深度学习 · causal inference

Structural causal models (SCMs) are a powerful tool for understanding the complex causal relationships that underlie many real-world systems. As these systems grow in size, the number of variables and complexity of interactions between them does, too. Thus, becoming convoluted and difficult to analyze. This is particularly true in the context of machine learning and artificial intelligence, where an ever increasing amount of data demands for new methods to simplify and compress large scale SCM. While methods for marginalizing and abstracting SCM already exist today, they may destroy the causality of the marginalized model. To alleviate this, we introduce the concept of consolidating causal mechanisms to transform large-scale SCM while preserving consistent interventional behaviour. We show consolidation is a powerful method for simplifying SCM, discuss reduction of computational complexity and give a perspective on generalizing abilities of consolidated SCM.

Causality is a central concept in a wide range of research areas, yet there is still no universally agreed axiomatisation of causality. We view causality both as an extension of probability theory and as a study of what happens when one intervenes on a system, and argue in favour of taking Kolmogorov's measure-theoretic axiomatisation of probability as the starting point towards an axiomatisation of causality. To that end, we propose the notion of a causal space, consisting of a probability space along with a collection of transition probability kernels, called causal kernels, that encode the causal information of the space. Our proposed framework is not only rigorously grounded in measure theory, but it also sheds light on long-standing limitations of existing frameworks including, for example, cycles, latent variables and stochastic processes.

Constraint-based causal discovery methods leverage conditional independence tests to infer causal relationships in a wide variety of applications. Just as the majority of machine learning methods, existing work focuses on studying $\textit{independent and identically distributed}$ data. However, it is known that even with infinite $i.i.d.\$ data, constraint-based methods can only identify causal structures up to broad Markov equivalence classes, posing a fundamental limitation for causal discovery. In this work, we observe that exchangeable data contains richer conditional independence structure than $i.i.d.\$ data, and show how the richer structure can be leveraged for causal discovery. We first present causal de Finetti theorems, which state that exchangeable distributions with certain non-trivial conditional independences can always be represented as $\textit{independent causal mechanism (ICM)}$ generative processes. We then present our main identifiability theorem, which shows that given data from an ICM generative process, its unique causal structure can be identified through performing conditional independence tests. We finally develop a causal discovery algorithm and demonstrate its applicability to inferring causal relationships from multi-environment data.

Causal disentanglement aims to uncover a representation of data using latent variables that are interrelated through a causal model. Such a representation is identifiable if the latent model that explains the data is unique. In this paper, we focus on the scenario where unpaired observational and interventional data are available, with each intervention changing the mechanism of a latent variable. When the causal variables are fully observed, statistically consistent algorithms have been developed to identify the causal model under faithfulness assumptions. We here show that identifiability can still be achieved with unobserved causal variables, given a generalized notion of faithfulness. Our results guarantee that we can recover the latent causal model up to an equivalence class and predict the effect of unseen combinations of interventions, in the limit of infinite data. We implement our causal disentanglement framework by developing an autoencoding variational Bayes algorithm and apply it to the problem of predicting combinatorial perturbation effects in genomics.

One of the fundamental challenges found throughout the data sciences is to explain why things happen in specific ways, or through which mechanisms a certain variable $X$ exerts influences over another variable $Y$. In statistics and machine learning, significant efforts have been put into developing machinery to estimate correlations across variables efficiently. In causal inference, a large body of literature is concerned with the decomposition of causal effects under the rubric of mediation analysis. However, many variations are spurious in nature, including different phenomena throughout the applied sciences. Despite the statistical power to estimate correlations and the identification power to decompose causal effects, there is still little understanding of the properties of spurious associations and how they can be decomposed in terms of the underlying causal mechanisms. In this manuscript, we develop formal tools for decomposing spurious variations in both Markovian and Semi-Markovian models. We prove the first results that allow a non-parametric decomposition of spurious effects and provide sufficient conditions for the identification of such decompositions. The described approach has several applications, ranging from explainable and fair AI to questions in epidemiology and medicine, and we empirically demonstrate its use.

Causal inference from observational data is crucial for many disciplines such as medicine and economics. However, sharp bounds for causal effects under relaxations of the unconfoundedness assumption (causal sensitivity analysis) are subject to ongoing research. So far, works with sharp bounds are restricted to fairly simple settings (e.g., a single binary treatment). In this paper, we propose a unified framework for causal sensitivity analysis under unobserved confounding in various settings. For this, we propose a flexible generalization of the marginal sensitivity model (MSM) and then derive sharp bounds for a large class of causal effects. This includes (conditional) average treatment effects, effects for mediation analysis and path analysis, and distributional effects. Furthermore, our sensitivity model is applicable to discrete, continuous, and time-varying treatments. It allows us to interpret the partial identification problem under unobserved confounding as a distribution shift in the latent confounders while evaluating the causal effect of interest. In the special case of a single binary treatment, our bounds for (conditional) average treatment effects coincide with recent optimality results for causal sensitivity analysis. Finally, we propose a scalable algorithm to estimate our sharp bounds from observational data.

