making based on these spurious correlations, it can become untrustable and lead to catastrophic outcomes when deployed in the real-world scene. In this paper, we explore and try to solve this problem in the context of skin cancer diagnosis. We introduce a human-in-the-loop framework in the model training process such that users can observe and correct the model's decision logic when confounding behaviors happen. Specifically, our method can automatically discover confounding factors by analyzing the co-occurrence behavior of the samples. It is capable of learning confounding concepts using easily obtained concept exemplars. By mapping the black-box model's feature representation onto an explainable concept space, human users can interpret the concept and intervene via first order-logic instruction. We systematically evaluate our method on our newly crafted, well-controlled skin lesion dataset and several public skin lesion datasets. Experiments show that our method can effectively detect and remove confounding factors from datasets without any prior knowledge about the category distribution and does not require fully annotated concept labels. We also show that our method enables the model to focus on clinical-related concepts, improving the model's performance and trustworthiness during model inference.

Large language models (LLM) have achieved impressive performance on medical question-answering benchmarks. However, high benchmark accuracy does not imply that the performance generalizes to real-world clinical settings. Medical question-answering benchmarks rely on assumptions consistent with quantifying LLM performance but that may not hold in the open world of the clinic. Yet LLMs learn broad knowledge that can help the LLM generalize to practical conditions regardless of unrealistic assumptions in celebrated benchmarks. We seek to quantify how well LLM medical question-answering benchmark performance generalizes when benchmark assumptions are violated. Specifically, we present an adversarial method that we call MedFuzz (for medical fuzzing). MedFuzz attempts to modify benchmark questions in ways aimed at confounding the LLM. We demonstrate the approach by targeting strong assumptions about patient characteristics presented in the MedQA benchmark. Successful "attacks" modify a benchmark item in ways that would be unlikely to fool a medical expert but nonetheless "trick" the LLM into changing from a correct to an incorrect answer. Further, we present a permutation test technique that can ensure a successful attack is statistically significant. We show how to use performance on a "MedFuzzed" benchmark, as well as individual successful attacks. The methods show promise at providing insights into the ability of an LLM to operate robustly in more realistic settings.

Pathology Foundation Models (FMs) hold great promise for healthcare. Before they can be used in clinical practice, it is essential to ensure they are robust to variations between medical centers. We measure whether pathology FMs focus on biological features like tissue and cancer type, or on the well known confounding medical center signatures introduced by staining procedure and other differences. We introduce the Robustness Index. This novel robustness metric reflects to what degree biological features dominate confounding features. Ten current publicly available pathology FMs are evaluated. We find that all current pathology foundation models evaluated represent the medical center to a strong degree. Significant differences in the robustness index are observed. Only one model so far has a robustness index greater than one, meaning biological features dominate confounding features, but only slightly. A quantitative approach to measure the influence of medical center differences on FM-based prediction performance is described. We analyze the impact of unrobustness on classification performance of downstream models, and find that cancer-type classification errors are not random, but specifically attributable to same-center confounders: images of other classes from the same medical center. We visualize FM embedding spaces, and find these are more strongly organized by medical centers than by biological factors. As a consequence, the medical center of origin is predicted more accurately than the tissue source and cancer type. The robustness index introduced here is provided with the aim of advancing progress towards clinical adoption of robust and reliable pathology FMs.

Temporally dense single-person "small data" have become widely available thanks to mobile apps and wearable sensors. Many caregivers and self-trackers want to use these data to help a specific person change their behavior to achieve desired health outcomes. Ideally, this involves discerning possible causes from correlations using that person's own observational time series data. In this paper, we estimate within-individual average treatment effects of physical activity on sleep duration, and vice-versa. We introduce the model twin randomization (MoTR; "motor") method for analyzing an individual's intensive longitudinal data. Formally, MoTR is an application of the g-formula (i.e., standardization, back-door adjustment) under serial interference. It estimates stable recurring effects, as is done in n-of-1 trials and single case experimental designs. We compare our approach to standard methods (with possible confounding) to show how to use causal inference to make better personalized recommendations for health behavior change, and analyze 222 days of Fitbit sleep and steps data for one of the authors.

Adapter-based training has emerged as a key mechanism for extending the capabilities of powerful foundation image generators, enabling personalized and stylized text-to-image synthesis. These adapters are typically trained to capture a specific target attribute, such as subject identity, using single-image reconstruction objectives. However, because the input image inevitably contains a mixture of visual factors, adapters are prone to entangle the target attribute with incidental ones, such as pose, expression, and lighting. This spurious correlation problem limits generalization and obstructs the model's ability to adhere to the input text prompt. In this work, we uncover a simple yet effective solution: provide the very shortcuts we wish to eliminate during adapter training. In Shortcut-Rerouted Adapter Training, confounding factors are routed through auxiliary modules, such as ControlNet or LoRA, eliminating the incentive for the adapter to internalize them. The auxiliary modules are then removed during inference. When applied to tasks like facial and full-body identity injection, our approach improves generation quality, diversity, and prompt adherence. These results point to a general design principle in the era of large models: when seeking disentangled representations, the most effective path may be to establish shortcuts for what should NOT be learned.

Recommendation systems (RS) aim to provide personalized content, but they face a challenge in unbiased learning due to selection bias, where users only interact with items they prefer. This bias leads to a distorted representation of user preferences, which hinders the accuracy and fairness of recommendations. To address the issue, various methods such as error imputation based, inverse propensity scoring, and doubly robust techniques have been developed. Despite the progress, from the structural causal model perspective, previous debiasing methods in RS assume the independence of the exogenous variables. In this paper, we release this assumption and propose a learning algorithm based on likelihood maximization to learn a prediction model. We first discuss the correlation and difference between unmeasured confounding and our scenario, then we propose a unified method that effectively handles latent exogenous variables. Specifically, our method models the data generation process with latent exogenous variables under mild normality assumptions. We then develop a Monte Carlo algorithm to numerically estimate the likelihood function. Extensive experiments on synthetic datasets and three real-world datasets demonstrate the effectiveness of our proposed method. The code is at https://github.com/WallaceSUI/kdd25-background-variable.

Though notable progress has been made, neural-based aspect-based sentiment analysis (ABSA) models are prone to learn spurious correlations from annotation biases, resulting in poor robustness on adversarial data transformations. Among the debiasing solutions, causal inference-based methods have attracted much research attention, which can be mainly categorized into causal intervention methods and counterfactual reasoning methods. However, most of the present debiasing methods focus on single-variable causal inference, which is not suitable for ABSA with two input variables (the target aspect and the review). In this paper, we propose a novel framework based on multi-variable causal inference for debiasing ABSA. In this framework, different types of biases are tackled based on different causal intervention methods. For the review branch, the bias is modeled as indirect confounding from context, where backdoor adjustment intervention is employed for debiasing. For the aspect branch, the bias is described as a direct correlation with labels, where counterfactual reasoning is adopted for debiasing. Extensive experiments demonstrate the effectiveness of the proposed method compared to various baselines on the two widely used real-world aspect robustness test set datasets.

