Daily Papers

A major barrier to deploying current machine learning models lies in their non-reliability to dataset shifts. To resolve this problem, most existing studies attempted to transfer stable information to unseen environments. Particularly, independent causal mechanisms-based methods proposed to remove mutable causal mechanisms via the do-operator. Compared to previous methods, the obtained stable predictors are more effective in identifying stable information. However, a key question remains: which subset of this whole stable information should the model transfer, in order to achieve optimal generalization ability? To answer this question, we present a comprehensive minimax analysis from a causal perspective. Specifically, we first provide a graphical condition for the whole stable set to be optimal. When this condition fails, we surprisingly find with an example that this whole stable set, although can fully exploit stable information, is not the optimal one to transfer. To identify the optimal subset under this case, we propose to estimate the worst-case risk with a novel optimization scheme over the intervention functions on mutable causal mechanisms. We then propose an efficient algorithm to search for the subset with minimal worst-case risk, based on a newly defined equivalence relation between stable subsets. Compared to the exponential cost of exhaustively searching over all subsets, our searching strategy enjoys a polynomial complexity. The effectiveness and efficiency of our methods are demonstrated on synthetic data and the diagnosis of Alzheimer's disease.

We present a general causal generative modelling framework for accurate estimation of high fidelity image counterfactuals with deep structural causal models. Estimation of interventional and counterfactual queries for high-dimensional structured variables, such as images, remains a challenging task. We leverage ideas from causal mediation analysis and advances in generative modelling to design new deep causal mechanisms for structured variables in causal models. Our experiments demonstrate that our proposed mechanisms are capable of accurate abduction and estimation of direct, indirect and total effects as measured by axiomatic soundness of counterfactuals.

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

Learning causal structure from observational data often assumes that we observe independent and identically distributed (i.\,i.\,d) data. The traditional approach aims to find a graphical representation that encodes the same set of conditional independence relationships as those present in the observed distribution. It is known that under i.\,i.\,d assumption, even with infinite data, there is a limit to how fine-grained a causal structure we can identify. To overcome this limitation, recent work has explored using data originating from different, related environments to learn richer causal structure. These approaches implicitly rely on the independent causal mechanisms (ICM) principle, which postulates that the mechanism giving rise to an effect given its causes and the mechanism which generates the causes do not inform or influence each other. Thus, components of the causal model can independently change from environment to environment. Despite its wide application in machine learning and causal inference, there is a lack of statistical formalization of the ICM principle and how it enables identification of richer causal structures from grouped data. Here we present new causal de Finetti theorems which offer a first statistical formalization of ICM principle and show how causal structure identification is possible from exchangeable data. Our work provides theoretical justification for a broad range of techniques leveraging multi-environment data to learn causal structure.

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.

We address causal reasoning in multivariate time series data generated by stochastic processes. Existing approaches are largely restricted to static settings, ignoring the continuity and emission of variations across time. In contrast, we propose a learning paradigm that directly establishes causation between events in the course of time. We present two key lemmas to compute causal contributions and frame them as reinforcement learning problems. Our approach offers formal and computational tools for uncovering and quantifying causal relationships in diffusion processes, subsuming various important settings such as discrete-time Markov decision processes. Finally, in fairly intricate experiments and through sheer learning, our framework reveals and quantifies causal links, which otherwise seem inexplicable.

Diffusion probabilistic models (DPMs) have become the state-of-the-art in high-quality image generation. However, DPMs have an arbitrary noisy latent space with no interpretable or controllable semantics. Although there has been significant research effort to improve image sample quality, there is little work on representation-controlled generation using diffusion models. Specifically, causal modeling and controllable counterfactual generation using DPMs is an underexplored area. In this work, we propose CausalDiffAE, a diffusion-based causal representation learning framework to enable counterfactual generation according to a specified causal model. Our key idea is to use an encoder to extract high-level semantically meaningful causal variables from high-dimensional data and model stochastic variation using reverse diffusion. We propose a causal encoding mechanism that maps high-dimensional data to causally related latent factors and parameterize the causal mechanisms among latent factors using neural networks. To enforce the disentanglement of causal variables, we formulate a variational objective and leverage auxiliary label information in a prior to regularize the latent space. We propose a DDIM-based counterfactual generation procedure subject to do-interventions. Finally, to address the limited label supervision scenario, we also study the application of CausalDiffAE when a part of the training data is unlabeled, which also enables granular control over the strength of interventions in generating counterfactuals during inference. We empirically show that CausalDiffAE learns a disentangled latent space and is capable of generating high-quality counterfactual images.

Inferring causal structures from experimentation is a central task in many domains. For example, in biology, recent advances allow us to obtain single-cell expression data under multiple interventions such as drugs or gene knockouts. However, the targets of the interventions are often uncertain or unknown and the number of observations limited. As a result, standard causal discovery methods can no longer be reliably used. To fill this gap, we propose a Bayesian framework (BaCaDI) for discovering and reasoning about the causal structure that underlies data generated under various unknown experimental or interventional conditions. BaCaDI is fully differentiable, which allows us to infer the complex joint posterior over the intervention targets and the causal structure via efficient gradient-based variational inference. In experiments on synthetic causal discovery tasks and simulated gene-expression data, BaCaDI outperforms related methods in identifying causal structures and intervention targets.

The principle of independent causal mechanisms (ICM) states that generative processes of real world data consist of independent modules which do not influence or inform each other. While this idea has led to fruitful developments in the field of causal inference, it is not widely-known in the NLP community. In this work, we argue that the causal direction of the data collection process bears nontrivial implications that can explain a number of published NLP findings, such as differences in semi-supervised learning (SSL) and domain adaptation (DA) performance across different settings. We categorize common NLP tasks according to their causal direction and empirically assay the validity of the ICM principle for text data using minimum description length. We conduct an extensive meta-analysis of over 100 published SSL and 30 DA studies, and find that the results are consistent with our expectations based on causal insights. This work presents the first attempt to analyze the ICM principle in NLP, and provides constructive suggestions for future modeling choices. Code available at https://github.com/zhijing-jin/icm4nlp

A faithful and interpretable explanation of an AI model's behavior and internal structure is a high-level explanation that is human-intelligible but also consistent with the known, but often opaque low-level causal details of the model. We argue that the theory of causal abstraction provides the mathematical foundations for the desired kinds of model explanations. In causal abstraction analysis, we use interventions on model-internal states to rigorously assess whether an interpretable high-level causal model is a faithful description of an AI model. Our contributions in this area are: (1) We generalize causal abstraction to cyclic causal structures and typed high-level variables. (2) We show how multi-source interchange interventions can be used to conduct causal abstraction analyses. (3) We define a notion of approximate causal abstraction that allows us to assess the degree to which a high-level causal model is a causal abstraction of a lower-level one. (4) We prove constructive causal abstraction can be decomposed into three operations we refer to as marginalization, variable-merge, and value-merge. (5) We formalize the XAI methods of LIME, causal effect estimation, causal mediation analysis, iterated nullspace projection, and circuit-based explanations as special cases of causal abstraction analysis.

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.

It is commonplace to encounter heterogeneous or nonstationary data, of which the underlying generating process changes across domains or over time. Such a distribution shift feature presents both challenges and opportunities for causal discovery. In this paper, we develop a framework for causal discovery from such data, called Constraint-based causal Discovery from heterogeneous/NOnstationary Data (CD-NOD), to find causal skeleton and directions and estimate the properties of mechanism changes. First, we propose an enhanced constraint-based procedure to detect variables whose local mechanisms change and recover the skeleton of the causal structure over observed variables. Second, we present a method to determine causal orientations by making use of independent changes in the data distribution implied by the underlying causal model, benefiting from information carried by changing distributions. After learning the causal structure, next, we investigate how to efficiently estimate the "driving force" of the nonstationarity of a causal mechanism. That is, we aim to extract from data a low-dimensional representation of changes. The proposed methods are nonparametric, with no hard restrictions on data distributions and causal mechanisms, and do not rely on window segmentation. Furthermore, we find that data heterogeneity benefits causal structure identification even with particular types of confounders. Finally, we show the connection between heterogeneity/nonstationarity and soft intervention in causal discovery. Experimental results on various synthetic and real-world data sets (task-fMRI and stock market data) are presented to demonstrate the efficacy of the proposed methods.

In Causal Bayesian Optimization (CBO), an agent intervenes on an unknown structural causal model to maximize a downstream reward variable. In this paper, we consider the generalization where other agents or external events also intervene on the system, which is key for enabling adaptiveness to non-stationarities such as weather changes, market forces, or adversaries. We formalize this generalization of CBO as Adversarial Causal Bayesian Optimization (ACBO) and introduce the first algorithm for ACBO with bounded regret: Causal Bayesian Optimization with Multiplicative Weights (CBO-MW). Our approach combines a classical online learning strategy with causal modeling of the rewards. To achieve this, it computes optimistic counterfactual reward estimates by propagating uncertainty through the causal graph. We derive regret bounds for CBO-MW that naturally depend on graph-related quantities. We further propose a scalable implementation for the case of combinatorial interventions and submodular rewards. Empirically, CBO-MW outperforms non-causal and non-adversarial Bayesian optimization methods on synthetic environments and environments based on real-word data. Our experiments include a realistic demonstration of how CBO-MW can be used to learn users' demand patterns in a shared mobility system and reposition vehicles in strategic areas.

Conventional supervised learning methods typically assume i.i.d samples and are found to be sensitive to out-of-distribution (OOD) data. We propose Generative Causal Representation Learning (GCRL) which leverages causality to facilitate knowledge transfer under distribution shifts. While we evaluate the effectiveness of our proposed method in human trajectory prediction models, GCRL can be applied to other domains as well. First, we propose a novel causal model that explains the generative factors in motion forecasting datasets using features that are common across all environments and with features that are specific to each environment. Selection variables are used to determine which parts of the model can be directly transferred to a new environment without fine-tuning. Second, we propose an end-to-end variational learning paradigm to learn the causal mechanisms that generate observations from features. GCRL is supported by strong theoretical results that imply identifiability of the causal model under certain assumptions. Experimental results on synthetic and real-world motion forecasting datasets show the robustness and effectiveness of our proposed method for knowledge transfer under zero-shot and low-shot settings by substantially outperforming the prior motion forecasting models on out-of-distribution prediction. Our code is available at https://github.com/sshirahmad/GCRL.

We provide an optimization-based framework to perform counterfactual analysis in a dynamic model with hidden states. Our framework is grounded in the ``abduction, action, and prediction'' approach to answer counterfactual queries and handles two key challenges where (1) the states are hidden and (2) the model is dynamic. Recognizing the lack of knowledge on the underlying causal mechanism and the possibility of infinitely many such mechanisms, we optimize over this space and compute upper and lower bounds on the counterfactual quantity of interest. Our work brings together ideas from causality, state-space models, simulation, and optimization, and we apply it on a breast cancer case study. To the best of our knowledge, we are the first to compute lower and upper bounds on a counterfactual query in a dynamic latent-state model.

Mediation analysis learns the causal effect transmitted via mediator variables between treatments and outcomes and receives increasing attention in various scientific domains to elucidate causal relations. Most existing works focus on point-exposure studies where each subject only receives one treatment at a single time point. However, there are a number of applications (e.g., mobile health) where the treatments are sequentially assigned over time and the dynamic mediation effects are of primary interest. Proposing a reinforcement learning (RL) framework, we are the first to evaluate dynamic mediation effects in settings with infinite horizons. We decompose the average treatment effect into an immediate direct effect, an immediate mediation effect, a delayed direct effect, and a delayed mediation effect. Upon the identification of each effect component, we further develop robust and semi-parametrically efficient estimators under the RL framework to infer these causal effects. The superior performance of the proposed method is demonstrated through extensive numerical studies, theoretical results, and an analysis of a mobile health dataset.

Causal inference is a critical task across fields such as healthcare, economics, and the social sciences. While recent advances in machine learning, especially those based on the deep-learning architectures, have shown potential in estimating causal effects, existing approaches often fall short in handling complex causal structures and lack adaptability across various causal scenarios. In this paper, we present a novel transformer-based method for causal inference that overcomes these challenges. The core innovation of our model lies in its integration of causal Directed Acyclic Graphs (DAGs) directly into the attention mechanism, enabling it to accurately model the underlying causal structure. This allows for flexible estimation of both average treatment effects (ATE) and conditional average treatment effects (CATE). Extensive experiments on both synthetic and real-world datasets demonstrate that our approach surpasses existing methods in estimating causal effects across a wide range of scenarios. The flexibility and robustness of our model make it a valuable tool for researchers and practitioners tackling complex causal inference problems.

For text-based AI systems to interact in the real world, causal reasoning is an essential skill. Since interventional data is costly to generate, we study to what extent an agent can learn causal reasoning from passive data. Specifically, we consider an axiomatic training setup where an agent learns from multiple demonstrations of a causal axiom (or rule), rather than incorporating the axiom as an inductive bias or inferring it from data values. A key question is whether the agent would learn to generalize from the axiom demonstrations to new scenarios. For example, if a transformer model is trained on demonstrations of the causal transitivity axiom over small graphs, would it generalize to applying the transitivity axiom over large graphs? Our results, based on a novel axiomatic training scheme, indicate that such generalization is possible. We consider the task of inferring whether a variable causes another variable, given a causal graph structure. We find that a 67 million parameter transformer model, when trained on linear causal chains (along with some noisy variations) can generalize well to new kinds of graphs, including longer causal chains, causal chains with reversed order, and graphs with branching; even when it is not explicitly trained for such settings. Our model performs at par (or even better) than many larger language models such as GPT-4, Gemini Pro, and Phi-3. Overall, our axiomatic training framework provides a new paradigm of learning causal reasoning from passive data that can be used to learn arbitrary axioms, as long as sufficient demonstrations can be generated.

