As predictive models -- e.g., from machine learning -- give likely outcomes, they may be used to reason on the effect of an intervention, a causal-inference task. The increasing complexity of health data has opened the door to a plethora of models, but also the Pandora box of model selection: which of these models yield the most valid causal estimates? Here we highlight that classic machine-learning model selection does not select the best outcome models for causal inference. Indeed, causal model selection should control both outcome errors for each individual, treated or not treated, whereas only one outcome is observed. Theoretically, simple risks used in machine learning do not control causal effects when treated and non-treated population differ too much. More elaborate risks build proxies of the causal error using ``nuisance'' re-weighting to compute it on the observed data. But does computing these nuisance adds noise to model selection? Drawing from an extensive empirical study, we outline a good causal model-selection procedure: using the so-called $R\text{-risk}$; using flexible estimators to compute the nuisance models on the train set; and splitting out 10\% of the data to compute risks.
Cell type deconvolution is a computational approach to infer proportions of individual cell types from bulk transcriptomics data. Though many new methods have been developed for cell type deconvolution, most of them only provide point estimation of the cell type proportions. On the other hand, estimates of the cell type proportions can be very noisy due to various sources of bias and randomness, and ignoring their uncertainty may greatly affect the validity of downstream analyses. In this paper, we propose a comprehensive statistical framework for cell type deconvolution and construct asymptotically valid confidence intervals both for each individual's cell type proportion and for quantifying how cell type proportions change across multiple bulk individuals in downstream regression analyses. Our analysis takes into account various factors including the biological randomness of gene expressions across cells and individuals, gene-gene dependence, and the cross-platform biases and sequencing errors, and avoids any parametric assumptions on the data distributions. We also provide identification conditions of the cell type proportions when there are arbitrary platforms-specific bias across sequencing technologies.
Robust feature selection is vital for creating reliable and interpretable Machine Learning (ML) models. When designing statistical prediction models in cases where domain knowledge is limited and underlying interactions are unknown, choosing the optimal set of features is often difficult. To mitigate this issue, we introduce a Multidata (M) causal feature selection approach that simultaneously processes an ensemble of time series datasets and produces a single set of causal drivers. This approach uses the causal discovery algorithms PC1 or PCMCI that are implemented in the Tigramite Python package. These algorithms utilize conditional independence tests to infer parts of the causal graph. Our causal feature selection approach filters out causally-spurious links before passing the remaining causal features as inputs to ML models (Multiple linear regression, Random Forest) that predict the targets. We apply our framework to the statistical intensity prediction of Western Pacific Tropical Cyclones (TC), for which it is often difficult to accurately choose drivers and their dimensionality reduction (time lags, vertical levels, and area-averaging). Using more stringent significance thresholds in the conditional independence tests helps eliminate spurious causal relationships, thus helping the ML model generalize better to unseen TC cases. M-PC1 with a reduced number of features outperforms M-PCMCI, non-causal ML, and other feature selection methods (lagged correlation, random), even slightly outperforming feature selection based on eXplainable Artificial Intelligence. The optimal causal drivers obtained from our causal feature selection help improve our understanding of underlying relationships and suggest new potential drivers of TC intensification.
Our goal is to produce methods for observational causal inference that are auditable, easy to troubleshoot, accurate for treatment effect estimation, and scalable to high-dimensional data. We describe a general framework called Model-to-Match that achieves these goals by (i) learning a distance metric via outcome modeling, (ii) creating matched groups using the distance metric, and (iii) using the matched groups to estimate treatment effects. Model-to-Match uses variable importance measurements to construct a distance metric, making it a flexible framework that can be adapted to various applications. Concentrating on the scalability of the problem in the number of potential confounders, we operationalize the Model-to-Match framework with LASSO. We derive performance guarantees for settings where LASSO outcome modeling consistently identifies all confounders (importantly without requiring the linear model to be correctly specified). We also provide experimental results demonstrating the method's auditability, accuracy, and scalability as well as extensions to more general nonparametric outcome modeling.
We propose a new nonparametric modeling framework for causal inference when outcomes depend on how agents are linked in a social or economic network. Such network interference describes a large literature on treatment spillovers, social interactions, social learning, information diffusion, disease and financial contagion, social capital formation, and more. Our approach works by first characterizing how an agent is linked in the network using the configuration of other agents and connections nearby as measured by path distance. The impact of a policy or treatment assignment is then learned by pooling outcome data across similarly configured agents. We demonstrate the approach by proposing an asymptotically valid test for the hypothesis of policy irrelevance/no treatment effects and bounding the mean-squared error of a k-nearest-neighbor estimator for the average or distributional policy effect/treatment response.
