In causal estimation problems, the parameter of interest is often only partially identified, implying that the parameter cannot be recovered exactly, even with infinite data. Here, we study Bayesian inference for partially identified treatment effects in multi-treatment causal inference problems with unobserved confounding. In principle, inferring the partially identified treatment effects is natural under the Bayesian paradigm, but the results can be highly sensitive to parameterization and prior specification, often in surprising ways. It is thus essential to understand which aspects of the conclusions about treatment effects are driven entirely by the prior specification. We use a so-called transparent parameterization to contextualize the effects of more interpretable scientifically motivated prior specifications on the multiple effects. We demonstrate our analysis in an example quantifying the effects of gene expression levels on mouse obesity.
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Randomized controlled trials (RCTs) are considered as the gold standard for testing causal hypotheses in the clinical domain. However, the investigation of prognostic variables of patient outcome in a hypothesized cause-effect route is not feasible using standard statistical methods. Here, we propose a new automated causal inference method (AutoCI) built upon the invariant causal prediction (ICP) framework for the causal re-interpretation of clinical trial data. Compared to existing methods, we show that the proposed AutoCI allows to efficiently determine the causal variables with a clear differentiation on two real-world RCTs of endometrial cancer patients with mature outcome and extensive clinicopathological and molecular data. This is achieved via suppressing the causal probability of non-causal variables by a wide margin. In ablation studies, we further demonstrate that the assignment of causal probabilities by AutoCI remain consistent in the presence of confounders. In conclusion, these results confirm the robustness and feasibility of AutoCI for future applications in real-world clinical analysis.
We consider the design and analysis of multi-factor experiments using fractional factorial and incomplete designs within the potential outcome framework. These designs are particularly useful when limited resources make running a full factorial design infeasible. We connect our design-based methods to standard regression methods. We further motivate the usefulness of these designs in multi-factor observational studies, where certain treatment combinations may be so rare that there are no measured outcomes in the observed data corresponding to them. Therefore, conceptualizing a hypothetical fractional factorial experiment instead of a full factorial experiment allows for appropriate analysis in those settings. We illustrate our approach using biomedical data from the 2003-2004 cycle of the National Health and Nutrition Examination Survey to examine the effects of four common pesticides on body mass index.
Understanding treatment effect heterogeneity in observational studies is of great practical importance to many scientific fields. Quantile regression provides a natural framework for modeling such heterogeneity. In this paper, we propose a new method for inference on heterogeneous quantile treatment effects in the presence of high-dimensional covariates. Our estimator combines a $\ell_1$-penalized regression adjustment with a quantile-specific bias correction scheme based on quantile regression rank scores. We present a comprehensive study of the theoretical properties of this estimator, including weak convergence of the heterogeneous quantile treatment effect process to a Gaussian process. We illustrate the finite-sample performance of our approach through Monte Carlo experiments and an empirical example, dealing with the differential effect of statin usage for lowering low-density lipoprotein cholesterol levels for the Alzheimer's disease patients who participated in the UK Biobank study.
Since the average treatment effect (ATE) measures the change in social welfare, even if positive, there is a risk of negative effect on, say, some 10% of the population. Assessing such risk is difficult, however, because any one individual treatment effect (ITE) is never observed so the 10% worst-affected cannot be identified, while distributional treatment effects only compare the first deciles within each treatment group, which does not correspond to any 10%-subpopulation. In this paper we consider how to nonetheless assess this important risk measure, formalized as the conditional value at risk (CVaR) of the ITE distribution. We leverage the availability of pre-treatment covariates and characterize the tightest-possible upper and lower bounds on ITE-CVaR given by the covariate-conditional average treatment effect (CATE) function. Some bounds can also be interpreted as summarizing a complex CATE function into a single metric and are of interest independently of being a bound. We then proceed to study how to estimate these bounds efficiently from data and construct confidence intervals. This is challenging even in randomized experiments as it requires understanding the distribution of the unknown CATE function, which can be very complex if we use rich covariates so as to best control for heterogeneity. We develop a debiasing method that overcomes this and prove it enjoys favorable statistical properties even when CATE and other nuisances are estimated by black-box machine learning or even inconsistently. Studying a hypothetical change to French job-search counseling services, our bounds and inference demonstrate a small social benefit entails a negative impact on a substantial subpopulation.