We consider a setting where there are $N$ heterogeneous units and $p$ interventions. Our goal is to learn unit-specific potential outcomes for any combination of these $p$ interventions, i.e., $N \times 2^p$ causal parameters. Choosing a combination of interventions is a problem that naturally arises in a variety of applications such as factorial design experiments and recommendation engines (e.g., showing a set of movies that maximizes engagement for a given user). Running $N \times 2^p$ experiments to estimate the various parameters is likely expensive and/or infeasible as $N$ and $p$ grow. Further, with observational data there is likely confounding, i.e., whether or not a unit is seen under a combination is correlated with its potential outcome under that combination. We study this problem under a novel model that imposes latent structure across both units and combinations of interventions. Specifically, we assume latent similarity in potential outcomes across units (i.e., the matrix of potential outcomes is approximately rank $r$) and regularity in how combinations of interventions interact (i.e., the coefficients in the Fourier expansion of the potential outcomes is approximately $s$ sparse). We establish identification for all $N \times 2^p$ parameters despite unobserved confounding. We propose an estimation procedure, Synthetic Combinations, and establish finite-sample consistency under precise conditions on the observation pattern. We show that Synthetic Combinations is able to consistently estimate unit-specific potential outcomes given a total of $\text{poly}(r) \times \left( N + s^2p\right)$ observations. In comparison, previous methods that do not exploit structure across both units and combinations have poorer sample complexity scaling as $\min(N \times s^2p, \ \ r \times (N + 2^p))$.

Constructing a directed cyclic graph (DCG) is challenged by both algorithmic difficulty and computational burden. Comparing multiple DCGs is even more difficult, compounded by the need to identify dynamic causalities across graphs. We propose to unify multiple DCGs with a single structural model and develop a limited-information-based method to simultaneously construct multiple networks and infer their disparities, which can be visualized by appropriate correspondence analysis. The algorithm provides DCGs with robust non-asymptotic theoretical properties. It is designed with two sequential stages, each of which involves parallel computation tasks that are scalable to the network complexity. Taking advantage of high-performance clusters, our method makes it possible to evaluate the statistical significance of DCGs using the bootstrap method. We demonstrated the effectiveness of our method by applying it to synthetic and real datasets.

In computational social science (CSS), researchers analyze documents to explain social and political phenomena. In most scenarios, CSS researchers first obtain labels for documents and then explain labels using interpretable regression analyses in the second step. One increasingly common way to annotate documents cheaply at scale is through large language models (LLMs). However, like other scalable ways of producing annotations, such surrogate labels are often imperfect and biased. We present a new algorithm for using imperfect annotation surrogates for downstream statistical analyses while guaranteeing statistical properties—like asymptotic unbiasedness and proper uncertainty quantification—which are fundamental to CSS research. We show that direct use of surrogate labels in downstream statistical analyses leads to substantial bias and invalid confidence intervals, even with high surrogate accuracy of 80-90\%. To address this, we build on debiased machine learning to propose the design-based supervised learning (DSL) estimator. DSL employs a doubly-robust procedure to combine surrogate labels with a smaller number of high-quality, gold-standard labels. Our approach guarantees valid inference for downstream statistical analyses, even when surrogates are arbitrarily biased and without requiring stringent assumptions, by controlling the probability of sampling documents for gold-standard labeling. Both our theoretical analysis and experimental results show that DSL provides valid statistical inference while achieving root mean squared errors comparable to existing alternatives that focus only on prediction without inferential guarantees.

One of the grand challenges of cell biology is inferring the gene regulatory network (GRN) which describes interactions between genes and their products that control gene expression and cellular function. We can treat this as a causal discovery problem but with two non-standard challenges: (1) regulatory networks are inherently cyclic so we should not model a GRN as a directed acyclic graph (DAG), and (2) observations have significant measurement noise so for typical sample sizes, there will always be a large equivalence class of graphs that are likely given the data, and we want methods that capture this uncertainty. Existing methods either focus on challenge (1), identifying cyclic structure from dynamics, or on challenge (2) learning complex Bayesian posteriors over directed acyclic graphs, but not both. In this paper we leverage the fact that it is possible to estimate the ``velocity'' of the expression of a gene with RNA velocity techniques to develop an approach that addresses both challenges. Because we have access to velocity information, we can treat the Bayesian structure learning problem as a problem of sparse identification of a dynamical system, capturing cyclic feedback loops through time. We leverage Generative Flow Networks (GFlowNets) to estimate the posterior distribution over the combinatorial space of possible sparse dependencies. Our results indicate that our method learns posteriors that better encapsulate the distributions of cyclic structures compared to counterpart state-of-the-art Bayesian structure learning approaches.