Answering counterfactual queries has many important applications such as knowledge discovery and explainability, but is challenging when causal variables are unobserved and we only see a projection onto an observation space, for instance, image pixels. One approach is to recover the latent Structural Causal Model (SCM), but this typically needs unrealistic assumptions, such as linearity of the causal mechanisms. Another approach is to use na\"ive ML approximations, such as generative models, to generate counterfactual samples; however, these lack guarantees of accuracy. In this work, we strive to strike a balance between practicality and theoretical guarantees by focusing on a specific type of causal query called domain counterfactuals, which hypothesizes what a sample would have looked like if it had been generated in a different domain (or environment). Concretely, by only assuming invertibility, sparse domain interventions and access to observational data from different domains, we aim to improve domain counterfactual estimation both theoretically and practically with less restrictive assumptions. We define domain counterfactually equivalent models and prove necessary and sufficient properties for equivalent models that provide a tight characterization of the domain counterfactual equivalence classes. Building upon this result, we prove that every equivalence class contains a model where all intervened variables are at the end when topologically sorted by the causal DAG. This surprising result suggests that a model design that only allows intervention in the last k latent variables may improve model estimation for counterfactuals. We then test this model design on extensive simulated and image-based experiments which show the sparse canonical model indeed improves counterfactual estimation over baseline non-sparse models.

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.

Imitation learning suffers from causal confusion. This phenomenon occurs when learned policies attend to features that do not causally influence the expert actions but are instead spuriously correlated. Causally confused agents produce low open-loop supervised loss but poor closed-loop performance upon deployment. We consider the problem of masking observed confounders in a disentangled representation of the observation space. Our novel masking algorithm leverages the usual ability to intervene in the initial system state, avoiding any requirement involving expert querying, expert reward functions, or causal graph specification. Under certain assumptions, we theoretically prove that this algorithm is conservative in the sense that it does not incorrectly mask observations that causally influence the expert; furthermore, intervening on the initial state serves to strictly reduce excess conservatism. The masking algorithm is applied to behavior cloning for two illustrative control systems: CartPole and Reacher.

We explore algorithms to select actions in the causal bandit setting where the learner can choose to intervene on a set of random variables related by a causal graph, and the learner sequentially chooses interventions and observes a sample from the interventional distribution. The learner's goal is to quickly find the intervention, among all interventions on observable variables, that maximizes the expectation of an outcome variable. We depart from previous literature by assuming no knowledge of the causal graph except that latent confounders between the outcome and its ancestors are not present. We first show that the unknown graph problem can be exponentially hard in the parents of the outcome. To remedy this, we adopt an additional additive assumption on the outcome which allows us to solve the problem by casting it as an additive combinatorial linear bandit problem with full-bandit feedback. We propose a novel action-elimination algorithm for this setting, show how to apply this algorithm to the causal bandit problem, provide sample complexity bounds, and empirically validate our findings on a suite of randomly generated causal models, effectively showing that one does not need to explicitly learn the parents of the outcome to identify the best intervention.

Interpreting the inner function of neural networks is crucial for the trustworthy development and deployment of these black-box models. Prior interpretability methods focus on correlation-based measures to attribute model decisions to individual examples. However, these measures are susceptible to noise and spurious correlations encoded in the model during the training phase (e.g., biased inputs, model overfitting, or misspecification). Moreover, this process has proven to result in noisy and unstable attributions that prevent any transparent understanding of the model's behavior. In this paper, we develop a robust interventional-based method grounded by causal analysis to capture cause-effect mechanisms in pre-trained neural networks and their relation to the prediction. Our novel approach relies on path interventions to infer the causal mechanisms within hidden layers and isolate relevant and necessary information (to model prediction), avoiding noisy ones. The result is task-specific causal explanatory graphs that can audit model behavior and express the actual causes underlying its performance. We apply our method to vision models trained on classification tasks. On image classification tasks, we provide extensive quantitative experiments to show that our approach can capture more stable and faithful explanations than standard attribution-based methods. Furthermore, the underlying causal graphs reveal the neural interactions in the model, making it a valuable tool in other applications (e.g., model repair).

Understanding causality should be a core requirement of any attempt to build real impact through AI. Due to the inherent unobservability of counterfactuals, large randomised trials (RCTs) are the standard for causal inference. But large experiments are generically expensive, and randomisation carries its own costs, e.g. when suboptimal decisions are trialed. Recent work has proposed more sample-efficient alternatives to RCTs, but these are not adaptable to the downstream application for which the causal effect is sought. In this work, we develop a task-specific approach to experimental design and derive sampling strategies customised to particular downstream applications. Across a range of important tasks, real-world datasets, and sample sizes, our method outperforms other benchmarks, e.g. requiring an order-of-magnitude less data to match RCT performance on targeted marketing tasks.

We study neural network loss landscapes through the lens of mode connectivity, the observation that minimizers of neural networks retrieved via training on a dataset are connected via simple paths of low loss. Specifically, we ask the following question: are minimizers that rely on different mechanisms for making their predictions connected via simple paths of low loss? We provide a definition of mechanistic similarity as shared invariances to input transformations and demonstrate that lack of linear connectivity between two models implies they use dissimilar mechanisms for making their predictions. Relevant to practice, this result helps us demonstrate that naive fine-tuning on a downstream dataset can fail to alter a model's mechanisms, e.g., fine-tuning can fail to eliminate a model's reliance on spurious attributes. Our analysis also motivates a method for targeted alteration of a model's mechanisms, named connectivity-based fine-tuning (CBFT), which we analyze using several synthetic datasets for the task of reducing a model's reliance on spurious attributes.

It has long been hypothesised that causal reasoning plays a fundamental role in robust and general intelligence. However, it is not known if agents must learn causal models in order to generalise to new domains, or if other inductive biases are sufficient. We answer this question, showing that any agent capable of satisfying a regret bound under a large set of distributional shifts must have learned an approximate causal model of the data generating process, which converges to the true causal model for optimal agents. We discuss the implications of this result for several research areas including transfer learning and causal inference.

Heterogeneity and comorbidity are two interwoven challenges associated with various healthcare problems that greatly hampered research on developing effective treatment and understanding of the underlying neurobiological mechanism. Very few studies have been conducted to investigate heterogeneous causal effects (HCEs) in graphical contexts due to the lack of statistical methods. To characterize this heterogeneity, we first conceptualize heterogeneous causal graphs (HCGs) by generalizing the causal graphical model with confounder-based interactions and multiple mediators. Such confounders with an interaction with the treatment are known as moderators. This allows us to flexibly produce HCGs given different moderators and explicitly characterize HCEs from the treatment or potential mediators on the outcome. We establish the theoretical forms of HCEs and derive their properties at the individual level in both linear and nonlinear models. An interactive structural learning is developed to estimate the complex HCGs and HCEs with confidence intervals provided. Our method is empirically justified by extensive simulations and its practical usefulness is illustrated by exploring causality among psychiatric disorders for trauma survivors.

Effective root cause analysis (RCA) is vital for swiftly restoring services, minimizing losses, and ensuring the smooth operation and management of complex systems. Previous data-driven RCA methods, particularly those employing causal discovery techniques, have primarily focused on constructing dependency or causal graphs for backtracking the root causes. However, these methods often fall short as they rely solely on data from a single modality, thereby resulting in suboptimal solutions. In this work, we propose Mulan, a unified multi-modal causal structure learning method for root cause localization. We leverage a log-tailored language model to facilitate log representation learning, converting log sequences into time-series data. To explore intricate relationships across different modalities, we propose a contrastive learning-based approach to extract modality-invariant and modality-specific representations within a shared latent space. Additionally, we introduce a novel key performance indicator-aware attention mechanism for assessing modality reliability and co-learning a final causal graph. Finally, we employ random walk with restart to simulate system fault propagation and identify potential root causes. Extensive experiments on three real-world datasets validate the effectiveness of our proposed framework.

Recovering causal relationships from data is an important problem. Using observational data, one can typically only recover causal graphs up to a Markov equivalence class and additional assumptions or interventional data are needed for complete recovery. In this work, under some standard assumptions, we study causal graph discovery via adaptive interventions with node-dependent interventional costs. For this setting, we show that no algorithm can achieve an approximation guarantee that is asymptotically better than linear in the number of vertices with respect to the verification number; a well-established benchmark for adaptive search algorithms. Motivated by this negative result, we define a new benchmark that captures the worst-case interventional cost for any search algorithm. Furthermore, with respect to this new benchmark, we provide adaptive search algorithms that achieve logarithmic approximations under various settings: atomic, bounded size interventions and generalized cost objectives.

Conventional causal discovery methods rely on centralized data, which is inconsistent with the decentralized nature of data in many real-world situations. This discrepancy has motivated the development of federated causal discovery (FCD) approaches. However, existing FCD methods may be limited by their potentially restrictive assumptions of identifiable functional causal models or homogeneous data distributions, narrowing their applicability in diverse scenarios. In this paper, we propose a novel FCD method attempting to accommodate arbitrary causal models and heterogeneous data. We first utilize a surrogate variable corresponding to the client index to account for the data heterogeneity across different clients. We then develop a federated conditional independence test (FCIT) for causal skeleton discovery and establish a federated independent change principle (FICP) to determine causal directions. These approaches involve constructing summary statistics as a proxy of the raw data to protect data privacy. Owing to the nonparametric properties, FCIT and FICP make no assumption about particular functional forms, thereby facilitating the handling of arbitrary causal models. We conduct extensive experiments on synthetic and real datasets to show the efficacy of our method. The code is available at https://github.com/lokali/FedCDH.git.

Transfer learning has recently become the dominant paradigm of machine learning. Pre-trained models fine-tuned for downstream tasks achieve better performance with fewer labelled examples. Nonetheless, it remains unclear how to develop models that specialise towards multiple tasks without incurring negative interference and that generalise systematically to non-identically distributed tasks. Modular deep learning has emerged as a promising solution to these challenges. In this framework, units of computation are often implemented as autonomous parameter-efficient modules. Information is conditionally routed to a subset of modules and subsequently aggregated. These properties enable positive transfer and systematic generalisation by separating computation from routing and updating modules locally. We offer a survey of modular architectures, providing a unified view over several threads of research that evolved independently in the scientific literature. Moreover, we explore various additional purposes of modularity, including scaling language models, causal inference, programme induction, and planning in reinforcement learning. Finally, we report various concrete applications where modularity has been successfully deployed such as cross-lingual and cross-modal knowledge transfer. Related talks and projects to this survey, are available at https://www.modulardeeplearning.com/.

Current Reinforcement Learning (RL) methods often suffer from sample-inefficiency, resulting from blind exploration strategies that neglect causal relationships among states, actions, and rewards. Although recent causal approaches aim to address this problem, they lack grounded modeling of reward-guided causal understanding of states and actions for goal-orientation, thus impairing learning efficiency. To tackle this issue, we propose a novel method named Causal Information Prioritization (CIP) that improves sample efficiency by leveraging factored MDPs to infer causal relationships between different dimensions of states and actions with respect to rewards, enabling the prioritization of causal information. Specifically, CIP identifies and leverages causal relationships between states and rewards to execute counterfactual data augmentation to prioritize high-impact state features under the causal understanding of the environments. Moreover, CIP integrates a causality-aware empowerment learning objective, which significantly enhances the agent's execution of reward-guided actions for more efficient exploration in complex environments. To fully assess the effectiveness of CIP, we conduct extensive experiments across 39 tasks in 5 diverse continuous control environments, encompassing both locomotion and manipulation skills learning with pixel-based and sparse reward settings. Experimental results demonstrate that CIP consistently outperforms existing RL methods across a wide range of scenarios.

Convergent Cross Mapping (CCM) is a powerful method for detecting causality in coupled nonlinear dynamical systems, providing a model-free approach to capture dynamic causal interactions. Partial Cross Mapping (PCM) was introduced as an extension of CCM to address indirect causality in three-variable systems by comparing cross-mapping quality between direct cause-effect mapping and indirect mapping through an intermediate conditioning variable. However, PCM remains limited to univariate delay embeddings in its cross-mapping processes. In this work, we extend PCM to the multivariate setting, introducing multiPCM, which leverages multivariate embeddings to more effectively distinguish indirect causal relationships. We further propose a multivariate cross-mapping framework (MXMap) for causal discovery in dynamical systems. This two-phase framework combines (1) pairwise CCM tests to establish an initial causal graph and (2) multiPCM to refine the graph by pruning indirect causal connections. Through experiments on simulated data and the ERA5 Reanalysis weather dataset, we demonstrate the effectiveness of MXMap. Additionally, MXMap is compared against several baseline methods, showing advantages in accuracy and causal graph refinement.

