Treatment Effect

Time-varying counterfactual prediction (TCP) from observational data supports the answer of when and how to assign multiple sequential treatments, yielding importance in various applications. Despite the progress achieved by recent advances, e.g., LSTM or Transformer based causal approaches, their capability of capturing interactions in long sequences remains to be improved in both prediction performance and running efficiency. In parallel with the development of TCP, the success of the state-space models (SSMs) has achieved remarkable progress toward long-sequence modeling with saved running time. Consequently, studying how Mamba simultaneously benefits the effectiveness and efficiency of TCP becomes a compelling research direction. In this paper, we propose to exploit advantages of the SSMs to tackle the TCP task, by introducing a counterfactual Mamba model with Covariate-based Decorrelation towards Selective Parameters (Mamba-CDSP). Motivated by the over-balancing problem in TCP of the direct covariate balancing methods, we propose to de-correlate between the current treatment and the representation of historical covariates, treatments, and outcomes, which can mitigate the confounding bias while preserve more covariate information. In addition, we show that the overall de-correlation in TCP is equivalent to regularizing the selective parameters of Mamba over each time step, which leads our approach to be effective and lightweight. We conducted extensive experiments on both synthetic and real-world datasets, demonstrating that Mamba-CDSP not only outperforms baselines by a large margin, but also exhibits prominent running efficiency.

Causal inference from observational data has attracted considerable attention among researchers. One main obstacle is the handling of confounders. As direct measurement of confounders may not be feasible, recent methods seek to address the confounding bias via proxy variables, i.e., covariates postulated to be conducive to the inference of latent confounders. However, the selected proxies may scramble both confounders and post-treatment variables in practice, which risks biasing the estimation by controlling for variables affected by the treatment. In this paper, we systematically investigate the bias due to latent post-treatment variables, i.e., latent post-treatment bias, in causal effect estimation. Specifically, we first derive the bias when selected proxies scramble both latent confounders and post-treatment variables, which we demonstrate can be arbitrarily bad. We then propose a Confounder-identifiable VAE (CiVAE) to address the bias. Based on a mild assumption that the prior of latent variables that generate the proxy belongs to a general exponential family with at least one invertible sufficient statistic in the factorized part, CiVAE individually identifies latent confounders and latent post-treatment variables up to bijective transformations. We then prove that with individual identification, the intractable disentanglement problem of latent confounders and post-treatment variables can be transformed into a tractable independence test problem despite arbitrary dependence may exist among them. Finally, we prove that the true causal effects can be unbiasedly estimated with transformed confounders inferred by CiVAE. Experiments on both simulated and real-world datasets demonstrate significantly improved robustness of CiVAE.

We address the individualized treatment effect (ITE) estimation problem, focusing on continuous, multidimensional, and time-dependent treatments for precision medicine. The central challenge lies in modeling these complex treatment scenarios while capturing dynamic patient responses and minimizing reliance on control data. We propose the Gaussian Mixture Counterfactual Generator (GMCG), a generative model that transforms the Gaussian mixture model—traditionally a tool for clustering and density estimation—into a new tool explicitly geared toward causal inference. This approach generates robust counterfactuals by effectively handling continuous and multidimensional treatment spaces. We evaluate GMCG on synthetic crossover trial data and simulated datasets, demonstrating its superior performance over existing methods, particularly in scenarios with limited control data. GMCG derives its effectiveness from modeling the joint distribution of covariates, treatments, and outcomes using a latent state vector while employing a conditional distribution of the state vector to suppress confounding and isolate treatment-outcome relationships.