An essential and challenging problem in causal inference is causal effect estimation from observational data. The problem becomes more difficult with the presence of unobserved confounding variables. The front-door adjustment is a practical approach for dealing with unobserved confounding variables. However, the restriction for the standard front-door adjustment is difficult to satisfy in practice. In this paper, we relax some of the restrictions by proposing the concept of conditional front-door (CFD) adjustment and develop the theorem that guarantees the causal effect identifiability of CFD adjustment. Furthermore, as it is often impossible for a CFD variable to be given in practice, it is desirable to learn it from data. By leveraging the ability of deep generative models, we propose CFDiVAE to learn the representation of the CFD adjustment variable directly from data with the identifiable Variational AutoEncoder and formally prove the model identifiability. Extensive experiments on synthetic datasets validate the effectiveness of CFDiVAE and its superiority over existing methods. The experiments also show that the performance of CFDiVAE is less sensitive to the causal strength of unobserved confounding variables. We further apply CFDiVAE to a real-world dataset to demonstrate its potential application.

The causalimages R package enables causal inference with image and image sequence data, providing new tools for integrating novel data sources like satellite and bio-medical imagery into the study of cause and effect. One set of functions enables image-based causal inference analyses. For example, one key function decomposes treatment effect heterogeneity by images using an interpretable Bayesian framework. This allows for determining which types of images or image sequences are most responsive to interventions. A second modeling function allows researchers to control for confounding using images. The package also allows investigators to produce embeddings that serve as vector summaries of the image or video content. Finally, infrastructural functions are also provided, such as tools for writing large-scale image and image sequence data as sequentialized byte strings for more rapid image analysis. causalimages therefore opens new capabilities for causal inference in R, letting researchers use informative imagery in substantive analyses in a fast and accessible manner.

This work presents a first evaluation of two state-of-the-art Large Reasoning Models (LRMs), OpenAI's o3-mini and DeepSeek R1, on analogical reasoning, focusing on well-established nonverbal human IQ tests based on Raven's progressive matrices. We benchmark with the I-RAVEN dataset and its more difficult extension, I-RAVEN-X, which tests the ability to generalize to longer reasoning rules and ranges of the attribute values. To assess the influence of visual uncertainties on these nonverbal analogical reasoning tests, we extend the I-RAVEN-X dataset, which otherwise assumes an oracle perception. We adopt a two-fold strategy to simulate this imperfect visual perception: 1) we introduce confounding attributes which, being sampled at random, do not contribute to the prediction of the correct answer of the puzzles and 2) smoothen the distributions of the input attributes' values. We observe a sharp decline in OpenAI's o3-mini task accuracy, dropping from 86.6% on the original I-RAVEN to just 17.0% -- approaching random chance -- on the more challenging I-RAVEN-X, which increases input length and range and emulates perceptual uncertainty. This drop occurred despite spending 3.4x more reasoning tokens. A similar trend is also observed for DeepSeek R1: from 80.6% to 23.2%. On the other hand, a neuro-symbolic probabilistic abductive model, ARLC, that achieves state-of-the-art performances on I-RAVEN, can robustly reason under all these out-of-distribution tests, maintaining strong accuracy with only a modest reduction from 98.6% to 88.0%. Our code is available at https://github.com/IBM/raven-large-language-models.

Mathematical researchers, especially those in early-career positions, face critical decisions about topic specialization with limited information about the collaborative environments of different research areas. The aim of this paper is to study how the popularity of a research topic is associated with the structure of that topic's collaboration network, as observed by a suite of measures capturing organizational structure at several scales. We apply these measures to 1,938 algorithmically discovered topics across 121,391 papers sourced from arXiv metadata during the period 2020--2025. Our analysis, which controls for the confounding effects of network size, reveals a structural dichotomy--we find that popular topics organize into modular "schools of thought," while niche topics maintain hierarchical core-periphery structures centered around established experts. This divide is not an artifact of scale, but represents a size-independent structural pattern correlated with popularity. We also document a "constraint reversal": after controlling for size, researchers in popular fields face greater structural constraints on collaboration opportunities, contrary to conventional expectations. Our findings suggest that topic selection is an implicit choice between two fundamentally different collaborative environments, each with distinct implications for a researcher's career. To make these structural patterns transparent to the research community, we developed the Math Research Compass (https://mathresearchcompass.com), an interactive platform providing data on topic popularity and collaboration patterns across mathematical topics.

Logical reasoning is a critical component of Large Language Models (LLMs), and substantial research efforts in recent years have aimed to enhance their deductive reasoning capabilities. However, existing deductive reasoning benchmarks, which are crucial for evaluating and advancing LLMs, are inadequate due to their lack of task complexity, presence of prior knowledge as a confounder, and superficial error analysis. To address these deficiencies, we introduce JustLogic, a synthetically generated deductive reasoning benchmark designed for rigorous evaluation of LLMs. JustLogic is (i) highly complex, capable of generating a diverse range of linguistic patterns, vocabulary, and argument structures; (ii) prior knowledge independent, eliminating the advantage of models possessing prior knowledge and ensuring that only deductive reasoning is used to answer questions; and (iii) capable of in-depth error analysis on the heterogeneous effects of reasoning depth and argument form on model accuracy. Our experimental results on JustLogic reveal that most state-of-the-art (SOTA) LLMs perform significantly worse than the human average, demonstrating substantial room for model improvement. All code and data are available at https://github.com/michaelchen-lab/JustLogic

Instrumental variable (IV) methods are used to estimate causal effects in settings with unobserved confounding, where we cannot directly experiment on the treatment variable. Instruments are variables which only affect the outcome indirectly via the treatment variable(s). Most IV applications focus on low-dimensional treatments and crucially require at least as many instruments as treatments. This assumption is restrictive: in the natural sciences we often seek to infer causal effects of high-dimensional treatments (e.g., the effect of gene expressions or microbiota on health and disease), but can only run few experiments with a limited number of instruments (e.g., drugs or antibiotics). In such underspecified problems, the full treatment effect is not identifiable in a single experiment even in the linear case. We show that one can still reliably recover the projection of the treatment effect onto the instrumented subspace and develop techniques to consistently combine such partial estimates from different sets of instruments. We then leverage our combined estimators in an algorithm that iteratively proposes the most informative instruments at each round of experimentation to maximize the overall information about the full causal effect.

We study counterfactual identifiability in causal models with bijective generation mechanisms (BGM), a class that generalizes several widely-used causal models in the literature. We establish their counterfactual identifiability for three common causal structures with unobserved confounding, and propose a practical learning method that casts learning a BGM as structured generative modeling. Learned BGMs enable efficient counterfactual estimation and can be obtained using a variety of deep conditional generative models. We evaluate our techniques in a visual task and demonstrate its application in a real-world video streaming simulation task.

Aspect-based sentiment analysis (ABSA) aims to predict the sentiment towards a specific aspect in the text. However, existing ABSA test sets cannot be used to probe whether a model can distinguish the sentiment of the target aspect from the non-target aspects. To solve this problem, we develop a simple but effective approach to enrich ABSA test sets. Specifically, we generate new examples to disentangle the confounding sentiments of the non-target aspects from the target aspect's sentiment. Based on the SemEval 2014 dataset, we construct the Aspect Robustness Test Set (ARTS) as a comprehensive probe of the aspect robustness of ABSA models. Over 92% data of ARTS show high fluency and desired sentiment on all aspects by human evaluation. Using ARTS, we analyze the robustness of nine ABSA models, and observe, surprisingly, that their accuracy drops by up to 69.73%. We explore several ways to improve aspect robustness, and find that adversarial training can improve models' performance on ARTS by up to 32.85%. Our code and new test set are available at https://github.com/zhijing-jin/ARTS_TestSet

Deep neural networks have shown excellent performances in many real-world applications. Unfortunately, they may show "Clever Hans"-like behavior---making use of confounding factors within datasets---to achieve high performance. In this work, we introduce the novel learning setting of "explanatory interactive learning" (XIL) and illustrate its benefits on a plant phenotyping research task. XIL adds the scientist into the training loop such that she interactively revises the original model via providing feedback on its explanations. Our experimental results demonstrate that XIL can help avoiding Clever Hans moments in machine learning and encourages (or discourages, if appropriate) trust into the underlying model.