We study the problem of model selection in causal inference, specifically for the case of conditional average treatment effect (CATE) estimation under binary treatments. Unlike model selection in machine learning, there is no perfect analogue of cross-validation as we do not observe the counterfactual potential outcome for any data point. Towards this, there have been a variety of proxy metrics proposed in the literature, that depend on auxiliary nuisance models estimated from the observed data (propensity score model, outcome regression model). However, the effectiveness of these metrics has only been studied on synthetic datasets as we can access the counterfactual data for them. We conduct an extensive empirical analysis to judge the performance of these metrics introduced in the literature, and novel ones introduced in this work, where we utilize the latest advances in generative modeling to incorporate multiple realistic datasets. Our analysis suggests novel model selection strategies based on careful hyperparameter tuning of CATE estimators and causal ensembling.

Causal discovery, i.e., inferring underlying cause-effect relationships from observations of a scene or system, is an inherent mechanism in human cognition, but has been shown to be highly challenging to automate. The majority of approaches in the literature aiming for this task consider constrained scenarios with fully observed variables or data from stationary time-series. In this work we aim for causal discovery in a more general class of scenarios, scenes with non-stationary behavior over time. For our purposes we here regard a scene as a composition objects interacting with each other over time. Non-stationarity is modeled as stationarity conditioned on an underlying variable, a state, which can be of varying dimension, more or less hidden given observations of the scene, and also depend more or less directly on these observations. We propose a probabilistic deep learning approach called State-Dependent Causal Inference (SDCI) for causal discovery in such conditionally stationary time-series data. Results in two different synthetic scenarios show that this method is able to recover the underlying causal dependencies with high accuracy even in cases with hidden states.

We tackle the challenge of large-scale network intervention for guiding excitatory point processes, such as infectious disease spread or traffic congestion control. Our model-based reinforcement learning utilizes neural ODEs to capture how the networked excitatory point processes will evolve subject to the time-varying changes in network topology. Our approach incorporates Gradient-Descent based Model Predictive Control (GD-MPC), offering policy flexibility to accommodate prior knowledge and constraints. To address the intricacies of planning and overcome the high dimensionality inherent to such decision-making problems, we design an Amortize Network Interventions (ANI) framework, allowing for the pooling of optimal policies from history and other contexts, while ensuring a permutation equivalent property. This property enables efficient knowledge transfer and sharing across diverse contexts. Our approach has broad applications, from curbing infectious disease spread to reducing carbon emissions through traffic light optimization, and thus has the potential to address critical societal and environmental challenges.

Mechanistic interpretability seeks to understand the internal mechanisms of machine learning models, where localization -- identifying the important model components -- is a key step. Activation patching, also known as causal tracing or interchange intervention, is a standard technique for this task (Vig et al., 2020), but the literature contains many variants with little consensus on the choice of hyperparameters or methodology. In this work, we systematically examine the impact of methodological details in activation patching, including evaluation metrics and corruption methods. In several settings of localization and circuit discovery in language models, we find that varying these hyperparameters could lead to disparate interpretability results. Backed by empirical observations, we give conceptual arguments for why certain metrics or methods may be preferred. Finally, we provide recommendations for the best practices of activation patching going forwards.

We develop a method for generating causal post-hoc explanations of black-box classifiers based on a learned low-dimensional representation of the data. The explanation is causal in the sense that changing learned latent factors produces a change in the classifier output statistics. To construct these explanations, we design a learning framework that leverages a generative model and information-theoretic measures of causal influence. Our objective function encourages both the generative model to faithfully represent the data distribution and the latent factors to have a large causal influence on the classifier output. Our method learns both global and local explanations, is compatible with any classifier that admits class probabilities and a gradient, and does not require labeled attributes or knowledge of causal structure. Using carefully controlled test cases, we provide intuition that illuminates the function of our objective. We then demonstrate the practical utility of our method on image recognition tasks.

Interpretability provides a toolset for understanding how and why neural networks behave in certain ways. However, there is little unity in the field: most studies employ ad-hoc evaluations and do not share theoretical foundations, making it difficult to measure progress and compare the pros and cons of different techniques. Furthermore, while mechanistic understanding is frequently discussed, the basic causal units underlying these mechanisms are often not explicitly defined. In this paper, we propose a perspective on interpretability research grounded in causal mediation analysis. Specifically, we describe the history and current state of interpretability taxonomized according to the types of causal units (mediators) employed, as well as methods used to search over mediators. We discuss the pros and cons of each mediator, providing insights as to when particular kinds of mediators and search methods are most appropriate depending on the goals of a given study. We argue that this framing yields a more cohesive narrative of the field, as well as actionable insights for future work. Specifically, we recommend a focus on discovering new mediators with better trade-offs between human-interpretability and compute-efficiency, and which can uncover more sophisticated abstractions from neural networks than the primarily linear mediators employed in current work. We also argue for more standardized evaluations that enable principled comparisons across mediator types, such that we can better understand when particular causal units are better suited to particular use cases.

Causal abstraction is a promising theoretical framework for explainable artificial intelligence that defines when an interpretable high-level causal model is a faithful simplification of a low-level deep learning system. However, existing causal abstraction methods have two major limitations: they require a brute-force search over alignments between the high-level model and the low-level one, and they presuppose that variables in the high-level model will align with disjoint sets of neurons in the low-level one. In this paper, we present distributed alignment search (DAS), which overcomes these limitations. In DAS, we find the alignment between high-level and low-level models using gradient descent rather than conducting a brute-force search, and we allow individual neurons to play multiple distinct roles by analyzing representations in non-standard bases-distributed representations. Our experiments show that DAS can discover internal structure that prior approaches miss. Overall, DAS removes previous obstacles to conducting causal abstraction analyses and allows us to find conceptual structure in trained neural nets.

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.

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.

Causal representation learning seeks to extract high-level latent factors from low-level sensory data. Most existing methods rely on observational data and structural assumptions (e.g., conditional independence) to identify the latent factors. However, interventional data is prevalent across applications. Can interventional data facilitate causal representation learning? We explore this question in this paper. The key observation is that interventional data often carries geometric signatures of the latent factors' support (i.e. what values each latent can possibly take). For example, when the latent factors are causally connected, interventions can break the dependency between the intervened latents' support and their ancestors'. Leveraging this fact, we prove that the latent causal factors can be identified up to permutation and scaling given data from perfect do interventions. Moreover, we can achieve block affine identification, namely the estimated latent factors are only entangled with a few other latents if we have access to data from imperfect interventions. These results highlight the unique power of interventional data in causal representation learning; they can enable provable identification of latent factors without any assumptions about their distributions or dependency structure.

We investigate causal computations taking sequences of inputs to sequences of outputs where the nth output depends on the first n inputs only. We model these in category theory via a construction taking a Cartesian category C to another category St(C) with a novel trace-like operation called "delayed trace", which misses yanking and dinaturality axioms of the usual trace. The delayed trace operation provides a feedback mechanism in St(C) with an implicit guardedness guarantee. When C is equipped with a Cartesian differential operator, we construct a differential operator for St(C) using an abstract version of backpropagation through time, a technique from machine learning based on unrolling of functions. This obtains a swath of properties for backpropagation through time, including a chain rule and Schwartz theorem. Our differential operator is also able to compute the derivative of a stateful network without requiring the network to be unrolled.

Discovering causal structures from data is a challenging inference problem of fundamental importance in all areas of science. The appealing properties of neural networks have recently led to a surge of interest in differentiable neural network-based methods for learning causal structures from data. So far, differentiable causal discovery has focused on static datasets of observational or fixed interventional origin. In this work, we introduce an active intervention targeting (AIT) method which enables a quick identification of the underlying causal structure of the data-generating process. Our method significantly reduces the required number of interactions compared with random intervention targeting and is applicable for both discrete and continuous optimization formulations of learning the underlying directed acyclic graph (DAG) from data. We examine the proposed method across multiple frameworks in a wide range of settings and demonstrate superior performance on multiple benchmarks from simulated to real-world data.

The prevalent use of commercial and open-source diffusion models (DMs) for text-to-image generation prompts risk mitigation to prevent undesired behaviors. Existing concept erasing methods in academia are all based on full parameter or specification-based fine-tuning, from which we observe the following issues: 1) Generation alternation towards erosion: Parameter drift during target elimination causes alternations and potential deformations across all generations, even eroding other concepts at varying degrees, which is more evident with multi-concept erased; 2) Transfer inability & deployment inefficiency: Previous model-specific erasure impedes the flexible combination of concepts and the training-free transfer towards other models, resulting in linear cost growth as the deployment scenarios increase. To achieve non-invasive, precise, customizable, and transferable elimination, we ground our erasing framework on one-dimensional adapters to erase multiple concepts from most DMs at once across versatile erasing applications. The concept-SemiPermeable structure is injected as a Membrane (SPM) into any DM to learn targeted erasing, and meantime the alteration and erosion phenomenon is effectively mitigated via a novel Latent Anchoring fine-tuning strategy. Once obtained, SPMs can be flexibly combined and plug-and-play for other DMs without specific re-tuning, enabling timely and efficient adaptation to diverse scenarios. During generation, our Facilitated Transport mechanism dynamically regulates the permeability of each SPM to respond to different input prompts, further minimizing the impact on other concepts. Quantitative and qualitative results across ~40 concepts, 7 DMs and 4 erasing applications have demonstrated the superior erasing of SPM. Our code and pre-tuned SPMs will be available on the project page https://lyumengyao.github.io/projects/spm.

Mechanistic interpretability aims to understand model behaviors in terms of specific, interpretable features, often hypothesized to manifest as low-dimensional subspaces of activations. Specifically, recent studies have explored subspace interventions (such as activation patching) as a way to simultaneously manipulate model behavior and attribute the features behind it to given subspaces. In this work, we demonstrate that these two aims diverge, potentially leading to an illusory sense of interpretability. Counterintuitively, even if a subspace intervention makes the model's output behave as if the value of a feature was changed, this effect may be achieved by activating a dormant parallel pathway leveraging another subspace that is causally disconnected from model outputs. We demonstrate this phenomenon in a distilled mathematical example, in two real-world domains (the indirect object identification task and factual recall), and present evidence for its prevalence in practice. In the context of factual recall, we further show a link to rank-1 fact editing, providing a mechanistic explanation for previous work observing an inconsistency between fact editing performance and fact localization. However, this does not imply that activation patching of subspaces is intrinsically unfit for interpretability. To contextualize our findings, we also show what a success case looks like in a task (indirect object identification) where prior manual circuit analysis informs an understanding of the location of a feature. We explore the additional evidence needed to argue that a patched subspace is faithful.

Recent work has shown promising results in causal discovery by leveraging interventional data with gradient-based methods, even when the intervened variables are unknown. However, previous work assumes that the correspondence between samples and interventions is known, which is often unrealistic. We envision a scenario with an extensive dataset sampled from multiple intervention distributions and one observation distribution, but where we do not know which distribution originated each sample and how the intervention affected the system, i.e., interventions are entirely latent. We propose a method based on neural networks and variational inference that addresses this scenario by framing it as learning a shared causal graph among an infinite mixture (under a Dirichlet process prior) of intervention structural causal models. Experiments with synthetic and real data show that our approach and its semi-supervised variant are able to discover causal relations in this challenging scenario.

Causal structures for observational survival data provide crucial information regarding the relationships between covariates and time-to-event. We derive motivation from the information theoretic source coding argument, and show that incorporating the knowledge of the directed acyclic graph (DAG) can be beneficial if suitable source encoders are employed. As a possible source encoder in this context, we derive a variational inference based conditional variational autoencoder for causal structured survival prediction, which we refer to as DAGSurv. We illustrate the performance of DAGSurv on low and high-dimensional synthetic datasets, and real-world datasets such as METABRIC and GBSG. We demonstrate that the proposed method outperforms other survival analysis baselines such as Cox Proportional Hazards, DeepSurv and Deephit, which are oblivious to the underlying causal relationship between data entities.

In this paper, we propose REASON, a novel framework that enables the automatic discovery of both intra-level (i.e., within-network) and inter-level (i.e., across-network) causal relationships for root cause localization. REASON consists of Topological Causal Discovery and Individual Causal Discovery. The Topological Causal Discovery component aims to model the fault propagation in order to trace back to the root causes. To achieve this, we propose novel hierarchical graph neural networks to construct interdependent causal networks by modeling both intra-level and inter-level non-linear causal relations. Based on the learned interdependent causal networks, we then leverage random walks with restarts to model the network propagation of a system fault. The Individual Causal Discovery component focuses on capturing abrupt change patterns of a single system entity. This component examines the temporal patterns of each entity's metric data (i.e., time series), and estimates its likelihood of being a root cause based on the Extreme Value theory. Combining the topological and individual causal scores, the top K system entities are identified as root causes. Extensive experiments on three real-world datasets with case studies demonstrate the effectiveness and superiority of the proposed framework.

The origin of adversarial examples is still inexplicable in research fields, and it arouses arguments from various viewpoints, albeit comprehensive investigations. In this paper, we propose a way of delving into the unexpected vulnerability in adversarially trained networks from a causal perspective, namely adversarial instrumental variable (IV) regression. By deploying it, we estimate the causal relation of adversarial prediction under an unbiased environment dissociated from unknown confounders. Our approach aims to demystify inherent causal features on adversarial examples by leveraging a zero-sum optimization game between a casual feature estimator (i.e., hypothesis model) and worst-case counterfactuals (i.e., test function) disturbing to find causal features. Through extensive analyses, we demonstrate that the estimated causal features are highly related to the correct prediction for adversarial robustness, and the counterfactuals exhibit extreme features significantly deviating from the correct prediction. In addition, we present how to effectively inoculate CAusal FEatures (CAFE) into defense networks for improving adversarial robustness.