Networked interference, also known as the peer effect in social science and spillover effect in economics, has drawn increasing interest across various domains. This phenomenon arises when a unit’s treatment and outcome are influenced by the actions of its peers, posing significant challenges to causal inference, particularly in treatment assignment and effect estimation in real applications, due to the violation of the SUTVA assumption. While extensive graph models have been developed to identify treatment effects, these models often rely on structural assumptions about networked interference, assuming it to be identical to the social network, which can lead to misspecification issues in real applications. To address these challenges, we propose an Interference-Agnostic Causal Graph Transformer (CauGramer), which aggregates peers information via $L$-order Graph Transformer and employs cross-attention to infer aggregation function for learning interference representations. By integrating confounder balancing and minimax moment constraints, CauGramer fully incorporates peer information, enabling robust treatment effect estimation. Extensive experiments on two widely-used benchmarks demonstrate the effectiveness and superiority of CauGramer. The code is available at https://github.com/anpwu/CauGramer.

In gradient descent dynamics of neural networks, the top eigenvalue of the Hessian of the loss (sharpness) displays a variety of robust phenomena throughout training. This includes early time regimes where the sharpness may decrease during early periods of training (sharpness reduction), and later time behavior such as progressive sharpening and edge of stability. We demonstrate that a simple -layer linear network (UV model) trained on a single training example exhibits all of the essential sharpness phenomenology observed in real-world scenarios. By analyzing the structure of dynamical fixed points in function space and the vector field of function updates, we uncover the underlying mechanisms behind these sharpness trends. Our analysis reveals (i) the mechanism behind early sharpness reduction and progressive sharpening, (ii) the required conditions for edge of stability, and (iii) a period-doubling route to chaos on the edge of stability manifold as learning rate is increased. Finally, we demonstrate that various predictions from this simplified model generalize to real-world scenarios and discuss its limitations.

Models of Virtual Cells and Virtual Tissues at single-cell resolution would allow us to test perturbations in silico and accelerate progress in tissue and cell engineering. However, most such models are not rooted in causal inference and as a result, could mistake correlation for causation. We introduce Celcomen, a novel generative graph neural network grounded in mathematical causality to disentangle intra- and inter-cellular gene regulation in spatial transcriptomics and single-cell data. Celcomen can also be prompted by perturbations to generate spatial counterfactuals, thus offering insights into experimentally inaccessible states, with potential applications in human health. We validate the model's disentanglement and identifiability through simulations, and demonstrate its counterfactual predictions in clinically relevant settings, including human glioblastoma and fetal spleen, recovering inflammation-related gene programs post immune system perturbation. Moreover, it supports mechanistic interpretability, as its parameters can be reverse-engineered from observed behavior, making it an accessible model for understanding both neural networks and complex biological systems.

Estimating heterogeneous treatment effects (HTEs) over time is crucial in many disciplines such as personalized medicine. Existing works for this task have mostly focused on *model-based* learners that adapt specific machine-learning models and adjustment mechanisms. In contrast, model-agnostic learners - so-called *meta-learners* - are largely unexplored. In our paper, we propose several meta-learners that are model-agnostic and thus can be used in combination with arbitrary machine learning models (e.g., transformers) to estimate HTEs over time. We then provide a comprehensive theoretical analysis that characterizes the different learners and that allows us to offer insights into when specific learners are preferable. Furthermore, we propose a novel IVW-DR-learner that (i) uses a doubly robust (DR) and orthogonal loss; and (ii) leverages inverse-variance weights (IVWs) that we derive to stabilize the DR-loss over time. Our IVWs downweight extreme trajectories due to *products* of inverse-propensities in the DR-loss, resulting in a lower estimation variance. Our IVW-DR-learner achieves superior performance in our experiments, particularly in regimes with low overlap and long time horizons.

We study Bayesian neural networks (BNNs) in the theoretical limits of infinitely increasing number of training examples, network width and input space dimension. Our findings establish new bridges between kernel-theoretic approaches and techniques derived from statistical mechanics through the correspondence between Mercer's eigenvalues and limiting spectral distributions of covariance matrices studied in random matrix theory. Our theoretical contributions first consist in novel integral formulas that accurately describe the predictors of BNNs in the asymptotic linear-width and sublinear-width regimes. Moreover, we extend the recently developed renormalisation theory of deep linear neural networks, enabling a rigorous explanation of the mounting empirical evidence that hints at the theory's applicability to nonlinear BNNs with ReLU activations in the linear-width regime. From a practical standpoint, our results introduce a novel technique for estimating the predictor statistics of a trained BNN that is applicable to the sublinear-width regime where the predictions of the renormalisation theory are inaccurate.