To process novel sentences, language models (LMs) must generalize compositionally -- combine familiar elements in new ways. What aspects of a model's structure promote compositional generalization? Focusing on transformers, we test the hypothesis, motivated by recent theoretical and empirical work, that transformers generalize more compositionally when they are deeper (have more layers). Because simply adding layers increases the total number of parameters, confounding depth and size, we construct three classes of models which trade off depth for width such that the total number of parameters is kept constant (41M, 134M and 374M parameters). We pretrain all models as LMs and fine-tune them on tasks that test for compositional generalization. We report three main conclusions: (1) after fine-tuning, deeper models generalize better out-of-distribution than shallower models do, but the relative benefit of additional layers diminishes rapidly; (2) within each family, deeper models show better language modeling performance, but returns are similarly diminishing; (3) the benefits of depth for compositional generalization cannot be attributed solely to better performance on language modeling or on in-distribution data.

Recent studies show that large language models (LLMs) exhibit self-preference bias when serving as judges, meaning they tend to favor their own responses over those generated by other models. Existing methods typically measure this bias by calculating the difference between the scores a judge model assigns to its own responses and those it assigns to responses from other models. However, this approach conflates self-preference bias with response quality, as higher-quality responses from the judge model may also lead to positive score differences, even in the absence of bias. To address this issue, we introduce gold judgments as proxies for the actual quality of responses and propose the DBG score, which measures self-preference bias as the difference between the scores assigned by the judge model to its own responses and the corresponding gold judgments. Since gold judgments reflect true response quality, the DBG score mitigates the confounding effect of response quality on bias measurement. Using the DBG score, we conduct comprehensive experiments to assess self-preference bias across LLMs of varying versions, sizes, and reasoning abilities. Additionally, we investigate two factors that influence and help alleviate self-preference bias: response text style and the post-training data of judge models. Finally, we explore potential underlying mechanisms of self-preference bias from an attention-based perspective. Our code and data are available at https://github.com/zhiyuanc2001/self-preference.

Faithful evaluation of language model capabilities is crucial for deriving actionable insights that can inform model development. However, rigorous causal evaluations in this domain face significant methodological challenges, including complex confounding effects and prohibitive computational costs associated with extensive retraining. To tackle these challenges, we propose a causal representation learning framework wherein observed benchmark performance is modeled as a linear transformation of a few latent capability factors. Crucially, these latent factors are identified as causally interrelated after appropriately controlling for the base model as a common confounder. Applying this approach to a comprehensive dataset encompassing over 1500 models evaluated across six benchmarks from the Open LLM Leaderboard, we identify a concise three-node linear causal structure that reliably explains the observed performance variations. Further interpretation of this causal structure provides substantial scientific insights beyond simple numerical rankings: specifically, we reveal a clear causal direction starting from general problem-solving capabilities, advancing through instruction-following proficiency, and culminating in mathematical reasoning ability. Our results underscore the essential role of carefully controlling base model variations during evaluation, a step critical to accurately uncovering the underlying causal relationships among latent model capabilities.

The origins of the colours of Trans-Neptunian Objects (TNOs) represent a crucial unresolved question, central to understanding the history of our Solar System. Recent observational surveys revealed correlations between the eccentricity and inclination of TNOs, and their colours. This rekindled the long-standing debate on whether these colours reflect the conditions of TNO formation or their subsequent evolution. We address this question using a model-agnostic, data-driven approach that unanimously converges to a common causal graph from the analysis of two different datasets, each from two different conditional independence test methods. For evaluation, we demonstrate how our model is consistent with the currently-accepted paradigms of TNOs' dynamical histories, without involving any orbital modelling or physics-based assumptions. Our causal model (with no knowledge of the existence of Neptune) predicts the need for an unknown confounding variable, consistent with Neptune's effects. The model predicts that the colour of TNOs is the root cause of their inclination distribution, rather than the other way around. This strongly suggests that the colours of TNOs reflect an underlying dynamical property, most likely their formation location. Our model excludes formation scenarios that invoke substantial colour modification by subsequent evolution. We conclude that the colours of TNOs are predominantly primordial.

Large language models (LLMs) have demonstrated significant improvements in contextual understanding. However, their ability to attend to truly critical information during long-context reasoning and generation still falls behind the pace. Specifically, our preliminary experiments reveal that certain distracting patterns can misdirect the model's attention during inference, and removing these patterns substantially improves reasoning accuracy and generation quality. We attribute this phenomenon to spurious correlations in the training data, which obstruct the model's capacity to infer authentic causal instruction-response relationships. This phenomenon may induce redundant reasoning processes, potentially resulting in significant inference overhead and, more critically, the generation of erroneous or suboptimal responses. To mitigate this, we introduce a two-stage framework called Learning to Focus (LeaF) leveraging intervention-based inference to disentangle confounding factors. In the first stage, LeaF employs gradient-based comparisons with an advanced teacher to automatically identify confounding tokens based on causal relationships in the training corpus. Then, in the second stage, it prunes these tokens during distillation to enact intervention, aligning the student's attention with the teacher's focus distribution on truly critical context tokens. Experimental results demonstrate that LeaF not only achieves an absolute improvement in various mathematical reasoning, code generation and multi-hop question answering benchmarks but also effectively suppresses attention to confounding tokens during inference, yielding a more interpretable and reliable reasoning model.

Objective: fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always clear that all demographic confounds, such as age, sex, and race, have been removed from fMRI data. Additionally, many fMRI datasets are restricted to authorized researchers, making dissemination of these valuable data sources challenging. Methods: We create a variational autoencoder (VAE)-based model, DemoVAE, to decorrelate fMRI features from demographics and generate high-quality synthetic fMRI data based on user-supplied demographics. We train and validate our model using two large, widely used datasets, the Philadelphia Neurodevelopmental Cohort (PNC) and Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP). Results: We find that DemoVAE recapitulates group differences in fMRI data while capturing the full breadth of individual variations. Significantly, we also find that most clinical and computerized battery fields that are correlated with fMRI data are not correlated with DemoVAE latents. An exception are several fields related to schizophrenia medication and symptom severity. Conclusion: Our model generates fMRI data that captures the full distribution of FC better than traditional VAE or GAN models. We also find that most prediction using fMRI data is dependent on correlation with, and prediction of, demographics. Significance: Our DemoVAE model allows for generation of high quality synthetic data conditioned on subject demographics as well as the removal of the confounding effects of demographics. We identify that FC-based prediction tasks are highly influenced by demographic confounds.

The reliability of deep time series models is often compromised by their tendency to rely on confounding factors, which may lead to misleading results. Our newly recorded, naturally confounded dataset named P2S from a real mechanical production line emphasizes this. To tackle the challenging problem of mitigating confounders in time series data, we introduce Right on Time (RioT). Our method enables interactions with model explanations across both the time and frequency domain. Feedback on explanations in both domains is then used to constrain the model, steering it away from the annotated confounding factors. The dual-domain interaction strategy is crucial for effectively addressing confounders in time series datasets. We empirically demonstrate that RioT can effectively guide models away from the wrong reasons in P2S as well as popular time series classification and forecasting datasets.