We propose constrained causal Bayesian optimization (cCBO), an approach for finding interventions in a known causal graph that optimize a target variable under some constraints. cCBO first reduces the search space by exploiting the graph structure and, if available, an observational dataset; and then solves the restricted optimization problem by modelling target and constraint quantities using Gaussian processes and by sequentially selecting interventions via a constrained expected improvement acquisition function. We propose different surrogate models that enable to integrate observational and interventional data while capturing correlation among effects with increasing levels of sophistication. We evaluate cCBO on artificial and real-world causal graphs showing successful trade off between fast convergence and percentage of feasible interventions.

Causal representation learning aims to unveil latent high-level causal representations from observed low-level data. One of its primary tasks is to provide reliable assurance of identifying these latent causal models, known as identifiability. A recent breakthrough explores identifiability by leveraging the change of causal influences among latent causal variables across multiple environments liu2022identifying. However, this progress rests on the assumption that the causal relationships among latent causal variables adhere strictly to linear Gaussian models. In this paper, we extend the scope of latent causal models to involve nonlinear causal relationships, represented by polynomial models, and general noise distributions conforming to the exponential family. Additionally, we investigate the necessity of imposing changes on all causal parameters and present partial identifiability results when part of them remains unchanged. Further, we propose a novel empirical estimation method, grounded in our theoretical finding, that enables learning consistent latent causal representations. Our experimental results, obtained from both synthetic and real-world data, validate our theoretical contributions concerning identifiability and consistency.

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.

In this paper, the causal bandit problem is investigated, in which the objective is to select an optimal sequence of interventions on nodes in a causal graph. It is assumed that the graph is governed by linear structural equations; it is further assumed that both the causal topology and the distribution of interventions are unknown. By exploiting the causal relationships between the nodes whose signals contribute to the reward, interventions are optimized. First, based on the difference between the two types of graph identification errors (false positives and negatives), a causal graph learning method is proposed, which strongly reduces sample complexity relative to the prior art by learning sub-graphs. Under the assumption of Gaussian exogenous inputs and minimum-mean squared error weight estimation, a new uncertainty bound tailored to the causal bandit problem is derived. This uncertainty bound drives an upper confidence bound based intervention selection to optimize the reward. To cope with non-stationary bandits, a sub-graph change detection mechanism is proposed, with high sample efficiency. Numerical results compare the new methodology to existing schemes and show a substantial performance improvement in both stationary and non-stationary settings. Compared to existing approaches, the proposed scheme takes 67% fewer samples to learn the causal structure and achieves an average reward gain of 85%.

Many social and environmental phenomena are associated with macroscopic changes in the built environment, captured by satellite imagery on a global scale and with daily temporal resolution. While widely used for prediction, these images and especially image sequences remain underutilized for causal inference, especially in the context of randomized controlled trials (RCTs), where causal identification is established by design. In this paper, we develop and compare a set of general tools for analyzing Conditional Average Treatment Effects (CATEs) from temporal satellite data that can be applied to any RCT where geographical identifiers are available. Through a simulation study, we analyze different modeling strategies for estimating CATE in sequences of satellite images. We find that image sequence representation models with more parameters generally yield a greater ability to detect heterogeneity. To explore the role of model and data choice in practice, we apply the approaches to two influential RCTs -- Banerjee et al. (2015), a poverty study in Cusco, Peru, and Bolsen et al. (2014), a water conservation experiment in Georgia, USA. We benchmark our image sequence models against image-only, tabular-only, and combined image-tabular data sources, summarizing practical implications for investigators in a multivariate analysis. Land cover classifications over satellite images facilitate interpretation of what image features drive heterogeneity. We also show robustness to data and model choice of satellite-based generalization of the RCT results to larger geographical areas outside the original. Overall, this paper shows how satellite sequence data can be incorporated into the analysis of RCTs, and provides evidence about the implications of data, model, and evaluation metric choice for causal analysis.

We introduce a gradient-based approach for the problem of Bayesian optimal experimental design to learn causal models in a batch setting -- a critical component for causal discovery from finite data where interventions can be costly or risky. Existing methods rely on greedy approximations to construct a batch of experiments while using black-box methods to optimize over a single target-state pair to intervene with. In this work, we completely dispose of the black-box optimization techniques and greedy heuristics and instead propose a conceptually simple end-to-end gradient-based optimization procedure to acquire a set of optimal intervention target-state pairs. Such a procedure enables parameterization of the design space to efficiently optimize over a batch of multi-target-state interventions, a setting which has hitherto not been explored due to its complexity. We demonstrate that our proposed method outperforms baselines and existing acquisition strategies in both single-target and multi-target settings across a number of synthetic datasets.

We study experiment design for unique identification of the causal graph of a simple SCM, where the graph may contain cycles. The presence of cycles in the structure introduces major challenges for experiment design as, unlike acyclic graphs, learning the skeleton of causal graphs with cycles may not be possible from merely the observational distribution. Furthermore, intervening on a variable in such graphs does not necessarily lead to orienting all the edges incident to it. In this paper, we propose an experiment design approach that can learn both cyclic and acyclic graphs and hence, unifies the task of experiment design for both types of graphs. We provide a lower bound on the number of experiments required to guarantee the unique identification of the causal graph in the worst case, showing that the proposed approach is order-optimal in terms of the number of experiments up to an additive logarithmic term. Moreover, we extend our result to the setting where the size of each experiment is bounded by a constant. For this case, we show that our approach is optimal in terms of the size of the largest experiment required for uniquely identifying the causal graph in the worst case.

Most existing causal discovery methods rely on the assumption of no latent confounders, limiting their applicability in solving real-life problems. In this paper, we introduce a novel, versatile framework for causal discovery that accommodates the presence of causally-related hidden variables almost everywhere in the causal network (for instance, they can be effects of observed variables), based on rank information of covariance matrix over observed variables. We start by investigating the efficacy of rank in comparison to conditional independence and, theoretically, establish necessary and sufficient conditions for the identifiability of certain latent structural patterns. Furthermore, we develop a Rank-based Latent Causal Discovery algorithm, RLCD, that can efficiently locate hidden variables, determine their cardinalities, and discover the entire causal structure over both measured and hidden ones. We also show that, under certain graphical conditions, RLCD correctly identifies the Markov Equivalence Class of the whole latent causal graph asymptotically. Experimental results on both synthetic and real-world personality data sets demonstrate the efficacy of the proposed approach in finite-sample cases.

Within the field of causal inference, we consider the problem of estimating heterogeneous treatment effects from data. We propose and validate a novel approach for learning feature representations to aid the estimation of the conditional average treatment effect or CATE. Our method focuses on an intermediate layer in a neural network trained to predict the outcome from the features. In contrast to previous approaches that encourage the distribution of representations to be treatment-invariant, we leverage a genetic algorithm that optimizes over representations useful for predicting the outcome to select those less useful for predicting the treatment. This allows us to retain information within the features useful for predicting outcome even if that information may be related to treatment assignment. We validate our method on synthetic examples and illustrate its use on a real life dataset.

Epidemiologists often wish to estimate quantities that are easy to communicate and correspond to the results of realistic public health scenarios. Methods from causal inference can answer these questions. We adopt the language of potential outcomes under Rubin's original Bayesian framework and show that the parametric g-formula is easily amenable to a Bayesian approach. We show that the frequentist properties of the Bayesian g-formula suggest it improves the accuracy of estimates of causal effects in small samples or when data may be sparse. We demonstrate our approach to estimate the effect of environmental tobacco smoke on body mass index z-scores among children aged 4-9 years who were enrolled in a longitudinal birth cohort in New York, USA. We give a general algorithm and supply SAS and Stan code that can be adopted to implement our computational approach in both time-fixed and longitudinal data.

Forecasting on sparse multivariate time series (MTS) aims to model the predictors of future values of time series given their incomplete past, which is important for many emerging applications. However, most existing methods process MTS's individually, and do not leverage the dynamic distributions underlying the MTS's, leading to sub-optimal results when the sparsity is high. To address this challenge, we propose a novel generative model, which tracks the transition of latent clusters, instead of isolated feature representations, to achieve robust modeling. It is characterized by a newly designed dynamic Gaussian mixture distribution, which captures the dynamics of clustering structures, and is used for emitting timeseries. The generative model is parameterized by neural networks. A structured inference network is also designed for enabling inductive analysis. A gating mechanism is further introduced to dynamically tune the Gaussian mixture distributions. Extensive experimental results on a variety of real-life datasets demonstrate the effectiveness of our method.

In causal bandit problems, the action set consists of interventions on variables of a causal graph. Several researchers have recently studied such bandit problems and pointed out their practical applications. However, all existing works rely on a restrictive and impractical assumption that the learner is given full knowledge of the causal graph structure upfront. In this paper, we develop novel causal bandit algorithms without knowing the causal graph. Our algorithms work well for causal trees, causal forests and a general class of causal graphs. The regret guarantees of our algorithms greatly improve upon those of standard multi-armed bandit (MAB) algorithms under mild conditions. Lastly, we prove our mild conditions are necessary: without them one cannot do better than standard MAB algorithms.

When users can benefit from certain predictive outcomes, they may be prone to act to achieve those outcome, e.g., by strategically modifying their features. The goal in strategic classification is therefore to train predictive models that are robust to such behavior. However, the conventional framework assumes that changing features does not change actual outcomes, which depicts users as "gaming" the system. Here we remove this assumption, and study learning in a causal strategic setting where true outcomes do change. Focusing on accuracy as our primary objective, we show how strategic behavior and causal effects underlie two complementing forms of distribution shift. We characterize these shifts, and propose a learning algorithm that balances between these two forces and over time, and permits end-to-end training. Experiments on synthetic and semi-synthetic data demonstrate the utility of our approach.

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.

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.

Fair machine learning aims to prevent discrimination against individuals or sub-populations based on sensitive attributes such as gender and race. In recent years, causal inference methods have been increasingly used in fair machine learning to measure unfairness by causal effects. However, current methods assume that the true causal graph is given, which is often not true in real-world applications. To address this limitation, this paper proposes a framework for achieving causal fairness based on the notion of interventions when the true causal graph is partially known. The proposed approach involves modeling fair prediction using a Partially Directed Acyclic Graph (PDAG), specifically, a class of causal DAGs that can be learned from observational data combined with domain knowledge. The PDAG is used to measure causal fairness, and a constrained optimization problem is formulated to balance between fairness and accuracy. Results on both simulated and real-world datasets demonstrate the effectiveness of this method.

We present a constraint-based algorithm for learning causal structures from observational time-series data, in the presence of latent confounders. We assume a discrete-time, stationary structural vector autoregressive process, with both temporal and contemporaneous causal relations. One may ask if temporal and contemporaneous relations should be treated differently. The presented algorithm gradually refines a causal graph by learning long-term temporal relations before short-term ones, where contemporaneous relations are learned last. This ordering of causal relations to be learnt leads to a reduction in the required number of statistical tests. We validate this reduction empirically and demonstrate that it leads to higher accuracy for synthetic data and more plausible causal graphs for real-world data compared to state-of-the-art algorithms.

Learning behavioral patterns from observational data has been a de-facto approach to motion forecasting. Yet, the current paradigm suffers from two shortcomings: brittle under distribution shifts and inefficient for knowledge transfer. In this work, we propose to address these challenges from a causal representation perspective. We first introduce a causal formalism of motion forecasting, which casts the problem as a dynamic process with three groups of latent variables, namely invariant variables, style confounders, and spurious features. We then introduce a learning framework that treats each group separately: (i) unlike the common practice mixing datasets collected from different locations, we exploit their subtle distinctions by means of an invariance loss encouraging the model to suppress spurious correlations; (ii) we devise a modular architecture that factorizes the representations of invariant mechanisms and style confounders to approximate a sparse causal graph; (iii) we introduce a style contrastive loss that not only enforces the structure of style representations but also serves as a self-supervisory signal for test-time refinement on the fly. Experiments on synthetic and real datasets show that our proposed method improves the robustness and reusability of learned motion representations, significantly outperforming prior state-of-the-art motion forecasting models for out-of-distribution generalization and low-shot transfer.

Gene regulatory network inference (GRNI) is a challenging problem, particularly owing to the presence of zeros in single-cell RNA sequencing data: some are biological zeros representing no gene expression, while some others are technical zeros arising from the sequencing procedure (aka dropouts), which may bias GRNI by distorting the joint distribution of the measured gene expressions. Existing approaches typically handle dropout error via imputation, which may introduce spurious relations as the true joint distribution is generally unidentifiable. To tackle this issue, we introduce a causal graphical model to characterize the dropout mechanism, namely, Causal Dropout Model. We provide a simple yet effective theoretical result: interestingly, the conditional independence (CI) relations in the data with dropouts, after deleting the samples with zero values (regardless if technical or not) for the conditioned variables, are asymptotically identical to the CI relations in the original data without dropouts. This particular test-wise deletion procedure, in which we perform CI tests on the samples without zeros for the conditioned variables, can be seamlessly integrated with existing structure learning approaches including constraint-based and greedy score-based methods, thus giving rise to a principled framework for GRNI in the presence of dropouts. We further show that the causal dropout model can be validated from data, and many existing statistical models to handle dropouts fit into our model as specific parametric instances. Empirical evaluation on synthetic, curated, and real-world experimental transcriptomic data comprehensively demonstrate the efficacy of our method.