Constructing confidence intervals (CIs) for the average treatment effect (ATE) from patient records is crucial to assess the effectiveness and safety of drugs. However, patient records typically come from different hospitals, thus raising the question of how multiple observational/experimental datasets can be effectively combined for this purpose. In our paper, we propose a new method that estimates the ATE from multiple observational/experimental datasets and provides valid CIs. Our method makes little assumptions about the observational datasets and is thus widely applicable in medical practice. The key idea of our method is that we leverage prediction-powered inferences and thereby essentially `shrink' the CIs so that we offer more precise uncertainty quantification as compared to na{\"i}ve approaches. We further prove the unbiasedness of our method and the validity of our CIs. We confirm our theoretical results through various numerical experiments.

Practical and ethical constraints often require the use of observational data for causal inference, particularly in medicine and social sciences. Yet, observational datasets are prone to confounding, potentially compromising the validity of causal conclusions. While it is possible to correct for biases if the underlying causal graph is known, this is rarely a feasible ask in practical scenarios. A common strategy is to adjust for all available covariates, yet this approach can yield biased treatment effect estimates, especially when post-treatment or unobserved variables are present. We propose RAMEN, an algorithm that produces unbiased treatment effect estimates by leveraging the heterogeneity of multiple data sources without the need to know or learn the underlying causal graph. Notably, RAMEN achieves *doubly robust identification*: it can identify the treatment effect whenever the causal parents of the treatment or those of the outcome are observed, and the node whose parents are observed satisfies an invariance assumption. Empirical evaluations across synthetic, semi-synthetic, and real-world datasets show that our approach significantly outperforms existing methods.

Recently, scaling images to high resolution has received much attention in multimodal large language models (MLLMs). Most existing practices adopt a sliding-window-style cropping strategy to adapt to resolution increase. Such a cropping strategy, however, can easily cut off objects and connected regions, which introduces semantic discontinuity and therefore impedes MLLMs from recognizing small or irregularly shaped objects or text, leading to a phenomenon we call the semantic sawtooth effect. This effect is particularly evident in lightweight MLLMs. To address this issue, we introduce a Complementary Image Pyramid (CIP), a simple, effective, and plug-and-play solution designed to mitigate semantic discontinuity during high-resolution image processing. In particular, CIP dynamically constructs an image pyramid to provide complementary semantic information for the cropping-based MLLMs, enabling it rich acquire semantics at all levels. Furthermore, we introduce a Scale Compression Mechanism (SCM) to reduce the additional computational overhead by compressing the redundant visual tokens. Our experiments demonstrate that CIP can consistently enhance the performance across diverse architectures (e.g., MiniCPM-V-2, InternVL2, and LLaVA-OneVision), various model capacity (1B$\rightarrow$8B), and different usage configurations (training-free and fine-tuning). Leveraging the proposed CIP and SCM, we introduce a lightweight MLLM, Mini-Monkey, which achieves remarkable performance in both general multimodal understanding and document understanding. On the OCRBench, the 2B-version Mini-Monkey even surpasses the 8B model InternVL2-8B by 12 score. Additionally, training Mini-Monkey is cheap, requiring only eight RTX 3090 GPUs. Code and models are available at https://github.com/Yuliang-Liu/Monkey.

Problems in fields such as healthcare, robotics, and finance requires reasoning about the value both of what decision or action to take and when to take it. The prevailing hope is that artificial intelligence will support such decisions by estimating the causal effect of policies such as how to treat patients or how to allocate resources over time. However, existing methods for estimating the effect of a policy struggle with \emph{irregular time}. They either discretize time, or disregard the effect of timing policies. We present a new deep-Q algorithm that estimates the effect of both when and what to do called Earliest Disagreement Q-Evaluation (EDQ). EDQ makes use of recursion for the Q-function that is compatible with flexible sequence models, such as transformers. EDQ provides accurate estimates under standard assumptions. We validate the approach through experiments on survival time and tumor growth tasks.