While pre-trained language models (PLMs) have shown evidence of acquiring vast amounts of knowledge, it remains unclear how much of this parametric knowledge is actually usable in performing downstream tasks. We propose a systematic framework to measure parametric knowledge utilization in PLMs. Our framework first extracts knowledge from a PLM's parameters and subsequently constructs a downstream task around this extracted knowledge. Performance on this task thus depends exclusively on utilizing the model's possessed knowledge, avoiding confounding factors like insufficient signal. As an instantiation, we study factual knowledge of PLMs and measure utilization across 125M to 13B parameter PLMs. We observe that: (1) PLMs exhibit two gaps - in acquired vs. utilized knowledge, (2) they show limited robustness in utilizing knowledge under distribution shifts, and (3) larger models close the acquired knowledge gap but the utilized knowledge gap remains. Overall, our study provides insights into PLMs' capabilities beyond their acquired knowledge.

The current literature on AI-advised decision making -- involving explainable AI systems advising human decision makers -- presents a series of inconclusive and confounding results. To synthesize these findings, we propose a simple theory that elucidates the frequent failure of AI explanations to engender appropriate reliance and complementary decision making performance. We argue explanations are only useful to the extent that they allow a human decision maker to verify the correctness of an AI's prediction, in contrast to other desiderata, e.g., interpretability or spelling out the AI's reasoning process. Prior studies find in many decision making contexts AI explanations do not facilitate such verification. Moreover, most tasks fundamentally do not allow easy verification, regardless of explanation method, limiting the potential benefit of any type of explanation. We also compare the objective of complementary performance with that of appropriate reliance, decomposing the latter into the notions of outcome-graded and strategy-graded reliance.

Human evaluation is the foundation upon which the evaluation of both summarization systems and automatic metrics rests. However, existing human evaluation studies for summarization either exhibit a low inter-annotator agreement or have insufficient scale, and an in-depth analysis of human evaluation is lacking. Therefore, we address the shortcomings of existing summarization evaluation along the following axes: (1) We propose a modified summarization salience protocol, Atomic Content Units (ACUs), which is based on fine-grained semantic units and allows for a high inter-annotator agreement. (2) We curate the Robust Summarization Evaluation (RoSE) benchmark, a large human evaluation dataset consisting of 22,000 summary-level annotations over 28 top-performing systems on three datasets. (3) We conduct a comparative study of four human evaluation protocols, underscoring potential confounding factors in evaluation setups. (4) We evaluate 50 automatic metrics and their variants using the collected human annotations across evaluation protocols and demonstrate how our benchmark leads to more statistically stable and significant results. The metrics we benchmarked include recent methods based on large language models (LLMs), GPTScore and G-Eval. Furthermore, our findings have important implications for evaluating LLMs, as we show that LLMs adjusted by human feedback (e.g., GPT-3.5) may overfit unconstrained human evaluation, which is affected by the annotators' prior, input-agnostic preferences, calling for more robust, targeted evaluation methods.

Instrumental variable methods have been widely used to identify causal effects in the presence of unmeasured confounding. A key identification condition known as the exclusion restriction states that the instrument cannot have a direct effect on the outcome which is not mediated by the exposure in view. In the health and social sciences, such an assumption is often not credible. To address this concern, we consider identification conditions of the population average treatment effect with an invalid instrumental variable which does not satisfy the exclusion restriction, and derive the efficient influence function targeting the identifying functional under a nonparametric observed data model. We propose a novel multiply robust locally efficient estimator of the average treatment effect that is consistent in the union of multiple parametric nuisance models, as well as a multiply debiased machine learning estimator for which the nuisance parameters are estimated using generic machine learning methods, that effectively exploit various forms of linear or nonlinear structured sparsity in the nuisance parameter space. When one cannot be confident that any of these machine learners is consistent at sufficiently fast rates to ensure n-consistency for the average treatment effect, we introduce a new criteria for selective machine learning which leverages the multiple robustness property in order to ensure small bias. The proposed methods are illustrated through extensive simulations and a data analysis evaluating the causal effect of 401(k) participation on savings.

Learning high-quality text representations is fundamental to a wide range of NLP tasks. While encoder pretraining has traditionally relied on Masked Language Modeling (MLM), recent evidence suggests that decoder models pretrained with Causal Language Modeling (CLM) can be effectively repurposed as encoders, often surpassing traditional encoders on text representation benchmarks. However, it remains unclear whether these gains reflect an inherent advantage of the CLM objective or arise from confounding factors such as model and data scale. In this paper, we address this question through a series of large-scale, carefully controlled pretraining ablations, training a total of 30 models ranging from 210 million to 1 billion parameters, and conducting over 15,000 fine-tuning and evaluation runs. We find that while training with MLM generally yields better performance across text representation tasks, CLM-trained models are more data-efficient and demonstrate improved fine-tuning stability. Building on these findings, we experimentally show that a biphasic training strategy that sequentially applies CLM and then MLM, achieves optimal performance under a fixed computational training budget. Moreover, we demonstrate that this strategy becomes more appealing when initializing from readily available pretrained CLM models (from the existing LLM ecosystem), reducing the computational burden needed to train best-in-class encoder models. We release all project artifacts at https://hf.co/MLMvsCLM to foster further research.

Contrastive Language-Image Pretraining (CLIP) is a popular foundation model, supporting from zero-shot classification, retrieval to encoders for multimodal large language models (MLLMs). Although CLIP is successfully trained on billion-scale image-text pairs from the English world, scaling CLIP's training further to learning from the worldwide web data is still challenging: (1) no curation method is available to handle data points from non-English world; (2) the English performance from existing multilingual CLIP is worse than its English-only counterpart, i.e., "curse of multilinguality" that is common in LLMs. Here, we present MetaCLIP 2, the first recipe training CLIP from scratch on worldwide web-scale image-text pairs. To generalize our findings, we conduct rigorous ablations with minimal changes that are necessary to address the above challenges and present a recipe enabling mutual benefits from English and non-English world data. In zero-shot ImageNet classification, MetaCLIP 2 ViT-H/14 surpasses its English-only counterpart by 0.8% and mSigLIP by 0.7%, and surprisingly sets new state-of-the-art without system-level confounding factors (e.g., translation, bespoke architecture changes) on multilingual benchmarks, such as CVQA with 57.4%, Babel-ImageNet with 50.2% and XM3600 with 64.3% on image-to-text retrieval.

Vision-Language Models (VLMs) such as GPT-4V have recently demonstrated incredible strides on diverse vision language tasks. We dig into vision-based deductive reasoning, a more sophisticated but less explored realm, and find previously unexposed blindspots in the current SOTA VLMs. Specifically, we leverage Raven's Progressive Matrices (RPMs), to assess VLMs' abilities to perform multi-hop relational and deductive reasoning relying solely on visual clues. We perform comprehensive evaluations of several popular VLMs employing standard strategies such as in-context learning, self-consistency, and Chain-of-thoughts (CoT) on three diverse datasets, including the Mensa IQ test, IntelligenceTest, and RAVEN. The results reveal that despite the impressive capabilities of LLMs in text-based reasoning, we are still far from achieving comparable proficiency in visual deductive reasoning. We found that certain standard strategies that are effective when applied to LLMs do not seamlessly translate to the challenges presented by visual reasoning tasks. Moreover, a detailed analysis reveals that VLMs struggle to solve these tasks mainly because they are unable to perceive and comprehend multiple, confounding abstract patterns in RPM examples.