The varying significance of distinct primitive behaviors during the policy learning process has been overlooked by prior model-free RL algorithms. Leveraging this insight, we explore the causal relationship between different action dimensions and rewards to evaluate the significance of various primitive behaviors during training. We introduce a causality-aware entropy term that effectively identifies and prioritizes actions with high potential impacts for efficient exploration. Furthermore, to prevent excessive focus on specific primitive behaviors, we analyze the gradient dormancy phenomenon and introduce a dormancy-guided reset mechanism to further enhance the efficacy of our method. Our proposed algorithm, ACE: Off-policy Actor-critic with Causality-aware Entropy regularization, demonstrates a substantial performance advantage across 29 diverse continuous control tasks spanning 7 domains compared to model-free RL baselines, which underscores the effectiveness, versatility, and efficient sample efficiency of our approach. Benchmark results and videos are available at https://ace-rl.github.io/.

We formalize constraint-based structure learning of the "true" causal graph from observed data when unobserved variables are also existent. We provide conditions for a "natural" family of constraint-based structure-learning algorithms that output graphs that are Markov equivalent to the causal graph. Under the faithfulness assumption, this natural family contains all exact structure-learning algorithms. We also provide a set of assumptions, under which any natural structure-learning algorithm outputs Markov equivalent graphs to the causal graph. These assumptions can be thought of as a relaxation of faithfulness, and most of them can be directly tested from (the underlying distribution) of the data, particularly when one focuses on structural causal models. We specialize the definitions and results for structural causal models.

Despite being self-supervised, protein language models have shown remarkable performance in fundamental biological tasks such as predicting impact of genetic variation on protein structure and function. The effectiveness of these models on diverse set of tasks suggests that they learn meaningful representations of fitness landscape that can be useful for downstream clinical applications. Here, we interrogate the use of these language models in characterizing known pathogenic mutations in curated, medically actionable genes through an exhaustive search of putative compensatory mutations on each variant's genetic background. Systematic analysis of the predicted effects of these compensatory mutations reveal unappreciated structural features of proteins that are missed by other structure predictors like AlphaFold. While deep mutational scan experiments provide an unbiased estimate of the mutational landscape, we encourage the community to generate and curate rescue mutation experiments to inform the design of more sophisticated co-masking strategies and leverage large language models more effectively for downstream clinical prediction tasks.

Transformers demonstrate impressive performance on a range of reasoning benchmarks. To evaluate the degree to which these abilities are a result of actual reasoning, existing work has focused on developing sophisticated benchmarks for behavioral studies. However, these studies do not provide insights into the internal mechanisms driving the observed capabilities. To improve our understanding of the internal mechanisms of transformers, we present a comprehensive mechanistic analysis of a transformer trained on a synthetic reasoning task. We identify a set of interpretable mechanisms the model uses to solve the task, and validate our findings using correlational and causal evidence. Our results suggest that it implements a depth-bounded recurrent mechanisms that operates in parallel and stores intermediate results in selected token positions. We anticipate that the motifs we identified in our synthetic setting can provide valuable insights into the broader operating principles of transformers and thus provide a basis for understanding more complex models.

This paper presents Diffusion Forcing, a new training paradigm where a diffusion model is trained to denoise a set of tokens with independent per-token noise levels. We apply Diffusion Forcing to sequence generative modeling by training a causal next-token prediction model to generate one or several future tokens without fully diffusing past ones. Our approach is shown to combine the strengths of next-token prediction models, such as variable-length generation, with the strengths of full-sequence diffusion models, such as the ability to guide sampling to desirable trajectories. Our method offers a range of additional capabilities, such as (1) rolling-out sequences of continuous tokens, such as video, with lengths past the training horizon, where baselines diverge and (2) new sampling and guiding schemes that uniquely profit from Diffusion Forcing's variable-horizon and causal architecture, and which lead to marked performance gains in decision-making and planning tasks. In addition to its empirical success, our method is proven to optimize a variational lower bound on the likelihoods of all subsequences of tokens drawn from the true joint distribution. Project website: https://boyuan.space/diffusion-forcing/

This paper proposes a Disentangled gEnerative cAusal Representation (DEAR) learning method under appropriate supervised information. Unlike existing disentanglement methods that enforce independence of the latent variables, we consider the general case where the underlying factors of interests can be causally related. We show that previous methods with independent priors fail to disentangle causally related factors even under supervision. Motivated by this finding, we propose a new disentangled learning method called DEAR that enables causal controllable generation and causal representation learning. The key ingredient of this new formulation is to use a structural causal model (SCM) as the prior distribution for a bidirectional generative model. The prior is then trained jointly with a generator and an encoder using a suitable GAN algorithm incorporated with supervised information on the ground-truth factors and their underlying causal structure. We provide theoretical justification on the identifiability and asymptotic convergence of the proposed method. We conduct extensive experiments on both synthesized and real data sets to demonstrate the effectiveness of DEAR in causal controllable generation, and the benefits of the learned representations for downstream tasks in terms of sample efficiency and distributional robustness.

Interference is ubiquitous when conducting causal experiments over networks. Except for certain network structures, causal inference on the network in the presence of interference is difficult due to the entanglement between the treatment assignments and the interference levels. In this article, we conduct causal inference under interference on an observed, sparse but connected network, and we propose a novel design of experiments based on an independent set. Compared to conventional designs, the independent-set design focuses on an independent subset of data and controls their interference exposures through the assignments to the rest (auxiliary set). We provide a lower bound on the size of the independent set from a greedy algorithm , and justify the theoretical performance of estimators under the proposed design. Our approach is capable of estimating both spillover effects and treatment effects. We justify its superiority over conventional methods and illustrate the empirical performance through simulations.

We study the problem of designing mechanisms for information acquisition scenarios. This setting models strategic interactions between an uniformed receiver and a set of informed senders. In our model the senders receive information about the underlying state of nature and communicate their observation (either truthfully or not) to the receiver, which, based on this information, selects an action. Our goal is to design mechanisms maximizing the receiver's utility while incentivizing the senders to report truthfully their information. First, we provide an algorithm that efficiently computes an optimal incentive compatible (IC) mechanism. Then, we focus on the online problem in which the receiver sequentially interacts in an unknown game, with the objective of minimizing the cumulative regret w.r.t. the optimal IC mechanism, and the cumulative violation of the incentive compatibility constraints. We investigate two different online scenarios, i.e., the full and bandit feedback settings. For the full feedback problem, we propose an algorithm that guarantees mathcal O(sqrt T) regret and violation, while for the bandit feedback setting we present an algorithm that attains mathcal O(T^{alpha}) regret and mathcal O(T^{1-alpha/2}) violation for any alphain[1/2, 1]. Finally, we complement our results providing a tight lower bound.

We consider the task of evaluating policies of algorithmic resource allocation through randomized controlled trials (RCTs). Such policies are tasked with optimizing the utilization of limited intervention resources, with the goal of maximizing the benefits derived. Evaluation of such allocation policies through RCTs proves difficult, notwithstanding the scale of the trial, because the individuals' outcomes are inextricably interlinked through resource constraints controlling the policy decisions. Our key contribution is to present a new estimator leveraging our proposed novel concept, that involves retrospective reshuffling of participants across experimental arms at the end of an RCT. We identify conditions under which such reassignments are permissible and can be leveraged to construct counterfactual trials, whose outcomes can be accurately ascertained, for free. We prove theoretically that such an estimator is more accurate than common estimators based on sample means -- we show that it returns an unbiased estimate and simultaneously reduces variance. We demonstrate the value of our approach through empirical experiments on synthetic, semi-synthetic as well as real case study data and show improved estimation accuracy across the board.

Image-generation diffusion models have been fine-tuned to unlock new capabilities such as image-editing and novel view synthesis. Can we similarly unlock image-generation models for visuomotor control? We present GENIMA, a behavior-cloning agent that fine-tunes Stable Diffusion to 'draw joint-actions' as targets on RGB images. These images are fed into a controller that maps the visual targets into a sequence of joint-positions. We study GENIMA on 25 RLBench and 9 real-world manipulation tasks. We find that, by lifting actions into image-space, internet pre-trained diffusion models can generate policies that outperform state-of-the-art visuomotor approaches, especially in robustness to scene perturbations and generalizing to novel objects. Our method is also competitive with 3D agents, despite lacking priors such as depth, keypoints, or motion-planners.

The recent phenomenal success of language models has reinvigorated machine learning research, and large sequence models such as transformers are being applied to a variety of domains. One important problem class that has remained relatively elusive however is purposeful adaptive behavior. Currently there is a common perception that sequence models "lack the understanding of the cause and effect of their actions" leading them to draw incorrect inferences due to auto-suggestive delusions. In this report we explain where this mismatch originates, and show that it can be resolved by treating actions as causal interventions. Finally, we show that in supervised learning, one can teach a system to condition or intervene on data by training with factual and counterfactual error signals respectively.

We study the class of location-scale or heteroscedastic noise models (LSNMs), in which the effect Y can be written as a function of the cause X and a noise source N independent of X, which may be scaled by a positive function g over the cause, i.e., Y = f(X) + g(X)N. Despite the generality of the model class, we show the causal direction is identifiable up to some pathological cases. To empirically validate these theoretical findings, we propose two estimators for LSNMs: an estimator based on (non-linear) feature maps, and one based on neural networks. Both model the conditional distribution of Y given X as a Gaussian parameterized by its natural parameters. When the feature maps are correctly specified, we prove that our estimator is jointly concave, and a consistent estimator for the cause-effect identification task. Although the the neural network does not inherit those guarantees, it can fit functions of arbitrary complexity, and reaches state-of-the-art performance across benchmarks.

Explainability methods for NLP systems encounter a version of the fundamental problem of causal inference: for a given ground-truth input text, we never truly observe the counterfactual texts necessary for isolating the causal effects of model representations on outputs. In response, many explainability methods make no use of counterfactual texts, assuming they will be unavailable. In this paper, we show that robust causal explainability methods can be created using approximate counterfactuals, which can be written by humans to approximate a specific counterfactual or simply sampled using metadata-guided heuristics. The core of our proposal is the Causal Proxy Model (CPM). A CPM explains a black-box model N because it is trained to have the same actual input/output behavior as N while creating neural representations that can be intervened upon to simulate the counterfactual input/output behavior of N. Furthermore, we show that the best CPM for N performs comparably to N in making factual predictions, which means that the CPM can simply replace N, leading to more explainable deployed models. Our code is available at https://github.com/frankaging/Causal-Proxy-Model.

Diffusion models have emerged as powerful generative models in the text-to-image domain. This paper studies their application as observation-to-action models for imitating human behaviour in sequential environments. Human behaviour is stochastic and multimodal, with structured correlations between action dimensions. Meanwhile, standard modelling choices in behaviour cloning are limited in their expressiveness and may introduce bias into the cloned policy. We begin by pointing out the limitations of these choices. We then propose that diffusion models are an excellent fit for imitating human behaviour, since they learn an expressive distribution over the joint action space. We introduce several innovations to make diffusion models suitable for sequential environments; designing suitable architectures, investigating the role of guidance, and developing reliable sampling strategies. Experimentally, diffusion models closely match human demonstrations in a simulated robotic control task and a modern 3D gaming environment.

With the advance of diffusion models, today's video generation has achieved impressive quality. But generating temporal consistent long videos is still challenging. A majority of video diffusion models (VDMs) generate long videos in an autoregressive manner, i.e., generating subsequent clips conditioned on last frames of previous clip. However, existing approaches all involve bidirectional computations, which restricts the receptive context of each autoregression step, and results in the model lacking long-term dependencies. Inspired from the huge success of large language models (LLMs) and following GPT (generative pre-trained transformer), we bring causal (i.e., unidirectional) generation into VDMs, and use past frames as prompt to generate future frames. For Causal Generation, we introduce causal temporal attention into VDM, which forces each generated frame to depend on its previous frames. For Frame as Prompt, we inject the conditional frames by concatenating them with noisy frames (frames to be generated) along the temporal axis. Consequently, we present Video Diffusion GPT (ViD-GPT). Based on the two key designs, in each autoregression step, it is able to acquire long-term context from prompting frames concatenated by all previously generated frames. Additionally, we bring the kv-cache mechanism to VDMs, which eliminates the redundant computation from overlapped frames, significantly boosting the inference speed. Extensive experiments demonstrate that our ViD-GPT achieves state-of-the-art performance both quantitatively and qualitatively on long video generation. Code will be available at https://github.com/Dawn-LX/Causal-VideoGen.

Implicit Personalization (IP) is a phenomenon of language models inferring a user's background from the implicit cues in the input prompts and tailoring the response based on this inference. While previous work has touched upon various instances of this problem, there lacks a unified framework to study this behavior. This work systematically studies IP through a rigorous mathematical formulation, a multi-perspective moral reasoning framework, and a set of case studies. Our theoretical foundation for IP relies on a structural causal model and introduces a novel method, indirect intervention, to estimate the causal effect of a mediator variable that cannot be directly intervened upon. Beyond the technical approach, we also introduce a set of moral reasoning principles based on three schools of moral philosophy to study when IP may or may not be ethically appropriate. Equipped with both mathematical and ethical insights, we present three diverse case studies illustrating the varied nature of the IP problem and offer recommendations for future research. Our code and data are at https://github.com/jiarui-liu/IP.