Inferring causal structure from data is a challenging task of fundamental importance in science. Often, observational data alone is not enough to uniquely identify a system’s causal structure. The use of interventional data can address this issue, however, acquiring these samples typically demands a considerable investment of time and physical or financial resources. In this work, we are concerned with the acquisition of interventional data in a targeted manner to minimize the number of required experiments. We propose a novel Gradient-based Intervention Targeting method, abbreviated GIT, that ’trusts’ the gradient estimator of a gradient-based causal discovery framework to provide signals for the intervention targeting function. We provide extensive experiments in simulated and real-world datasets and demonstrate that GIT performs on par with competitive baselines, surpassing them in the low-data regime.

Motivated by a recent literature on the double-descent phenomenon in machine learning, we consider highly over-parameterized models in causal inference, including synthetic control with many control units. In such models, there may be so many free parameters that the model fits the training data perfectly. We first investigate high-dimensional linear regression for imputing wage data and estimating average treatment effects, where we find that models with many more covariates than sample size can outperform simple ones. We then document the performance of high-dimensional synthetic control estimators with many control units. We find that adding control units can help improve imputation performance even beyond the point where the pre-treatment fit is perfect. We provide a unified theoretical perspective on the performance of these high-dimensional models. Specifically, we show that more complex models can be interpreted as model-averaging estimators over simpler ones, which we link to an improvement in average performance. This perspective yields concrete insights into the use of synthetic control when control units are many relative to the number of pre-treatment periods.

We provide the first convergence guarantee for black-box variational inference (BBVI) with the reparameterization gradient. While preliminary investigations worked on simplified versions of BBVI (e.g., bounded domain, bounded support, only optimizing for the scale, and such), our setup does not need any such algorithmic modifications. Our results hold for log-smooth posterior densities with and without strong log-concavity and the location-scale variational family. Notably, our analysis reveals that certain algorithm design choices commonly employed in practice, such as nonlinear parameterizations of the scale matrix, can result in suboptimal convergence rates. Fortunately, running BBVI with proximal stochastic gradient descent fixes these limitations and thus achieves the strongest known convergence guarantees. We evaluate this theoretical insight by comparing proximal SGD against other standard implementations of BBVI on large-scale Bayesian inference problems.

We study the problem of combining neural networks with symbolic reasoning. Recently introduced frameworks for Probabilistic Neurosymbolic Learning (PNL), such as DeepProbLog, perform exponential-time exact inference, limiting the scalability of PNL solutions. We introduce Approximate Neurosymbolic Inference (A-NeSI): a new framework for PNL that uses neural networks for scalable approximate inference. A-NeSI 1) performs approximate inference in polynomial time without changing the semantics of probabilistic logics; 2) is trained using data generated by the background knowledge; 3) can generate symbolic explanations of predictions; and 4) can guarantee the satisfaction of logical constraints at test time, which is vital in safety-critical applications. Our experiments show that A-NeSI is the first end-to-end method to solve three neurosymbolic tasks with exponential combinatorial scaling. Finally, our experiments show that A-NeSI achieves explainability and safety without a penalty in performance.

Conventional imitation learning assumes access to the actions of demonstrators, but these motor signals are often non-observable in naturalistic settings. Additionally, sequential decision-making behaviors in these settings can deviate from the assumptions of a standard Markov Decision Process (MDP). To address these challenges, we explore deep generative modeling of state-only sequences with non-Markov Decision Process (nMDP), where the policy is an energy-based prior in the latent space of the state transition generator. We develop maximum likelihood estimation to achieve model-based imitation, which involves short-run MCMC sampling from the prior and importance sampling for the posterior. The learned model enables $\textit{decision-making as inference}$: model-free policy execution is equivalent to prior sampling, model-based planning is posterior sampling initialized from the policy. We demonstrate the efficacy of the proposed method in a prototypical path planning task with non-Markovian constraints and show that the learned model exhibits strong performances in challenging domains from the MuJoCo suite.