Data scaling has driven remarkable success in foundation models for Natural Language Processing (NLP) and Computer Vision (CV), yet the principles of effective data scaling in robotic manipulation remain insufficiently understood. In this work, we investigate the nuanced role of data diversity in robot learning by examining three critical dimensions-task (what to do), embodiment (which robot to use), and expert (who demonstrates)-challenging the conventional intuition of "more diverse is better". Throughout extensive experiments on various robot platforms, we reveal that (1) task diversity proves more critical than per-task demonstration quantity, benefiting transfer from diverse pre-training tasks to novel downstream scenarios; (2) multi-embodiment pre-training data is optional for cross-embodiment transfer-models trained on high-quality single-embodiment data can efficiently transfer to different platforms, showing more desirable scaling property during fine-tuning than multi-embodiment pre-trained models; and (3) expert diversity, arising from individual operational preferences and stochastic variations in human demonstrations, can be confounding to policy learning, with velocity multimodality emerging as a key contributing factor. Based on this insight, we propose a distribution debiasing method to mitigate velocity ambiguity, the yielding GO-1-Pro achieves substantial performance gains of 15%, equivalent to using 2.5 times pre-training data. Collectively, these findings provide new perspectives and offer practical guidance on how to scale robotic manipulation datasets effectively.

We present a general strategy to aligning visual generation models -- both image and video generation -- with human preference. To start with, we build VisionReward -- a fine-grained and multi-dimensional reward model. We decompose human preferences in images and videos into multiple dimensions, each represented by a series of judgment questions, linearly weighted and summed to an interpretable and accurate score. To address the challenges of video quality assessment, we systematically analyze various dynamic features of videos, which helps VisionReward surpass VideoScore by 17.2% and achieve top performance for video preference prediction. Based on VisionReward, we develop a multi-objective preference learning algorithm that effectively addresses the issue of confounding factors within preference data. Our approach significantly outperforms existing image and video scoring methods on both machine metrics and human evaluation. All code and datasets are provided at https://github.com/THUDM/VisionReward.

We introduce Arboretum, the largest publicly accessible dataset designed to advance AI for biodiversity applications. This dataset, curated from the iNaturalist community science platform and vetted by domain experts to ensure accuracy, includes 134.6 million images, surpassing existing datasets in scale by an order of magnitude. The dataset encompasses image-language paired data for a diverse set of species from birds (Aves), spiders/ticks/mites (Arachnida), insects (Insecta), plants (Plantae), fungus/mushrooms (Fungi), snails (Mollusca), and snakes/lizards (Reptilia), making it a valuable resource for multimodal vision-language AI models for biodiversity assessment and agriculture research. Each image is annotated with scientific names, taxonomic details, and common names, enhancing the robustness of AI model training. We showcase the value of Arboretum by releasing a suite of CLIP models trained using a subset of 40 million captioned images. We introduce several new benchmarks for rigorous assessment, report accuracy for zero-shot learning, and evaluations across life stages, rare species, confounding species, and various levels of the taxonomic hierarchy. We anticipate that Arboretum will spur the development of AI models that can enable a variety of digital tools ranging from pest control strategies, crop monitoring, and worldwide biodiversity assessment and environmental conservation. These advancements are critical for ensuring food security, preserving ecosystems, and mitigating the impacts of climate change. Arboretum is publicly available, easily accessible, and ready for immediate use. Please see the https://baskargroup.github.io/Arboretum/{project website} for links to our data, models, and code.

Computer vision models have been shown to exhibit and amplify biases across a wide array of datasets and tasks. Existing methods for quantifying bias in classification models primarily focus on dataset distribution and model performance on subgroups, overlooking the internal workings of a model. We introduce the Attention-IoU (Attention Intersection over Union) metric and related scores, which use attention maps to reveal biases within a model's internal representations and identify image features potentially causing the biases. First, we validate Attention-IoU on the synthetic Waterbirds dataset, showing that the metric accurately measures model bias. We then analyze the CelebA dataset, finding that Attention-IoU uncovers correlations beyond accuracy disparities. Through an investigation of individual attributes through the protected attribute of Male, we examine the distinct ways biases are represented in CelebA. Lastly, by subsampling the training set to change attribute correlations, we demonstrate that Attention-IoU reveals potential confounding variables not present in dataset labels.

Human feedback has become the de facto standard for evaluating the performance of Large Language Models, and is increasingly being used as a training objective. However, it is not clear which properties of a generated output this single `preference' score captures. We hypothesise that preference scores are subjective and open to undesirable biases. We critically analyse the use of human feedback for both training and evaluation, to verify whether it fully captures a range of crucial error criteria. We find that while preference scores have fairly good coverage, they under-represent important aspects like factuality. We further hypothesise that both preference scores and error annotation may be affected by confounders, and leverage instruction-tuned models to generate outputs that vary along two possible confounding dimensions: assertiveness and complexity. We find that the assertiveness of an output skews the perceived rate of factuality errors, indicating that human annotations are not a fully reliable evaluation metric or training objective. Finally, we offer preliminary evidence that using human feedback as a training objective disproportionately increases the assertiveness of model outputs. We encourage future work to carefully consider whether preference scores are well aligned with the desired objective.

Deep learning-based medical image classification techniques are rapidly advancing in medical image analysis, making it crucial to develop accurate and trustworthy models that can be efficiently deployed across diverse clinical scenarios. Concept Bottleneck Models (CBMs), which first predict a set of explainable concepts from images and then perform classification based on these concepts, are increasingly being adopted for explainable medical image classification. However, the inherent explainability of CBMs introduces new challenges when deploying trained models to new environments. Variations in imaging protocols and staining methods may induce concept-level shifts, such as alterations in color distribution and scale. Furthermore, since CBM training requires explicit concept annotations, fine-tuning models solely with image-level labels could compromise concept prediction accuracy and faithfulness - a critical limitation given the high cost of acquiring expert-annotated concept labels in medical domains. To address these challenges, we propose a training-free confusion concept identification strategy. By leveraging minimal new data (e.g., 4 images per class) with only image-level labels, our approach enhances out-of-domain performance without sacrificing source domain accuracy through two key operations: masking misactivated confounding concepts and amplifying under-activated discriminative concepts. The efficacy of our method is validated on both skin and white blood cell images. Our code is available at: https://github.com/riverback/TF-TTI-XMed.

Recent advancements in long-context language models (LCLMs) promise to transform Retrieval-Augmented Generation (RAG) by simplifying pipelines. With their expanded context windows, LCLMs can process entire knowledge bases and perform retrieval and reasoning directly -- a capability we define as In-Context Retrieval and Reasoning (ICR^2). However, existing benchmarks like LOFT often overestimate LCLM performance by providing overly simplified contexts. To address this, we introduce ICR^2, a benchmark that evaluates LCLMs in more realistic scenarios by including confounding passages retrieved with strong retrievers. We then propose three methods to enhance LCLM performance: (1) retrieve-then-generate fine-tuning, (2) retrieval-attention-probing, which uses attention heads to filter and de-noise long contexts during decoding, and (3) joint retrieval head training alongside the generation head. Our evaluation of five well-known LCLMs on LOFT and ICR^2 demonstrates significant gains with our best approach applied to Mistral-7B: +17 and +15 points by Exact Match on LOFT, and +13 and +2 points on ICR^2, compared to vanilla RAG and supervised fine-tuning, respectively. It even outperforms GPT-4-Turbo on most tasks despite being a much smaller model.