A directed acyclic graph (DAG) provides valuable prior knowledge that is often discarded in regression tasks in machine learning. We show that the independences arising from the presence of collider structures in DAGs provide meaningful inductive biases, which constrain the regression hypothesis space and improve predictive performance. We introduce collider regression, a framework to incorporate probabilistic causal knowledge from a collider in a regression problem. When the hypothesis space is a reproducing kernel Hilbert space, we prove a strictly positive generalisation benefit under mild assumptions and provide closed-form estimators of the empirical risk minimiser. Experiments on synthetic and climate model data demonstrate performance gains of the proposed methodology.

Curating a large scale medical imaging dataset for machine learning applications is both time consuming and expensive. Balancing the workload between model development, data collection and annotations is difficult for machine learning practitioners, especially under time constraints. Causal analysis is often used in medicine and economics to gain insights about the effects of actions and policies. In this paper we explore the effect of dataset interventions on the output of image classification models. Through a causal approach we investigate the effects of the quantity and type of data we need to incorporate in a dataset to achieve better performance for specific subtasks. The main goal of this paper is to highlight the potential of causal analysis as a tool for resource optimization for developing medical imaging ML applications. We explore this concept with a synthetic dataset and an exemplary use-case for Diabetic Retinopathy image analysis.

Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic features), and present to clinicians interpretable models. In order to build more accurate and better interpretable machine learning models for genetic medicine, we introduce Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning (PANTHER). PANTHER selects informative genetic pathways that directly encode molecular mechanisms. We apply genetically motivated constrained tensor factorization to group pathways in a way that reflects molecular mechanism interactions. We then train a softmax classifier for disease types using the identified pathway groups. We evaluated PANTHER against multiple state-of-the-art constrained tensor/matrix factorization models, as well as group guided and Bayesian hierarchical models. PANTHER outperforms all state-of-the-art comparison models significantly (p<0.05). Our experiments on large scale Next Generation Sequencing (NGS) and whole-genome genotyping datasets also demonstrated wide applicability of PANTHER. We performed feature analysis in predicting disease types, which suggested insights and benefits of the identified pathway groups.

Seismic advances in generative AI algorithms for imagery, text, and other data types has led to the temptation to use synthetic data to train next-generation models. Repeating this process creates an autophagous (self-consuming) loop whose properties are poorly understood. We conduct a thorough analytical and empirical analysis using state-of-the-art generative image models of three families of autophagous loops that differ in how fixed or fresh real training data is available through the generations of training and in whether the samples from previous generation models have been biased to trade off data quality versus diversity. Our primary conclusion across all scenarios is that without enough fresh real data in each generation of an autophagous loop, future generative models are doomed to have their quality (precision) or diversity (recall) progressively decrease. We term this condition Model Autophagy Disorder (MAD), making analogy to mad cow disease.

Large Language Models (LLMs) have shown state-of-the-art performance in a variety of tasks, including arithmetic and reasoning; however, to gauge the intellectual capabilities of LLMs, causal reasoning has become a reliable proxy for validating a general understanding of the mechanics and intricacies of the world similar to humans. Previous works in natural language processing (NLP) have either focused on open-ended causal reasoning via causal commonsense reasoning (CCR) or framed a symbolic representation-based question answering for theoretically backed-up analysis via a causal inference engine. The former adds an advantage of real-world grounding but lacks theoretically backed-up analysis/validation, whereas the latter is far from real-world grounding. In this work, we bridge this gap by proposing the COLD (Causal reasOning in cLosed Daily activities) framework, which is built upon human understanding of daily real-world activities to reason about the causal nature of events. We show that the proposed framework facilitates the creation of enormous causal queries (~ 9 million) and comes close to the mini-turing test, simulating causal reasoning to evaluate the understanding of a daily real-world task. We evaluate multiple LLMs on the created causal queries and find that causal reasoning is challenging even for activities trivial to humans. We further explore (the causal reasoning abilities of LLMs) using the backdoor criterion to determine the causal strength between events.

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.

Activation Patching is a method of directly computing causal attributions of behavior to model components. However, applying it exhaustively requires a sweep with cost scaling linearly in the number of model components, which can be prohibitively expensive for SoTA Large Language Models (LLMs). We investigate Attribution Patching (AtP), a fast gradient-based approximation to Activation Patching and find two classes of failure modes of AtP which lead to significant false negatives. We propose a variant of AtP called AtP*, with two changes to address these failure modes while retaining scalability. We present the first systematic study of AtP and alternative methods for faster activation patching and show that AtP significantly outperforms all other investigated methods, with AtP* providing further significant improvement. Finally, we provide a method to bound the probability of remaining false negatives of AtP* estimates.

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.

Autoregressive models excel in modeling sequential dependencies by enforcing causal constraints, yet they struggle to capture complex bidirectional patterns due to their unidirectional nature. In contrast, mask-based models leverage bidirectional context, enabling richer dependency modeling. However, they often assume token independence during prediction, which undermines the modeling of sequential dependencies. Additionally, the corruption of sequences through masking or absorption can introduce unnatural distortions, complicating the learning process. To address these issues, we propose Bidirectional Autoregressive Diffusion (BAD), a novel approach that unifies the strengths of autoregressive and mask-based generative models. BAD utilizes a permutation-based corruption technique that preserves the natural sequence structure while enforcing causal dependencies through randomized ordering, enabling the effective capture of both sequential and bidirectional relationships. Comprehensive experiments show that BAD outperforms autoregressive and mask-based models in text-to-motion generation, suggesting a novel pre-training strategy for sequence modeling. The codebase for BAD is available on https://github.com/RohollahHS/BAD.

We propose a novel framework that leverages LLMs for full causal graph discovery. While previous LLM-based methods have used a pairwise query approach, this requires a quadratic number of queries which quickly becomes impractical for larger causal graphs. In contrast, the proposed framework uses a breadth-first search (BFS) approach which allows it to use only a linear number of queries. We also show that the proposed method can easily incorporate observational data when available, to improve performance. In addition to being more time and data-efficient, the proposed framework achieves state-of-the-art results on real-world causal graphs of varying sizes. The results demonstrate the effectiveness and efficiency of the proposed method in discovering causal relationships, showcasing its potential for broad applicability in causal graph discovery tasks across different domains.

Causal Inference plays an significant role in explaining the decisions taken by statistical models and artificial intelligence models. Of late, this field started attracting the attention of researchers and practitioners alike. This paper presents a comprehensive survey of 37 papers published during 1992-2023 and concerning the application of causal inference to banking, finance, and insurance. The papers are categorized according to the following families of domains: (i) Banking, (ii) Finance and its subdomains such as corporate finance, governance finance including financial risk and financial policy, financial economics, and Behavioral finance, and (iii) Insurance. Further, the paper covers the primary ingredients of causal inference namely, statistical methods such as Bayesian Causal Network, Granger Causality and jargon used thereof such as counterfactuals. The review also recommends some important directions for future research. In conclusion, we observed that the application of causal inference in the banking and insurance sectors is still in its infancy, and thus more research is possible to turn it into a viable method.

Learning the continuous dynamics of a system from snapshots of its temporal marginals is a problem which appears throughout natural sciences and machine learning, including in quantum systems, single-cell biological data, and generative modeling. In these settings, we assume access to cross-sectional samples that are uncorrelated over time, rather than full trajectories of samples. In order to better understand the systems under observation, we would like to learn a model of the underlying process that allows us to propagate samples in time and thereby simulate entire individual trajectories. In this work, we propose Action Matching, a method for learning a rich family of dynamics using only independent samples from its time evolution. We derive a tractable training objective, which does not rely on explicit assumptions about the underlying dynamics and does not require back-propagation through differential equations or optimal transport solvers. Inspired by connections with optimal transport, we derive extensions of Action Matching to learn stochastic differential equations and dynamics involving creation and destruction of probability mass. Finally, we showcase applications of Action Matching by achieving competitive performance in a diverse set of experiments from biology, physics, and generative modeling.

We incorporate discrete and continuous time Markov processes as building blocks into probabilistic graphical models with latent and observed variables. We introduce the automatic Backward Filtering Forward Guiding (BFFG) paradigm (Mider et al., 2021) for programmable inference on latent states and model parameters. Our starting point is a generative model, a forward description of the probabilistic process dynamics. We backpropagate the information provided by observations through the model to transform the generative (forward) model into a pre-conditional model guided by the data. It approximates the actual conditional model with known likelihood-ratio between the two. The backward filter and the forward change of measure are suitable to be incorporated into a probabilistic programming context because they can be formulated as a set of transformation rules. The guided generative model can be incorporated in different approaches to efficiently sample latent states and parameters conditional on observations. We show applicability in a variety of settings, including Markov chains with discrete state space, interacting particle systems, state space models, branching diffusions and Gamma processes.

Diffusion models are a class of generative models that learn to synthesize samples by inverting a diffusion process that gradually maps data into noise. While these models have enjoyed great success recently, a full theoretical understanding of their observed properties is still lacking, in particular, their weak sensitivity to the choice of noise family and the role of adequate scheduling of noise levels for good synthesis. By identifying a correspondence between diffusion models and a well-known paradigm in cognitive science known as serial reproduction, whereby human agents iteratively observe and reproduce stimuli from memory, we show how the aforementioned properties of diffusion models can be explained as a natural consequence of this correspondence. We then complement our theoretical analysis with simulations that exhibit these key features. Our work highlights how classic paradigms in cognitive science can shed light on state-of-the-art machine learning problems.

Diffusion-based imitation learning improves Behavioral Cloning (BC) on multi-modal decision-making, but comes at the cost of significantly slower inference due to the recursion in the diffusion process. It urges us to design efficient policy generators while keeping the ability to generate diverse actions. To address this challenge, we propose AdaFlow, an imitation learning framework based on flow-based generative modeling. AdaFlow represents the policy with state-conditioned ordinary differential equations (ODEs), which are known as probability flows. We reveal an intriguing connection between the conditional variance of their training loss and the discretization error of the ODEs. With this insight, we propose a variance-adaptive ODE solver that can adjust its step size in the inference stage, making AdaFlow an adaptive decision-maker, offering rapid inference without sacrificing diversity. Interestingly, it automatically reduces to a one-step generator when the action distribution is uni-modal. Our comprehensive empirical evaluation shows that AdaFlow achieves high performance with fast inference speed.

In recent years, microservices have gained widespread adoption in IT operations due to their scalability, maintenance, and flexibility. However, it becomes challenging for site reliability engineers (SREs) to pinpoint the root cause due to the complex relationships in microservices when facing system malfunctions. Previous research employed structured learning methods (e.g., PC-algorithm) to establish causal relationships and derive root causes from causal graphs. Nevertheless, they ignored the temporal order of time series data and failed to leverage the rich information inherent in the temporal relationships. For instance, in cases where there is a sudden spike in CPU utilization, it can lead to an increase in latency for other microservices. However, in this scenario, the anomaly in CPU utilization occurs before the latency increase, rather than simultaneously. As a result, the PC-algorithm fails to capture such characteristics. To address these challenges, we propose RUN, a novel approach for root cause analysis using neural Granger causal discovery with contrastive learning. RUN enhances the backbone encoder by integrating contextual information from time series, and leverages a time series forecasting model to conduct neural Granger causal discovery. In addition, RUN incorporates Pagerank with a personalization vector to efficiently recommend the top-k root causes. Extensive experiments conducted on the synthetic and real-world microservice-based datasets demonstrate that RUN noticeably outperforms the state-of-the-art root cause analysis methods. Moreover, we provide an analysis scenario for the sock-shop case to showcase the practicality and efficacy of RUN in microservice-based applications. Our code is publicly available at https://github.com/zmlin1998/RUN.

The fields of Origin of Life and Artificial Life both question what life is and how it emerges from a distinct set of "pre-life" dynamics. One common feature of most substrates where life emerges is a marked shift in dynamics when self-replication appears. While there are some hypotheses regarding how self-replicators arose in nature, we know very little about the general dynamics, computational principles, and necessary conditions for self-replicators to emerge. This is especially true on "computational substrates" where interactions involve logical, mathematical, or programming rules. In this paper we take a step towards understanding how self-replicators arise by studying several computational substrates based on various simple programming languages and machine instruction sets. We show that when random, non self-replicating programs are placed in an environment lacking any explicit fitness landscape, self-replicators tend to arise. We demonstrate how this occurs due to random interactions and self-modification, and can happen with and without background random mutations. We also show how increasingly complex dynamics continue to emerge following the rise of self-replicators. Finally, we show a counterexample of a minimalistic programming language where self-replicators are possible, but so far have not been observed to arise.