Undertaking causal inference with observational data is incredibly useful across a wide range of tasks including the development of medical treatments, advertisements and marketing, and policy making. There are two significant challenges associated with undertaking causal inference using observational data: treatment assignment heterogeneity (\textit{i.e.}, differences between the treated and untreated groups), and an absence of counterfactual data (\textit{i.e.}, not knowing what would have happened if an individual who did get treatment, were instead to have not been treated). We address these two challenges by combining structured inference and targeted learning. In terms of structure, we factorize the joint distribution into risk, confounding, instrumental, and miscellaneous factors, and in terms of targeted learning, we apply a regularizer derived from the influence curve in order to reduce residual bias. An ablation study is undertaken, and an evaluation on benchmark datasets demonstrates that TVAE has competitive and state of the art performance.
Recently, there has been great interest in estimating the conditional average treatment effect using flexible machine learning methods. However, in practice, investigators often have working hypotheses about effect heterogeneity across pre-defined subgroups of individuals, which we call the groupwise approach. The paper compares two modern ways to estimate groupwise treatment effects, a nonparametric approach and a semiparametric approach, with the goal of better informing practice. Specifically, we compare (a) the underlying assumptions, (b) efficiency characteristics, and (c) a way to combine the two approaches. We also discuss how to obtain cluster-robust standard errors if the study units in the same subgroups are not independent and identically distributed. We conclude by reanalyzing the National Educational Longitudinal Study of 1988.
Many scientific datasets are compositional in nature. Important examples include species abundances in ecology, rock compositions in geology, topic compositions in large-scale text corpora, and sequencing count data in molecular biology. Here, we provide a causal view on compositional data in an instrumental variable setting where the composition acts as the cause. First, we crisply articulate potential pitfalls for practitioners regarding the interpretation of compositional causes from the viewpoint of interventions and warn against attributing causal meaning to common summary statistics such as diversity indices. We then advocate for and develop multivariate methods using statistical data transformations and regression techniques that take the special structure of the compositional sample space into account. In a comparative analysis on synthetic and real data we show the advantages and limitations of our proposal. We posit that our framework provides a useful starting point and guidance for valid and informative cause-effect estimation in the context of compositional data.
When are inferences (whether Direct-Likelihood, Bayesian, or Frequentist) obtained from partial data valid? This paper answers this question by offering a new asymptotic theory about inference with missing data that is more general than existing theories. By using more powerful tools from real analysis and probability theory than those used in previous research, it proves that as the sample size increases and the extent of missingness decreases, the mean-loglikelihood function generated by partial data and that ignores the missingness mechanism will almost surely converge uniformly to that which would have been generated by complete data; and if the data are Missing at Random, this convergence depends only on sample size. Thus, inferences from partial data, such as posterior modes, uncertainty estimates, confidence intervals, likelihood ratios, test statistics, and indeed, all quantities or features derived from the partial-data loglikelihood function, will be consistently estimated. They will approximate their complete-data analogues. This adds to previous research which has only proved the consistency and asymptotic normality of the posterior mode, and developed separate theories for Direct-Likelihood, Bayesian, and Frequentist inference. Practical implications of this result are discussed, and the theory is verified using a previous study of International Human Rights Law.
The Bayesian paradigm has the potential to solve core issues of deep neural networks such as poor calibration and data inefficiency. Alas, scaling Bayesian inference to large weight spaces often requires restrictive approximations. In this work, we show that it suffices to perform inference over a small subset of model weights in order to obtain accurate predictive posteriors. The other weights are kept as point estimates. This subnetwork inference framework enables us to use expressive, otherwise intractable, posterior approximations over such subsets. In particular, we implement subnetwork linearized Laplace: We first obtain a MAP estimate of all weights and then infer a full-covariance Gaussian posterior over a subnetwork. We propose a subnetwork selection strategy that aims to maximally preserve the model's predictive uncertainty. Empirically, our approach is effective compared to ensembles and less expressive posterior approximations over full networks.
Discrete random structures are important tools in Bayesian nonparametrics and the resulting models have proven effective in density estimation, clustering, topic modeling and prediction, among others. In this paper, we consider nested processes and study the dependence structures they induce. Dependence ranges between homogeneity, corresponding to full exchangeability, and maximum heterogeneity, corresponding to (unconditional) independence across samples. The popular nested Dirichlet process is shown to degenerate to the fully exchangeable case when there are ties across samples at the observed or latent level. To overcome this drawback, inherent to nesting general discrete random measures, we introduce a novel class of latent nested processes. These are obtained by adding common and group-specific completely random measures and, then, normalising to yield dependent random probability measures. We provide results on the partition distributions induced by latent nested processes, and develop an Markov Chain Monte Carlo sampler for Bayesian inferences. A test for distributional homogeneity across groups is obtained as a by product. The results and their inferential implications are showcased on synthetic and real data.
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