Large language models are being widely used across industries to generate content that contributes directly to key performance metrics, such as conversion rates. Pretrained models, however, often fall short when it comes to aligning with human preferences or optimizing for business objectives. As a result, fine-tuning with good-quality labeled data is essential to guide models to generate content that achieves better results. Controlled experiments, like A/B tests, can provide such data, but they are often expensive and come with significant engineering and logistical challenges. Meanwhile, companies have access to a vast amount of historical (observational) data that remains underutilized. In this work, we study the challenges and opportunities of fine-tuning LLMs using observational data. We show that while observational outcomes can provide valuable supervision, directly fine-tuning models on such data can lead them to learn spurious correlations. We present empirical evidence of this issue using various real-world datasets and propose DeconfoundLM, a method that explicitly removes the effect of known confounders from reward signals. Using simulation experiments, we demonstrate that DeconfoundLM improves the recovery of causal relationships and mitigates failure modes found in fine-tuning methods that ignore or naively incorporate confounding variables. Our findings highlight that while observational data presents risks, with the right causal corrections, it can be a powerful source of signal for LLM alignment. Please refer to the project page for code and related resources.

Pretrained vision-language models, such as CLIP, show promising zero-shot performance across a wide variety of datasets. For closed-set classification tasks, however, there is an inherent limitation: CLIP image encoders are typically designed to extract generic image-level features that summarize superfluous or confounding information for the target tasks. This results in degradation of classification performance, especially when objects of interest cover small areas of input images. In this work, we propose CLIP with Guided Cropping (GC-CLIP), where we use an off-the-shelf zero-shot object detection model in a preprocessing step to increase focus of zero-shot classifier to the object of interest and minimize influence of extraneous image regions. We empirically show that our approach improves zero-shot classification results across architectures and datasets, favorably for small objects.

As social media becomes increasingly prominent in our day to day lives, it is increasingly important to detect informative content and prevent the spread of disinformation and unverified rumours. While many sophisticated and successful models have been proposed in the literature, they are often compared with older NLP baselines such as SVMs, CNNs, and LSTMs. In this paper, we examine the performance of a broad set of modern transformer-based language models and show that with basic fine-tuning, these models are competitive with and can even significantly outperform recently proposed state-of-the-art methods. We present our framework as a baseline for creating and evaluating new methods for misinformation detection. We further study a comprehensive set of benchmark datasets, and discuss potential data leakage and the need for careful design of the experiments and understanding of datasets to account for confounding variables. As an extreme case example, we show that classifying only based on the first three digits of tweet ids, which contain information on the date, gives state-of-the-art performance on a commonly used benchmark dataset for fake news detection --Twitter16. We provide a simple tool to detect this problem and suggest steps to mitigate it in future datasets.

To enhance controllability in text-to-image generation, ControlNet introduces image-based control signals, while ControlNet++ improves pixel-level cycle consistency between generated images and the input control signal. To avoid the prohibitive cost of back-propagating through the sampling process, ControlNet++ optimizes only low-noise timesteps (e.g., t < 200) using a single-step approximation, which not only ignores the contribution of high-noise timesteps but also introduces additional approximation errors. A straightforward alternative for optimizing controllability across all timesteps is Direct Preference Optimization (DPO), a fine-tuning method that increases model preference for more controllable images (I^{w}) over less controllable ones (I^{l}). However, due to uncertainty in generative models, it is difficult to ensure that win--lose image pairs differ only in controllability while keeping other factors, such as image quality, fixed. To address this, we propose performing preference learning over control conditions rather than generated images. Specifically, we construct winning and losing control signals, c^{w} and c^{l}, and train the model to prefer c^{w}. This method, which we term Condition Preference Optimization (CPO), eliminates confounding factors and yields a low-variance training objective. Our approach theoretically exhibits lower contrastive loss variance than DPO and empirically achieves superior results. Moreover, CPO requires less computation and storage for dataset curation. Extensive experiments show that CPO significantly improves controllability over the state-of-the-art ControlNet++ across multiple control types: over 10% error rate reduction in segmentation, 70--80% in human pose, and consistent 2--5% reductions in edge and depth maps.

Self-supervised learning has seen great success recently in unsupervised representation learning, enabling breakthroughs in natural language and image processing. However, these methods often rely on autoregressive and masked modeling, which aim to reproduce masked information in the input, which can be vulnerable to the presence of noise or confounding variables. To address this problem, Joint-Embedding Predictive Architectures (JEPA) has been introduced with the aim to perform self-supervised learning in the latent space. To leverage these advancements in the domain of time series, we introduce Time Series JEPA (TS-JEPA), an architecture specifically adapted for time series representation learning. We validate TS-JEPA on both classification and forecasting, showing that it can match or surpass current state-of-the-art baselines on different standard datasets. Notably, our approach demonstrates a strong performance balance across diverse tasks, indicating its potential as a robust foundation for learning general representations. Thus, this work lays the groundwork for developing future time series foundation models based on Joint Embedding.

Interpretability is critical in high-stakes domains such as medical imaging, where understanding model decisions is essential for clinical adoption. In this work, we introduce Sparse Autoencoder (SAE)-based interpretability to breast imaging by analyzing {Mammo-CLIP}, a vision--language foundation model pretrained on large-scale mammogram image--report pairs. We train a patch-level Mammo-SAE on Mammo-CLIP to identify and probe latent features associated with clinically relevant breast concepts such as mass and suspicious calcification. Our findings reveal that top activated class level latent neurons in the SAE latent space often tend to align with ground truth regions, and also uncover several confounding factors influencing the model's decision-making process. Additionally, we analyze which latent neurons the model relies on during downstream finetuning for improving the breast concept prediction. This study highlights the promise of interpretable SAE latent representations in providing deeper insight into the internal workings of foundation models at every layer for breast imaging. The code will be released at https://krishnakanthnakka.github.io/MammoSAE/

Visual language is a system of communication that conveys information through symbols, shapes, and spatial arrangements. Diagrams are a typical example of a visual language depicting complex concepts and their relationships in the form of an image. The symbolic nature of diagrams presents significant challenges for building models capable of understanding them. Yet, recent studies seem to suggest that Large Vision-Language Models (LVLMs) can even tackle complex reasoning tasks involving diagrams. In this paper, we investigate this phenomenon by developing a comprehensive test suite to evaluate the diagram comprehension capability of LVLMs. Our test suite uses a variety of questions focused on concept entities and their relationships over a set of synthetic as well as real diagrams across several domains to evaluate the recognition and reasoning abilities of models. Our evaluation of three LVLMs (GPT-4V, GPT-4o, and Gemini) shows that while these models can accurately identify and reason about entities, their ability to understand relationships is notably limited. Further testing reveals that the decent performance on diagram understanding largely stems from leveraging their background knowledge as shortcuts to identify and reason about the relational information. Thus, we conclude that LVLMs have a limited capability for genuine diagram understanding, and their impressive performance in diagram reasoning is an illusion emanating from other confounding factors, such as the background knowledge in the models.