Biomedical imaging datasets are often small and biased, meaning that real-world performance of predictive models can be substantially lower than expected from internal testing. This work proposes using generative image editing to simulate dataset shifts and diagnose failure modes of biomedical vision models; this can be used in advance of deployment to assess readiness, potentially reducing cost and patient harm. Existing editing methods can produce undesirable changes, with spurious correlations learned due to the co-occurrence of disease and treatment interventions, limiting practical applicability. To address this, we train a text-to-image diffusion model on multiple chest X-ray datasets and introduce a new editing method RadEdit that uses multiple masks, if present, to constrain changes and ensure consistency in the edited images. We consider three types of dataset shifts: acquisition shift, manifestation shift, and population shift, and demonstrate that our approach can diagnose failures and quantify model robustness without additional data collection, complementing more qualitative tools for explainable AI.

Modularization is a cornerstone of computer science, abstracting complex functions into atomic building blocks. In this paper, we introduce a new level of modularization by abstracting generative models into atomic generative modules. Analogous to fractals in mathematics, our method constructs a new type of generative model by recursively invoking atomic generative modules, resulting in self-similar fractal architectures that we call fractal generative models. As a running example, we instantiate our fractal framework using autoregressive models as the atomic generative modules and examine it on the challenging task of pixel-by-pixel image generation, demonstrating strong performance in both likelihood estimation and generation quality. We hope this work could open a new paradigm in generative modeling and provide a fertile ground for future research. Code is available at https://github.com/LTH14/fractalgen.

Intelligent agents must be generalists - showing the ability to quickly adapt and generalize to varying tasks. Within the framework of reinforcement learning (RL), model-based RL algorithms learn a task-agnostic dynamics model of the world, in principle allowing them to generalize to arbitrary rewards. However, one-step models naturally suffer from compounding errors, making them ineffective for problems with long horizons and large state spaces. In this work, we propose a novel class of models - generalized occupancy models (GOMs) - that retain the generality of model-based RL while avoiding compounding error. The key idea behind GOMs is to model the distribution of all possible long-term outcomes from a given state under the coverage of a stationary dataset, along with a policy that realizes a particular outcome from the given state. These models can then quickly be used to select the optimal action for arbitrary new tasks, without having to redo policy optimization. By directly modeling long-term outcomes, GOMs avoid compounding error while retaining generality across arbitrary reward functions. We provide a practical instantiation of GOMs using diffusion models and show its efficacy as a new class of transferable models, both theoretically and empirically across a variety of simulated robotics problems. Videos and code at https://weirdlabuw.github.io/gom/.

Predicting how different interventions will causally affect a specific individual is important in a variety of domains such as personalized medicine, public policy, and online marketing. There are a large number of methods to predict the effect of an existing intervention based on historical data from individuals who received it. However, in many settings it is important to predict the effects of novel interventions (e.g., a newly invented drug), which these methods do not address. Here, we consider zero-shot causal learning: predicting the personalized effects of a novel intervention. We propose CaML, a causal meta-learning framework which formulates the personalized prediction of each intervention's effect as a task. CaML trains a single meta-model across thousands of tasks, each constructed by sampling an intervention, along with its recipients and nonrecipients. By leveraging both intervention information (e.g., a drug's attributes) and individual features~(e.g., a patient's history), CaML is able to predict the personalized effects of novel interventions that do not exist at the time of training. Experimental results on real world datasets in large-scale medical claims and cell-line perturbations demonstrate the effectiveness of our approach. Most strikingly, CaML's zero-shot predictions outperform even strong baselines trained directly on data from the test interventions.

Being able to provide explanations for a model's decision has become a central requirement for the development, deployment, and adoption of machine learning models. However, we are yet to understand what explanation methods can and cannot do. How do upstream factors such as data, model prediction, hyperparameters, and random initialization influence downstream explanations? While previous work raised concerns that explanations (E) may have little relationship with the prediction (Y), there is a lack of conclusive study to quantify this relationship. Our work borrows tools from causal inference to systematically assay this relationship. More specifically, we study the relationship between E and Y by measuring the treatment effect when intervening on their causal ancestors, i.e., on hyperparameters and inputs used to generate saliency-based Es or Ys. Our results suggest that the relationships between E and Y is far from ideal. In fact, the gap between 'ideal' case only increase in higher-performing models -- models that are likely to be deployed. Our work is a promising first step towards providing a quantitative measure of the relationship between E and Y, which could also inform the future development of methods for E with a quantitative metric.

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.

Humans are highly adaptable, swiftly switching between different modes to progressively handle different tasks, situations and contexts. In Human-object interaction (HOI) activities, these modes can be attributed to two mechanisms: (1) the large-scale consistent plan for the whole activity and (2) the small-scale children interactive actions that start and end along the timeline. While neuroscience and cognitive science have confirmed this multi-mechanism nature of human behavior, machine modeling approaches for human motion are trailing behind. While attempted to use gradually morphing structures (e.g., graph attention networks) to model the dynamic HOI patterns, they miss the expeditious and discrete mode-switching nature of the human motion. To bridge that gap, this work proposes to model two concurrent mechanisms that jointly control human motion: the Persistent process that runs continually on the global scale, and the Transient sub-processes that operate intermittently on the local context of the human while interacting with objects. These two mechanisms form an interactive Persistent-Transient Duality that synergistically governs the activity sequences. We model this conceptual duality by a parent-child neural network of Persistent and Transient channels with a dedicated neural module for dynamic mechanism switching. The framework is trialed on HOI motion forecasting. On two rich datasets and a wide variety of settings, the model consistently delivers superior performances, proving its suitability for the challenge.

Motivated by equilibrium models of labor markets, we develop a formulation of causal strategic classification in which strategic agents can directly manipulate their outcomes. As an application, we compare employers that anticipate the strategic response of a labor force with employers that do not. We show through a combination of theory and experiment that employers with performatively optimal hiring policies improve employer reward, labor force skill level, and in some cases labor force equity. On the other hand, we demonstrate that performative employers harm labor force utility and fail to prevent discrimination in other cases.

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.

Formal proofs are challenging to write even for experienced experts. Recent progress in Neural Theorem Proving (NTP) shows promise in expediting this process. However, the formal corpora available on the Internet are limited compared to the general text, posing a significant data scarcity challenge for NTP. To address this issue, this work proposes Alchemy, a general framework for data synthesis that constructs formal theorems through symbolic mutation. Specifically, for each candidate theorem in Mathlib, we identify all invocable theorems that can be used to rewrite or apply to it. Subsequently, we mutate the candidate theorem by replacing the corresponding term in the statement with its equivalent form or antecedent. As a result, our method increases the number of theorems in Mathlib by an order of magnitude, from 110k to 6M. Furthermore, we perform continual pretraining and supervised finetuning on this augmented corpus for large language models. Experimental results demonstrate the effectiveness of our approach, achieving a 5% absolute performance improvement on Leandojo benchmark. Additionally, our synthetic data achieve a 2.5% absolute performance gain on the out-of-distribution miniF2F benchmark. To provide further insights, we conduct a comprehensive analysis of synthetic data composition and the training paradigm, offering valuable guidance for developing a strong theorem prover.

Research in cultural evolution aims at providing causal explanations for the change of culture over time. Over the past decades, this field has generated an important body of knowledge, using experimental, historical, and computational methods. While computational models have been very successful at generating testable hypotheses about the effects of several factors, such as population structure or transmission biases, some phenomena have so far been more complex to capture using agent-based and formal models. This is in particular the case for the effect of the transformations of social information induced by evolved cognitive mechanisms. We here propose that leveraging the capacity of Large Language Models (LLMs) to mimic human behavior may be fruitful to address this gap. On top of being an useful approximation of human cultural dynamics, multi-agents models featuring generative agents are also important to study for their own sake. Indeed, as artificial agents are bound to participate more and more to the evolution of culture, it is crucial to better understand the dynamics of machine-generated cultural evolution. We here present a framework for simulating cultural evolution in populations of LLMs, allowing the manipulation of variables known to be important in cultural evolution, such as network structure, personality, and the way social information is aggregated and transformed. The software we developed for conducting these simulations is open-source and features an intuitive user-interface, which we hope will help to build bridges between the fields of cultural evolution and generative artificial intelligence.

We introduce a framework for automatically defining and learning deep generative models with problem-specific structure. We tackle problem domains that are more traditionally solved by algorithms such as sorting, constraint satisfaction for Sudoku, and matrix factorization. Concretely, we train diffusion models with an architecture tailored to the problem specification. This problem specification should contain a graphical model describing relationships between variables, and often benefits from explicit representation of subcomputations. Permutation invariances can also be exploited. Across a diverse set of experiments we improve the scaling relationship between problem dimension and our model's performance, in terms of both training time and final accuracy. Our code can be found at https://github.com/plai-group/gsdm.

In the realm of machine learning, traditional model development and automated approaches like AutoML typically rely on layers of abstraction, such as tree-based or Cartesian genetic programming. Our study introduces "Guided Evolution" (GE), a novel framework that diverges from these methods by utilizing Large Language Models (LLMs) to directly modify code. GE leverages LLMs for a more intelligent, supervised evolutionary process, guiding mutations and crossovers. Our unique "Evolution of Thought" (EoT) technique further enhances GE by enabling LLMs to reflect on and learn from the outcomes of previous mutations. This results in a self-sustaining feedback loop that augments decision-making in model evolution. GE maintains genetic diversity, crucial for evolutionary algorithms, by leveraging LLMs' capability to generate diverse responses from expertly crafted prompts and modulate model temperature. This not only accelerates the evolution process but also injects expert like creativity and insight into the process. Our application of GE in evolving the ExquisiteNetV2 model demonstrates its efficacy: the LLM-driven GE autonomously produced variants with improved accuracy, increasing from 92.52% to 93.34%, without compromising model compactness. This underscores the potential of LLMs to accelerate the traditional model design pipeline, enabling models to autonomously evolve and enhance their own designs.

Causal representation learning has showed a variety of settings in which we can disentangle latent variables with identifiability guarantees (up to some reasonable equivalence class). Common to all of these approaches is the assumption that (1) the latent variables are represented as d-dimensional vectors, and (2) that the observations are the output of some injective generative function of these latent variables. While these assumptions appear benign, we show that when the observations are of multiple objects, the generative function is no longer injective and disentanglement fails in practice. We can address this failure by combining recent developments in object-centric learning and causal representation learning. By modifying the Slot Attention architecture arXiv:2006.15055, we develop an object-centric architecture that leverages weak supervision from sparse perturbations to disentangle each object's properties. This approach is more data-efficient in the sense that it requires significantly fewer perturbations than a comparable approach that encodes to a Euclidean space and we show that this approach successfully disentangles the properties of a set of objects in a series of simple image-based disentanglement experiments.

We introduce Causal Diffusion as the autoregressive (AR) counterpart of Diffusion models. It is a next-token(s) forecasting framework that is friendly to both discrete and continuous modalities and compatible with existing next-token prediction models like LLaMA and GPT. While recent works attempt to combine diffusion with AR models, we show that introducing sequential factorization to a diffusion model can substantially improve its performance and enables a smooth transition between AR and diffusion generation modes. Hence, we propose CausalFusion - a decoder-only transformer that dual-factorizes data across sequential tokens and diffusion noise levels, leading to state-of-the-art results on the ImageNet generation benchmark while also enjoying the AR advantage of generating an arbitrary number of tokens for in-context reasoning. We further demonstrate CausalFusion's multimodal capabilities through a joint image generation and captioning model, and showcase CausalFusion's ability for zero-shot in-context image manipulations. We hope that this work could provide the community with a fresh perspective on training multimodal models over discrete and continuous data.

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.

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.

Data-driven modelling and synthesis of motion is an active research area with applications that include animation, games, and social robotics. This paper introduces a new class of probabilistic, generative, and controllable motion-data models based on normalising flows. Models of this kind can describe highly complex distributions, yet can be trained efficiently using exact maximum likelihood, unlike GANs or VAEs. Our proposed model is autoregressive and uses LSTMs to enable arbitrarily long time-dependencies. Importantly, is is also causal, meaning that each pose in the output sequence is generated without access to poses or control inputs from future time steps; this absence of algorithmic latency is important for interactive applications with real-time motion control. The approach can in principle be applied to any type of motion since it does not make restrictive, task-specific assumptions regarding the motion or the character morphology. We evaluate the models on motion-capture datasets of human and quadruped locomotion. Objective and subjective results show that randomly-sampled motion from the proposed method outperforms task-agnostic baselines and attains a motion quality close to recorded motion capture.

Feature engineering has become one of the most important steps to improve model prediction performance, and to produce quality datasets. However, this process requires non-trivial domain-knowledge which involves a time-consuming process. Thereby, automating such process has become an active area of research and of interest in industrial applications. In this paper, a novel method, called Meta-learning and Causality Based Feature Engineering (MACFE), is proposed; our method is based on the use of meta-learning, feature distribution encoding, and causality feature selection. In MACFE, meta-learning is used to find the best transformations, then the search is accelerated by pre-selecting "original" features given their causal relevance. Experimental evaluations on popular classification datasets show that MACFE can improve the prediction performance across eight classifiers, outperforms the current state-of-the-art methods in average by at least 6.54%, and obtains an improvement of 2.71% over the best previous works.