Constraint-based causal discovery algorithms learn part of the causal graph structure by systematically testing conditional independences observed in the data. These algorithms, such as the PC algorithm and its variants, rely on graphical characterizations of the so-called equivalence class of causal graphs proposed by Pearl. However, constraint-based causal discovery algorithms struggle when data is limited since conditional independence tests quickly lose their statistical power, especially when the conditioning set is large. To address this, we propose using conditional independence tests where the size of the conditioning set is upper bounded by some integer k for robust causal discovery. The existing graphical characterizations of the equivalence classes of causal graphs are not applicable when we cannot leverage all the conditional independence statements. We first define the notion of k-Markov equivalence: Two causal graphs are k-Markov equivalent if they entail the same conditional independence constraints where the conditioning set size is upper bounded by k. We propose a novel representation that allows us to graphically characterize k-Markov equivalence between two causal graphs. We propose a sound constraint-based algorithm called the k-PC algorithm for learning this equivalence class. Finally, we conduct synthetic, and semi-synthetic experiments to demonstrate that the k-PC algorithm enables more robust causal discovery in the small sample regime compared to the baseline algorithms.

Injecting structure into neural networks enables learning functions that satisfy invariances with respect to subsets of inputs. For instance, when learning generative models using neural networks, it is advantageous to encode the conditional independence structure of observed variables, often in the form of Bayesian networks. We propose the Structured Neural Network (StrNN), which injects structure through masking pathways in a neural network. The masks are designed via a novel relationship we explore between neural network architectures and binary matrix factorization, to ensure that the desired independencies are respected. We devise and study practical algorithms for this otherwise NP-hard design problem based on novel objectives that control the model architecture. We demonstrate the utility of StrNN in three applications: (1) binary and Gaussian density estimation with StrNN, (2) real-valued density estimation with Structured Autoregressive Flows (StrAFs) and Structured Continuous Normalizing Flows (StrCNF), and (3) interventional and counterfactual analysis with StrAFs for causal inference. Our work opens up new avenues for learning neural networks that enable data-efficient generative modeling and the use of normalizing flows for causal effect estimation.

We propose Tree Variational Autoencoder (TreeVAE), a new generative hierarchical clustering model that learns a flexible tree-based posterior distribution over latent variables. TreeVAE hierarchically divides samples according to their intrinsic characteristics, shedding light on hidden structures in the data. It adapts its architecture to discover the optimal tree for encoding dependencies between latent variables. The proposed tree-based generative architecture enables lightweight conditional inference and improves generative performance by utilizing specialized leaf decoders. We show that TreeVAE uncovers underlying clusters in the data and finds meaningful hierarchical relations between the different groups on a variety of datasets, including real-world imaging data. We present empirically that TreeVAE provides a more competitive log-likelihood lower bound than the sequential counterparts. Finally, due to its generative nature, TreeVAE is able to generate new samples from the discovered clusters via conditional sampling.

Machine learning (ML) models have been widely used to make predictions. Instead of a predictive statement about future outcomes, in many situations we want to pursue a decision: what can we do to avoid the undesired future if an ML model predicts so? In this paper, we present a rehearsal learning framework, in which decisions that can persuasively avoid the happening of undesired outcomes can be found and recommended. Based on the influence relation, we characterize the generative process of variables with structural rehearsal models, consisting of a probabilistic graphical model called rehearsal graphs and structural equations, and find actionable decisions that can alter the outcome by reasoning under a Bayesian framework. Moreover, we present a probably approximately correct bound to quantify the associated risk of a decision. Experiments validate the effectiveness of the proposed rehearsal learning framework and the informativeness of the bound.

Bayesian neural networks (BNNs) provide a formalism to quantify and calibrate uncertainty in deep learning. Current inference approaches for BNNs often resort to few-sample estimation for scalability, which can harm predictive performance, while its alternatives tend to be computationally prohibitively expensive. We tackle this challenge by revealing a previously unseen connection between inference on BNNs and volume computation problems. With this observation, we introduce a novel collapsed inference scheme that performs Bayesian model averaging using collapsed samples. It improves over a Monte-Carlo sample by limiting sampling to a subset of the network weights while pairing it with some closed-form conditional distribution over the rest. A collapsed sample represents uncountably many models drawn from the approximate posterior and thus yields higher sample efficiency. Further, we show that the marginalization of a collapsed sample can be solved analytically and efficiently despite the non-linearity of neural networks by leveraging existing volume computation solvers. Our proposed use of collapsed samples achieves a balance between scalability and accuracy. On various regression and classification tasks, our collapsed Bayesian deep learning approach demonstrates significant improvements over existing methods and sets a new state of the art in terms of uncertainty estimation as well as predictive performance.