Large Vision-Language Models (LVLMs) have demonstrated outstanding performance across various multimodal tasks. However, they suffer from a problem known as language prior, where responses are generated based solely on textual patterns while disregarding image information. Addressing the issue of language prior is crucial, as it can lead to undesirable biases or hallucinations when dealing with images that are out of training distribution. Despite its importance, current methods for accurately measuring language priors in LVLMs are poorly studied. Although existing benchmarks based on counterfactual or out-of-distribution images can partially be used to measure language priors, they fail to disentangle language priors from other confounding factors. To this end, we propose a new benchmark called VLind-Bench, which is the first benchmark specifically designed to measure the language priors, or blindness, of LVLMs. It not only includes tests on counterfactual images to assess language priors but also involves a series of tests to evaluate more basic capabilities such as commonsense knowledge, visual perception, and commonsense biases. For each instance in our benchmark, we ensure that all these basic tests are passed before evaluating the language priors, thereby minimizing the influence of other factors on the assessment. The evaluation and analysis of recent LVLMs in our benchmark reveal that almost all models exhibit a significant reliance on language priors, presenting a strong challenge in the field.

Despite the remarkable success of deep neural networks in a myriad of settings, several works have demonstrated their overwhelming sensitivity to near-imperceptible perturbations, known as adversarial attacks. On the other hand, prior works have also observed that deep networks can be under-sensitive, wherein large-magnitude perturbations in input space do not induce appreciable changes to network activations. In this work, we study in detail the phenomenon of under-sensitivity in vision models such as CNNs and Transformers, and present techniques to study the geometry and extent of "equi-confidence" level sets of such networks. We propose a Level Set Traversal algorithm that iteratively explores regions of high confidence with respect to the input space using orthogonal components of the local gradients. Given a source image, we use this algorithm to identify inputs that lie in the same equi-confidence level set as the source image despite being perceptually similar to arbitrary images from other classes. We further observe that the source image is linearly connected by a high-confidence path to these inputs, uncovering a star-like structure for level sets of deep networks. Furthermore, we attempt to identify and estimate the extent of these connected higher-dimensional regions over which the model maintains a high degree of confidence. The code for this project is publicly available at https://github.com/SriramB-98/blindspots-neurips-sub

Causal explanations of the predictions of NLP systems are essential to ensure safety and establish trust. Yet, existing methods often fall short of explaining model predictions effectively or efficiently and are often model-specific. In this paper, we address model-agnostic explanations, proposing two approaches for counterfactual (CF) approximation. The first approach is CF generation, where a large language model (LLM) is prompted to change a specific text concept while keeping confounding concepts unchanged. While this approach is demonstrated to be very effective, applying LLM at inference-time is costly. We hence present a second approach based on matching, and propose a method that is guided by an LLM at training-time and learns a dedicated embedding space. This space is faithful to a given causal graph and effectively serves to identify matches that approximate CFs. After showing theoretically that approximating CFs is required in order to construct faithful explanations, we benchmark our approaches and explain several models, including LLMs with billions of parameters. Our empirical results demonstrate the excellent performance of CF generation models as model-agnostic explainers. Moreover, our matching approach, which requires far less test-time resources, also provides effective explanations, surpassing many baselines. We also find that Top-K techniques universally improve every tested method. Finally, we showcase the potential of LLMs in constructing new benchmarks for model explanation and subsequently validate our conclusions. Our work illuminates new pathways for efficient and accurate approaches to interpreting NLP systems.

In recent years, we have witnessed the great advancement of Deep neural networks (DNNs) in image restoration. However, a critical limitation is that they cannot generalize well to real-world degradations with different degrees or types. In this paper, we are the first to propose a novel training strategy for image restoration from the causality perspective, to improve the generalization ability of DNNs for unknown degradations. Our method, termed Distortion Invariant representation Learning (DIL), treats each distortion type and degree as one specific confounder, and learns the distortion-invariant representation by eliminating the harmful confounding effect of each degradation. We derive our DIL with the back-door criterion in causality by modeling the interventions of different distortions from the optimization perspective. Particularly, we introduce counterfactual distortion augmentation to simulate the virtual distortion types and degrees as the confounders. Then, we instantiate the intervention of each distortion with a virtual model updating based on corresponding distorted images, and eliminate them from the meta-learning perspective. Extensive experiments demonstrate the effectiveness of our DIL on the generalization capability for unseen distortion types and degrees. Our code will be available at https://github.com/lixinustc/Causal-IR-DIL.

This work demonstrates that Legal Judgement Prediction systems without expert-informed adjustments can be vulnerable to shallow, distracting surface signals that arise from corpus construction, case distribution, and confounding factors. To mitigate this, we use domain expertise to strategically identify statistically predictive but legally irrelevant information. We adopt adversarial training to prevent the system from relying on it. We evaluate our deconfounded models by employing interpretability techniques and comparing to expert annotations. Quantitative experiments and qualitative analysis show that our deconfounded model consistently aligns better with expert rationales than baselines trained for prediction only. We further contribute a set of reference expert annotations to the validation and testing partitions of an existing benchmark dataset of European Court of Human Rights cases.

Previous works on Treatment Effect Estimation (TEE) are not in widespread use because they are predominantly theoretical, where strong parametric assumptions are made but untractable for practical application. Recent work uses multilayer perceptron (MLP) for modeling casual relationships, however, MLPs lag far behind recent advances in ML methodology, which limits their applicability and generalizability. To extend beyond the single domain formulation and towards more realistic learning scenarios, we explore model design spaces beyond MLPs, i.e., transformer backbones, which provide flexibility where attention layers govern interactions among treatments and covariates to exploit structural similarities of potential outcomes for confounding control. Through careful model design, Transformers as Treatment Effect Estimators (TransTEE) is proposed. We show empirically that TransTEE can: (1) serve as a general purpose treatment effect estimator that significantly outperforms competitive baselines in a variety of challenging TEE problems (e.g., discrete, continuous, structured, or dosage-associated treatments) and is applicable to both when covariates are tabular and when they consist of structural data (e.g., texts, graphs); (2) yield multiple advantages: compatibility with propensity score modeling, parameter efficiency, robustness to continuous treatment value distribution shifts, explainable in covariate adjustment, and real-world utility in auditing pre-trained language models

Commonsense causality reasoning (CCR) aims at identifying plausible causes and effects in natural language descriptions that are deemed reasonable by an average person. Although being of great academic and practical interest, this problem is still shadowed by the lack of a well-posed theoretical framework; existing work usually relies on deep language models wholeheartedly, and is potentially susceptible to confounding co-occurrences. Motivated by classical causal principles, we articulate the central question of CCR and draw parallels between human subjects in observational studies and natural languages to adopt CCR to the potential-outcomes framework, which is the first such attempt for commonsense tasks. We propose a novel framework, ROCK, to Reason O(A)bout Commonsense K(C)ausality, which utilizes temporal signals as incidental supervision, and balances confounding effects using temporal propensities that are analogous to propensity scores. The ROCK implementation is modular and zero-shot, and demonstrates good CCR capabilities.

Existing open-domain dialog models are generally trained to minimize the perplexity of target human responses. However, some human replies are more engaging than others, spawning more followup interactions. Current conversational models are increasingly capable of producing turns that are context-relevant, but in order to produce compelling agents, these models need to be able to predict and optimize for turns that are genuinely engaging. We leverage social media feedback data (number of replies and upvotes) to build a large-scale training dataset for feedback prediction. To alleviate possible distortion between the feedback and engagingness, we convert the ranking problem to a comparison of response pairs which involve few confounding factors. We trained DialogRPT, a set of GPT-2 based models on 133M pairs of human feedback data and the resulting ranker outperformed several baselines. Particularly, our ranker outperforms the conventional dialog perplexity baseline with a large margin on predicting Reddit feedback. We finally combine the feedback prediction models and a human-like scoring model to rank the machine-generated dialog responses. Crowd-sourced human evaluation shows that our ranking method correlates better with real human preferences than baseline models.