Most existing debiasing methods for multimodal models, including causal intervention and inference methods, utilize approximate heuristics to represent the biases, such as shallow features from early stages of training or unimodal features for multimodal tasks like VQA, etc., which may not be accurate. In this paper, we study bias arising from confounders in a causal graph for multimodal data and examine a novel approach that leverages causally-motivated information minimization to learn the confounder representations. Robust predictive features contain diverse information that helps a model generalize to out-of-distribution data. Hence, minimizing the information content of features obtained from a pretrained biased model helps learn the simplest predictive features that capture the underlying data distribution. We treat these features as confounder representations and use them via methods motivated by causal theory to remove bias from models. We find that the learned confounder representations indeed capture dataset biases, and the proposed debiasing methods improve out-of-distribution (OOD) performance on multiple multimodal datasets without sacrificing in-distribution performance. Additionally, we introduce a novel metric to quantify the sufficiency of spurious features in models' predictions that further demonstrates the effectiveness of our proposed methods. Our code is available at: https://github.com/Vaidehi99/CausalInfoMin

Epidemiologists aiming to model the dynamics of global events face a significant challenge in identifying the factors linked with anomalies such as disease outbreaks. In this paper, we present a novel method for identifying the most important development sectors sensitive to disease outbreaks by using global development indicators as markers. We use statistical methods to assess the causative linkages between these indicators and disease outbreaks, as well as to find the most often ranked indicators. We used data imputation techniques in addition to statistical analysis to convert raw real-world data sets into meaningful data for causal inference. The application of various algorithms for the detection of causal linkages between the indicators is the subject of this research. Despite the fact that disparities in governmental policies between countries account for differences in causal linkages, several indicators emerge as important determinants sensitive to disease outbreaks over the world in the 21st Century.

The Right to Explanation and the Right to be Forgotten are two important principles outlined to regulate algorithmic decision making and data usage in real-world applications. While the right to explanation allows individuals to request an actionable explanation for an algorithmic decision, the right to be forgotten grants them the right to ask for their data to be deleted from all the databases and models of an organization. Intuitively, enforcing the right to be forgotten may trigger model updates which in turn invalidate previously provided explanations, thus violating the right to explanation. In this work, we investigate the technical implications arising due to the interference between the two aforementioned regulatory principles, and propose the first algorithmic framework to resolve the tension between them. To this end, we formulate a novel optimization problem to generate explanations that are robust to model updates due to the removal of training data instances by data deletion requests. We then derive an efficient approximation algorithm to handle the combinatorial complexity of this optimization problem. We theoretically demonstrate that our method generates explanations that are provably robust to worst-case data deletion requests with bounded costs in case of linear models and certain classes of non-linear models. Extensive experimentation with real-world datasets demonstrates the efficacy of the proposed framework.

Recent advances in generative AI have brought incredible breakthroughs in several areas, including medical imaging. These generative models have tremendous potential not only to help safely share medical data via synthetic datasets but also to perform an array of diverse applications, such as anomaly detection, image-to-image translation, denoising, and MRI reconstruction. However, due to the complexity of these models, their implementation and reproducibility can be difficult. This complexity can hinder progress, act as a use barrier, and dissuade the comparison of new methods with existing works. In this study, we present MONAI Generative Models, a freely available open-source platform that allows researchers and developers to easily train, evaluate, and deploy generative models and related applications. Our platform reproduces state-of-art studies in a standardised way involving different architectures (such as diffusion models, autoregressive transformers, and GANs), and provides pre-trained models for the community. We have implemented these models in a generalisable fashion, illustrating that their results can be extended to 2D or 3D scenarios, including medical images with different modalities (like CT, MRI, and X-Ray data) and from different anatomical areas. Finally, we adopt a modular and extensible approach, ensuring long-term maintainability and the extension of current applications for future features.

Procedural planning aims to implement complex high-level goals by decomposition into sequential simpler low-level steps. Although procedural planning is a basic skill set for humans in daily life, it remains a challenge for large language models (LLMs) that lack a deep understanding of the cause-effect relations in procedures. Previous methods require manual exemplars to acquire procedural planning knowledge from LLMs in the zero-shot setting. However, such elicited pre-trained knowledge in LLMs induces spurious correlations between goals and steps, which impair the model generalization to unseen tasks. In contrast, this paper proposes a neuro-symbolic procedural PLANner (PLAN) that elicits procedural planning knowledge from the LLMs with commonsense-infused prompting. To mitigate spurious goal-step correlations, we use symbolic program executors on the latent procedural representations to formalize prompts from commonsense knowledge bases as a causal intervention toward the Structural Causal Model. Both automatic and human evaluations on WikiHow and RobotHow show the superiority of PLAN on procedural planning without further training or manual exemplars.

We introduce the concept of Automated Causal Discovery (AutoCD), defined as any system that aims to fully automate the application of causal discovery and causal reasoning methods. AutoCD's goal is to deliver all causal information that an expert human analyst would and answer a user's causal queries. We describe the architecture of such a platform, and illustrate its performance on synthetic data sets. As a case study, we apply it on temporal telecommunication data. The system is general and can be applied to a plethora of causal discovery problems.

The paradigm of pretrained deep learning models has recently emerged in artificial intelligence practice, allowing deployment in numerous societal settings with limited computational resources, but also embedding biases and enabling unintended negative uses. In this paper, we treat pretrained models as objects of study and discuss the ethical impacts of their sociological position. We discuss how pretrained models are developed and compared under the common task framework, but that this may make self-regulation inadequate. Further how pretrained models may have a performative effect on society that exacerbates biases. We then discuss how pretrained models move through actor networks as a kind of computationally immutable mobile, but that users also act as agents of technological change by reinterpreting them via fine-tuning and transfer. We further discuss how users may use pretrained models in malicious ways, drawing a novel connection between the responsible innovation and user-centered innovation literatures. We close by discussing how this sociological understanding of pretrained models can inform AI governance frameworks for fairness, accountability, and transparency.

Scientific discovery relies on scientists generating novel hypotheses that undergo rigorous experimental validation. To augment this process, we introduce an AI co-scientist, a multi-agent system built on Gemini 2.0. The AI co-scientist is intended to help uncover new, original knowledge and to formulate demonstrably novel research hypotheses and proposals, building upon prior evidence and aligned to scientist-provided research objectives and guidance. The system's design incorporates a generate, debate, and evolve approach to hypothesis generation, inspired by the scientific method and accelerated by scaling test-time compute. Key contributions include: (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling; (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute, improving hypothesis quality. While general purpose, we focus development and validation in three biomedical areas: drug repurposing, novel target discovery, and explaining mechanisms of bacterial evolution and anti-microbial resistance. For drug repurposing, the system proposes candidates with promising validation findings, including candidates for acute myeloid leukemia that show tumor inhibition in vitro at clinically applicable concentrations. For novel target discovery, the AI co-scientist proposed new epigenetic targets for liver fibrosis, validated by anti-fibrotic activity and liver cell regeneration in human hepatic organoids. Finally, the AI co-scientist recapitulated unpublished experimental results via a parallel in silico discovery of a novel gene transfer mechanism in bacterial evolution. These results, detailed in separate, co-timed reports, demonstrate the potential to augment biomedical and scientific discovery and usher an era of AI empowered scientists.

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.

Recognizing the prevalence of domain shift as a common challenge in machine learning, various domain generalization (DG) techniques have been developed to enhance the performance of machine learning systems when dealing with out-of-distribution (OOD) data. Furthermore, in real-world scenarios, data distributions can gradually change across a sequence of sequential domains. While current methodologies primarily focus on improving model effectiveness within these new domains, they often overlook fairness issues throughout the learning process. In response, we introduce an innovative framework called Counterfactual Fairness-Aware Domain Generalization with Sequential Autoencoder (CDSAE). This approach effectively separates environmental information and sensitive attributes from the embedded representation of classification features. This concurrent separation not only greatly improves model generalization across diverse and unfamiliar domains but also effectively addresses challenges related to unfair classification. Our strategy is rooted in the principles of causal inference to tackle these dual issues. To examine the intricate relationship between semantic information, sensitive attributes, and environmental cues, we systematically categorize exogenous uncertainty factors into four latent variables: 1) semantic information influenced by sensitive attributes, 2) semantic information unaffected by sensitive attributes, 3) environmental cues influenced by sensitive attributes, and 4) environmental cues unaffected by sensitive attributes. By incorporating fairness regularization, we exclusively employ semantic information for classification purposes. Empirical validation on synthetic and real-world datasets substantiates the effectiveness of our approach, demonstrating improved accuracy levels while ensuring the preservation of fairness in the evolving landscape of continuous domains.

We have recently witnessed a number of impressive results on hard mathematical reasoning problems with language models. At the same time, the robustness of these models has also been called into question; recent works have shown that models can rely on shallow patterns in the problem description when generating a solution. Building on the idea of behavioral testing, we propose a novel framework, which pins down the causal effect of various factors in the input, e.g., the surface form of the problem text, the operands, and math operators on the output solution. By grounding the behavioral analysis in a causal graph describing an intuitive reasoning process, we study the behavior of language models in terms of robustness and sensitivity to direct interventions in the input space. We apply our framework on a test bed of math word problems. Our analysis shows that robustness does not appear to continuously improve as a function of size, but the GPT-3 Davinci models (175B) achieve a dramatic improvement in both robustness and sensitivity compared to all other GPT variants.

Learning from off-policy data is essential for sample-efficient reinforcement learning. In the present work, we build on the insight that the advantage function can be understood as the causal effect of an action on the return, and show that this allows us to decompose the return of a trajectory into parts caused by the agent's actions (skill) and parts outside of the agent's control (luck). Furthermore, this decomposition enables us to naturally extend Direct Advantage Estimation (DAE) to off-policy settings (Off-policy DAE). The resulting method can learn from off-policy trajectories without relying on importance sampling techniques or truncating off-policy actions. We draw connections between Off-policy DAE and previous methods to demonstrate how it can speed up learning and when the proposed off-policy corrections are important. Finally, we use the MinAtar environments to illustrate how ignoring off-policy corrections can lead to suboptimal policy optimization performance.

Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of molecular trajectories as a paradigm for learning flexible multi-task surrogate models of MD from data. By conditioning on appropriately chosen frames of the trajectory, we show such generative models can be adapted to diverse tasks such as forward simulation, transition path sampling, and trajectory upsampling. By alternatively conditioning on part of the molecular system and inpainting the rest, we also demonstrate the first steps towards dynamics-conditioned molecular design. We validate the full set of these capabilities on tetrapeptide simulations and show that our model can produce reasonable ensembles of protein monomers. Altogether, our work illustrates how generative modeling can unlock value from MD data towards diverse downstream tasks that are not straightforward to address with existing methods or even MD itself. Code is available at https://github.com/bjing2016/mdgen.

Conditional generative models typically demand large annotated training sets to achieve high-quality synthesis. As a result, there has been significant interest in designing models that perform plug-and-play generation, i.e., to use a predefined or pretrained model, which is not explicitly trained on the generative task, to guide the generative process (e.g., using language). However, such guidance is typically useful only towards synthesizing high-level semantics rather than editing fine-grained details as in image-to-image translation tasks. To this end, and capitalizing on the powerful fine-grained generative control offered by the recent diffusion-based generative models, we introduce Steered Diffusion, a generalized framework for photorealistic zero-shot conditional image generation using a diffusion model trained for unconditional generation. The key idea is to steer the image generation of the diffusion model at inference time via designing a loss using a pre-trained inverse model that characterizes the conditional task. This loss modulates the sampling trajectory of the diffusion process. Our framework allows for easy incorporation of multiple conditions during inference. We present experiments using steered diffusion on several tasks including inpainting, colorization, text-guided semantic editing, and image super-resolution. Our results demonstrate clear qualitative and quantitative improvements over state-of-the-art diffusion-based plug-and-play models while adding negligible additional computational cost.

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.

Machine learning (ML) recourse techniques are increasingly used in high-stakes domains, providing end users with actions to alter ML predictions, but they assume ML developers understand what input variables can be changed. However, a recourse plan's actionability is subjective and unlikely to match developers' expectations completely. We present GAM Coach, a novel open-source system that adapts integer linear programming to generate customizable counterfactual explanations for Generalized Additive Models (GAMs), and leverages interactive visualizations to enable end users to iteratively generate recourse plans meeting their needs. A quantitative user study with 41 participants shows our tool is usable and useful, and users prefer personalized recourse plans over generic plans. Through a log analysis, we explore how users discover satisfactory recourse plans, and provide empirical evidence that transparency can lead to more opportunities for everyday users to discover counterintuitive patterns in ML models. GAM Coach is available at: https://poloclub.github.io/gam-coach/.

We investigate the mechanism design problem faced by a principal who hires multiple agents to gather and report costly information. Then, the principal exploits the information to make an informed decision. We model this problem as a game, where the principal announces a mechanism consisting in action recommendations and a payment function, a.k.a. scoring rule. Then, each agent chooses an effort level and receives partial information about an underlying state of nature based on the effort. Finally, the agents report the information (possibly non-truthfully), the principal takes a decision based on this information, and the agents are paid according to the scoring rule. While previous work focuses on single-agent problems, we consider multi-agents settings. This poses the challenge of coordinating the agents' efforts and aggregating correlated information. Indeed, we show that optimal mechanisms must correlate agents' efforts, which introduces externalities among the agents, and hence complex incentive compatibility constraints and equilibrium selection problems. First, we design a polynomial-time algorithm to find an optimal incentive compatible mechanism. Then, we study an online problem, where the principal repeatedly interacts with a group of unknown agents. We design a no-regret algorithm that provides mathcal{O}(T^{2/3}) regret with respect to an optimal mechanism, matching the state-of-the-art bound for single-agent settings.