Causal discovery and causal reasoning are classically treated as separate and consecutive tasks: one first infers the causal graph, and then uses it to estimate causal effects of interventions. However, such a two-stage approach is uneconomical, especially in terms of actively collected interventional data, since the causal query of interest may not require a fully-specified causal model. From a Bayesian perspective, it is also unnatural, since a causal query (e.g., the causal graph or some causal effect) can be viewed as a latent quantity subject to posterior inference -- other unobserved quantities that are not of direct interest (e.g., the full causal model) ought to be marginalized out in this process and contribute to our epistemic uncertainty. In this work, we propose Active Bayesian Causal Inference (ABCI), a fully-Bayesian active learning framework for integrated causal discovery and reasoning, which jointly infers a posterior over causal models and queries of interest. In our approach to ABCI, we focus on the class of causally-sufficient, nonlinear additive noise models, which we model using Gaussian processes. We sequentially design experiments that are maximally informative about our target causal query, collect the corresponding interventional data, and update our beliefs to choose the next experiment. Through simulations, we demonstrate that our approach is more data-efficient than several baselines that only focus on learning the full causal graph. This allows us to accurately learn downstream causal queries from fewer samples while providing well-calibrated uncertainty estimates for the quantities of interest.
We consider the problem of discovering $K$ related Gaussian directed acyclic graphs (DAGs), where the involved graph structures share a consistent causal order and sparse unions of supports. Under the multi-task learning setting, we propose a $l_1/l_2$-regularized maximum likelihood estimator (MLE) for learning $K$ linear structural equation models. We theoretically show that the joint estimator, by leveraging data across related tasks, can achieve a better sample complexity for recovering the causal order (or topological order) than separate estimations. Moreover, the joint estimator is able to recover non-identifiable DAGs, by estimating them together with some identifiable DAGs. Lastly, our analysis also shows the consistency of union support recovery of the structures. To allow practical implementation, we design a continuous optimization problem whose optimizer is the same as the joint estimator and can be approximated efficiently by an iterative algorithm. We validate the theoretical analysis and the effectiveness of the joint estimator in experiments.
A fundamental goal of scientific research is to learn about causal relationships. However, despite its critical role in the life and social sciences, causality has not had the same importance in Natural Language Processing (NLP), which has traditionally placed more emphasis on predictive tasks. This distinction is beginning to fade, with an emerging area of interdisciplinary research at the convergence of causal inference and language processing. Still, research on causality in NLP remains scattered across domains without unified definitions, benchmark datasets and clear articulations of the remaining challenges. In this survey, we consolidate research across academic areas and situate it in the broader NLP landscape. We introduce the statistical challenge of estimating causal effects, encompassing settings where text is used as an outcome, treatment, or as a means to address confounding. In addition, we explore potential uses of causal inference to improve the performance, robustness, fairness, and interpretability of NLP models. We thus provide a unified overview of causal inference for the computational linguistics community.
This paper focuses on the expected difference in borrower's repayment when there is a change in the lender's credit decisions. Classical estimators overlook the confounding effects and hence the estimation error can be magnificent. As such, we propose another approach to construct the estimators such that the error can be greatly reduced. The proposed estimators are shown to be unbiased, consistent, and robust through a combination of theoretical analysis and numerical testing. Moreover, we compare the power of estimating the causal quantities between the classical estimators and the proposed estimators. The comparison is tested across a wide range of models, including linear regression models, tree-based models, and neural network-based models, under different simulated datasets that exhibit different levels of causality, different degrees of nonlinearity, and different distributional properties. Most importantly, we apply our approaches to a large observational dataset provided by a global technology firm that operates in both the e-commerce and the lending business. We find that the relative reduction of estimation error is strikingly substantial if the causal effects are accounted for correctly.
Causal inference is a critical research topic across many domains, such as statistics, computer science, education, public policy and economics, for decades. Nowadays, estimating causal effect from observational data has become an appealing research direction owing to the large amount of available data and low budget requirement, compared with randomized controlled trials. Embraced with the rapidly developed machine learning area, various causal effect estimation methods for observational data have sprung up. In this survey, we provide a comprehensive review of causal inference methods under the potential outcome framework, one of the well known causal inference framework. The methods are divided into two categories depending on whether they require all three assumptions of the potential outcome framework or not. For each category, both the traditional statistical methods and the recent machine learning enhanced methods are discussed and compared. The plausible applications of these methods are also presented, including the applications in advertising, recommendation, medicine and so on. Moreover, the commonly used benchmark datasets as well as the open-source codes are also summarized, which facilitate researchers and practitioners to explore, evaluate and apply the causal inference methods.
Many current applications use recommendations in order to modify the natural user behavior, such as to increase the number of sales or the time spent on a website. This results in a gap between the final recommendation objective and the classical setup where recommendation candidates are evaluated by their coherence with past user behavior, by predicting either the missing entries in the user-item matrix, or the most likely next event. To bridge this gap, we optimize a recommendation policy for the task of increasing the desired outcome versus the organic user behavior. We show this is equivalent to learning to predict recommendation outcomes under a fully random recommendation policy. To this end, we propose a new domain adaptation algorithm that learns from logged data containing outcomes from a biased recommendation policy and predicts recommendation outcomes according to random exposure. We compare our method against state-of-the-art factorization methods, in addition to new approaches of causal recommendation and show significant improvements.