Algorithmic approaches to interpreting machine learning models have proliferated in recent years. We carry out human subject tests that are the first of their kind to isolate the effect of algorithmic explanations on a key aspect of model interpretability, simulatability, while avoiding important confounding experimental factors. A model is simulatable when a person can predict its behavior on new inputs. Through two kinds of simulation tests involving text and tabular data, we evaluate five explanations methods: (1) LIME, (2) Anchor, (3) Decision Boundary, (4) a Prototype model, and (5) a Composite approach that combines explanations from each method. Clear evidence of method effectiveness is found in very few cases: LIME improves simulatability in tabular classification, and our Prototype method is effective in counterfactual simulation tests. We also collect subjective ratings of explanations, but we do not find that ratings are predictive of how helpful explanations are. Our results provide the first reliable and comprehensive estimates of how explanations influence simulatability across a variety of explanation methods and data domains. We show that (1) we need to be careful about the metrics we use to evaluate explanation methods, and (2) there is significant room for improvement in current methods. All our supporting code, data, and models are publicly available at: https://github.com/peterbhase/InterpretableNLP-ACL2020

Social bias in machine learning has drawn significant attention, with work ranging from demonstrations of bias in a multitude of applications, curating definitions of fairness for different contexts, to developing algorithms to mitigate bias. In natural language processing, gender bias has been shown to exist in context-free word embeddings. Recently, contextual word representations have outperformed word embeddings in several downstream NLP tasks. These word representations are conditioned on their context within a sentence, and can also be used to encode the entire sentence. In this paper, we analyze the extent to which state-of-the-art models for contextual word representations, such as BERT and GPT-2, encode biases with respect to gender, race, and intersectional identities. Towards this, we propose assessing bias at the contextual word level. This novel approach captures the contextual effects of bias missing in context-free word embeddings, yet avoids confounding effects that underestimate bias at the sentence encoding level. We demonstrate evidence of bias at the corpus level, find varying evidence of bias in embedding association tests, show in particular that racial bias is strongly encoded in contextual word models, and observe that bias effects for intersectional minorities are exacerbated beyond their constituent minority identities. Further, evaluating bias effects at the contextual word level captures biases that are not captured at the sentence level, confirming the need for our novel approach.

Extracting causal relationships from observed correlations is a growing area in probabilistic reasoning, originating with the seminal work of Pearl and others from the early 1990s. This paper develops a new, categorically oriented view based on a clear distinction between syntax (string diagrams) and semantics (stochastic matrices), connected via interpretations as structure-preserving functors. A key notion in the identification of causal effects is that of an intervention, whereby a variable is forcefully set to a particular value independent of any prior propensities. We represent the effect of such an intervention as an endofunctor which performs `string diagram surgery' within the syntactic category of string diagrams. This diagram surgery in turn yields a new, interventional distribution via the interpretation functor. While in general there is no way to compute interventional distributions purely from observed data, we show that this is possible in certain special cases using a calculational tool called comb disintegration. We demonstrate the use of this technique on a well-known toy example, where we predict the causal effect of smoking on cancer in the presence of a confounding common cause. After developing this specific example, we show this technique provides simple sufficient conditions for computing interventions which apply to a wide variety of situations considered in the causal inference literature.

Estimating causal effect using machine learning (ML) algorithms can help to relax functional form assumptions if used within appropriate frameworks. However, most of these frameworks assume settings with cross-sectional data, whereas researchers often have access to panel data, which in traditional methods helps to deal with unobserved heterogeneity between units. In this paper, we explore how we can adapt double/debiased machine learning (DML) (Chernozhukov et al., 2018) for panel data in the presence of unobserved heterogeneity. This adaptation is challenging because DML's cross-fitting procedure assumes independent data and the unobserved heterogeneity is not necessarily additively separable in settings with nonlinear observed confounding. We assess the performance of several intuitively appealing estimators in a variety of simulations. While we find violations of the cross-fitting assumptions to be largely inconsequential for the accuracy of the effect estimates, many of the considered methods fail to adequately account for the presence of unobserved heterogeneity. However, we find that using predictive models based on the correlated random effects approach (Mundlak, 1978) within DML leads to accurate coefficient estimates across settings, given a sample size that is large relative to the number of observed confounders. We also show that the influence of the unobserved heterogeneity on the observed confounders plays a significant role for the performance of most alternative methods.

Existing machine learning methods for causal inference usually estimate quantities expressed via the mean of potential outcomes (e.g., average treatment effect). However, such quantities do not capture the full information about the distribution of potential outcomes. In this work, we estimate the density of potential outcomes after interventions from observational data. For this, we propose a novel, fully-parametric deep learning method called Interventional Normalizing Flows. Specifically, we combine two normalizing flows, namely (i) a nuisance flow for estimating nuisance parameters and (ii) a target flow for parametric estimation of the density of potential outcomes. We further develop a tractable optimization objective based on a one-step bias correction for efficient and doubly robust estimation of the target flow parameters. As a result, our Interventional Normalizing Flows offer a properly normalized density estimator. Across various experiments, we demonstrate that our Interventional Normalizing Flows are expressive and highly effective, and scale well with both sample size and high-dimensional confounding. To the best of our knowledge, our Interventional Normalizing Flows are the first proper fully-parametric, deep learning method for density estimation of potential outcomes.

AI agents hold the potential to revolutionize scientific productivity by automating literature reviews, replicating experiments, analyzing data, and even proposing new directions of inquiry; indeed, there are now many such agents, ranging from general-purpose "deep research" systems to specialized science-specific agents, such as AI Scientist and AIGS. Rigorous evaluation of these agents is critical for progress. Yet existing benchmarks fall short on several fronts: they (1) fail to provide holistic, product-informed measures of real-world use cases such as science research; (2) lack reproducible agent tools necessary for a controlled comparison of core agentic capabilities; (3) do not account for confounding variables such as model cost and tool access; (4) do not provide standardized interfaces for quick agent prototyping and evaluation; and (5) lack comprehensive baseline agents necessary to identify true advances. In response, we define principles and tooling for more rigorously benchmarking agents. Using these, we present AstaBench, a suite that provides the first holistic measure of agentic ability to perform scientific research, comprising 2400+ problems spanning the entire scientific discovery process and multiple scientific domains, and including many problems inspired by actual user requests to deployed Asta agents. Our suite comes with the first scientific research environment with production-grade search tools that enable controlled, reproducible evaluation, better accounting for confounders. Alongside, we provide a comprehensive suite of nine science-optimized classes of Asta agents and numerous baselines. Our extensive evaluation of 57 agents across 22 agent classes reveals several interesting findings, most importantly that despite meaningful progress on certain individual aspects, AI remains far from solving the challenge of science research assistance.

Reward modelling from preference data is a crucial step in aligning large language models (LLMs) with human values, requiring robust generalisation to novel prompt-response pairs. In this work, we propose to frame this problem in a causal paradigm, providing the rich toolbox of causality to identify the persistent challenges, such as causal misidentification, preference heterogeneity, and confounding due to user-specific factors. Inheriting from the literature of causal inference, we identify key assumptions necessary for reliable generalisation and contrast them with common data collection practices. We illustrate failure modes of naive reward models and demonstrate how causally-inspired approaches can improve model robustness. Finally, we outline desiderata for future research and practices, advocating targeted interventions to address inherent limitations of observational data.