Patient data is widely used to estimate heterogeneous treatment effects and understand the effectiveness and safety of drugs. Yet, patient data includes highly sensitive information that must be kept private. In this work, we aim to estimate the conditional average treatment effect (CATE) from observational data under differential privacy. Specifically, we present DP-CATE, a novel framework for CATE estimation that is *Neyman-orthogonal* and ensures *differential privacy* of the estimates. Our framework is highly general: it applies to any two-stage CATE meta-learner with a Neyman-orthogonal loss function and any machine learning model can be used for nuisance estimation. We further provide an extension of our DP-CATE, where we employ RKHS regression to release the complete CATE function while ensuring differential privacy. We demonstrate the effectiveness of DP-CATE across various experiments using synthetic and real-world datasets. To the best of our knowledge, we are the first to provide a framework for CATE estimation that is doubly robust and differentially private.

While Large Language Models (LLMs) excel at in-context learning (ICL) using just a few demonstrations, their performances are sensitive to demonstration orders. The reasons behind this sensitivity remain poorly understood. In this paper, we investigate the prompt embedding space to bridge the gap between the order sensitivity of ICL with inner workings of decoder-only LLMs, uncovering the clustering property: prompts sharing the first and last demonstrations have closer embeddings, with first-demonstration clustering usually being stronger in practice. We explain this property through extensive theoretical analyses and empirical evidences. Our finding suggests that the positional encoding and the causal attention mask are key contributors to the clustering phenomenon. Leveraging this clustering insight, we introduce Cluster-based Search, a novel method that accelerates the selection and ordering of demonstrations in self-adaptive ICL settings. Our approach substantially decreases the time complexity from factorial to quadratic, saving 92% to nearly 100% execution time while maintaining comparable performance to exhaustive search.

We consider time to treatment initialization. This can commonly occur in preventive medicine, such as disease screening and vaccination; it can also occur with non-fatal health conditions such as HIV infection without the onset of AIDS. While traditional causal inference focused on ‘when to treat’ and its effects, including their possible dependence on subject characteristics, we consider the incremental causal effect when the intensity of time to treatment initialization is intervened upon. We provide identification of the incremental causal effect without the commonly required positivity assumption, as well as an estimation framework using inverse probability weighting. We illustrate our approach via simulation, and apply it to a rheumatoid arthritis study to evaluate the incremental effect of time to start methotrexate on joint pain.

Machine learning is increasingly used to select which individuals receive limited-resource interventions in domains such as human services, education, development, and more. However, it is often not apparent what the right quantity is for models to predict. In particular, policymakers rarely have access to data from a randomized controlled trial (RCT) that would enable accurate estimates of treatment effects -- which individuals would benefit more from the intervention. Observational data is more likely to be available, creating a substantial risk of bias in treatment effect estimates. Practitioners instead commonly use a technique termed "risk-based targeting" where the model is just used to predict each individual's status quo outcome (an easier, non-causal task). Those with higher predicted risk are offered treatment. There is currently almost no empirical evidence to inform which choices lead to the most effect machine learning-informed targeting strategies in social domains. In this work, we use data from 5 real-world RCTs in a variety of domains to empirically assess such choices. We find that when treatment effects can be estimated reliably (which we simulate by using direct outcome observations), treatment effect based targeting substantially outperforms risk-based targeting, even when treatment effect estimates are biased. Moreover, these results hold even when the policymaker has strong normative preferences for assisting higher-risk individuals. However, when treatment effects must be predicted from features alone (as is always the case in practice), performance can degrade significantly due to limited data making it difficult to learn accurate mappings from features to treatment effects. Our results suggest treatment effect targeting has significant potential benefits, but realizing these benefits requires careful attention to model training and validation.