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We consider quantile estimation in a semi-supervised setting, characterized by two available data sets: (i) a small or moderate sized labeled data set containing observations for a response and a set of possibly high dimensional covariates, and (ii) a much larger unlabeled data set where only the covariates are observed. We propose a family of semi-supervised estimators for the response quantile(s) based on the two data sets, to improve the estimation accuracy compared to the supervised estimator, i.e., the sample quantile from the labeled data. These estimators use a flexible imputation strategy applied to the estimating equation along with a debiasing step that allows for full robustness against misspecification of the imputation model. Further, a one-step update strategy is adopted to enable easy implementation of our method and handle the complexity from the non-linear nature of the quantile estimating equation. Under mild assumptions, our estimators are fully robust to the choice of the nuisance imputation model, in the sense of always maintaining root-n consistency and asymptotic normality, while having improved efficiency relative to the supervised estimator. They also attain semi-parametric optimality if the relation between the response and the covariates is correctly specified via the imputation model. As an illustration of estimating the nuisance imputation function, we consider kernel smoothing type estimators on lower dimensional and possibly estimated transformations of the high dimensional covariates, and we establish novel results on their uniform convergence rates in high dimensions, involving responses indexed by a function class and usage of dimension reduction techniques. These results may be of independent interest. Numerical results on both simulated and real data confirm our semi-supervised approach's improved performance, in terms of both estimation and inference.

In this article, we aim to provide a general and complete understanding of semi-supervised (SS) causal inference for treatment effects. Specifically, we consider two such estimands: (a) the average treatment effect and (b) the quantile treatment effect, as prototype cases, in an SS setting, characterized by two available data sets: (i) a labeled data set of size $n$, providing observations for a response and a set of high dimensional covariates, as well as a binary treatment indicator; and (ii) an unlabeled data set of size $N$, much larger than $n$, but without the response observed. Using these two data sets, we develop a family of SS estimators which are ensured to be: (1) more robust and (2) more efficient than their supervised counterparts based on the labeled data set only. Beyond the 'standard' double robustness results (in terms of consistency) that can be achieved by supervised methods as well, we further establish root-n consistency and asymptotic normality of our SS estimators whenever the propensity score in the model is correctly specified, without requiring specific forms of the nuisance functions involved. Such an improvement of robustness arises from the use of the massive unlabeled data, so it is generally not attainable in a purely supervised setting. In addition, our estimators are shown to be semi-parametrically efficient as long as all the nuisance functions are correctly specified. Moreover, as an illustration of the nuisance estimators, we consider inverse-probability-weighting type kernel smoothing estimators involving unknown covariate transformation mechanisms, and establish in high dimensional scenarios novel results on their uniform convergence rates, which should be of independent interest. Numerical results on both simulated and real data validate the advantage of our methods over their supervised counterparts with respect to both robustness and efficiency.

Accurate identification of synergistic treatment combinations and their underlying biological mechanisms is critical across many disease domains, especially cancer. In translational oncology research, preclinical systems such as patient-derived xenografts (PDX) have emerged as a unique study design evaluating multiple treatments administered to samples from the same human tumor implanted into genetically identical mice. In this paper, we propose a novel Bayesian probabilistic tree-based framework for PDX data to investigate the hierarchical relationships between treatments by inferring treatment cluster trees, referred to as treatment trees (Rx-tree). The framework motivates a new metric of mechanistic similarity between two or more treatments accounting for inherent uncertainty in tree estimation; treatments with a high estimated similarity have potentially high mechanistic synergy. Building upon Dirichlet Diffusion Trees, we derive a closed-form marginal likelihood encoding the tree structure, which facilitates computationally efficient posterior inference via a new two-stage algorithm. Simulation studies demonstrate superior performance of the proposed method in recovering the tree structure and treatment similarities. Our analyses of a recently collated PDX dataset produce treatment similarity estimates that show a high degree of concordance with known biological mechanisms across treatments in five different cancers. More importantly, we uncover new and potentially effective combination therapies that confer synergistic regulation of specific downstream biological pathways for future clinical investigations. Our accompanying code, data, and shiny application for visualization of results are available at: //github.com/bayesrx/RxTree.

We study the problem of inferring heterogeneous treatment effects from time-to-event data. While both the related problems of (i) estimating treatment effects for binary or continuous outcomes and (ii) predicting survival outcomes have been well studied in the recent machine learning literature, their combination -- albeit of high practical relevance -- has received considerably less attention. With the ultimate goal of reliably estimating the effects of treatments on instantaneous risk and survival probabilities, we focus on the problem of learning (discrete-time) treatment-specific conditional hazard functions. We find that unique challenges arise in this context due to a variety of covariate shift issues that go beyond a mere combination of well-studied confounding and censoring biases. We theoretically analyse their effects by adapting recent generalization bounds from domain adaptation and treatment effect estimation to our setting and discuss implications for model design. We use the resulting insights to propose a novel deep learning method for treatment-specific hazard estimation based on balancing representations. We investigate performance across a range of experimental settings and empirically confirm that our method outperforms baselines by addressing covariate shifts from various sources.

Consider estimation of average treatment effects with multi-valued treatments using augmented inverse probability weighted (IPW) estimators, depending on outcome regression and propensity score models in high-dimensional settings. These regression models are often fitted by regularized likelihood-based estimation, while ignoring how the fitted functions are used in the subsequent inference about the treatment parameters. Such separate estimation can be associated with known difficulties in existing methods. We develop regularized calibrated estimation for fitting propensity score and outcome regression models, where sparsity-including penalties are employed to facilitate variable selection but the loss functions are carefully chosen such that valid confidence intervals can be obtained under possible model misspecification. Unlike in the case of binary treatments, the usual augmented IPW estimator is generalized by allowing different copies of coefficient estimators in outcome regression to ensure just-identification. For propensity score estimation, the new loss function and estimating functions are directly tied to achieving covariate balance between weighted treatment groups. We develop practical numerical algorithms for computing the regularized calibrated estimators with group Lasso by innovatively exploiting Fisher scoring, and provide rigorous high-dimensional analysis for the resulting augmented IPW estimators under suitable sparsity conditions, while tackling technical issues absent or overlooked in previous analyses. We present simulation studies and an empirical application to estimate the effects of maternal smoking on birth weights. The proposed methods are implemented in the R package mRCAL.

This paper studies treatment effect models in which individuals are classified into unobserved groups based on heterogeneous treatment rules. Using a finite mixture approach, we propose a marginal treatment effect (MTE) framework in which the treatment choice and outcome equations can be heterogeneous across groups. Under the availability of instrumental variables specific to each group, we show that the MTE for each group can be separately identified. Based on our identification result, we propose a two-step semiparametric procedure for estimating the group-wise MTE. We illustrate the usefulness of the proposed method with an application to economic returns to college education.

Multilevel regression and poststratification (MRP) is a flexible modeling technique that has been used in a broad range of small-area estimation problems. Traditionally, MRP studies have been focused on non-causal settings, where estimating a single population value using a nonrepresentative sample was of primary interest. In this manuscript, MRP-style estimators will be evaluated in an experimental causal inference setting. We simulate a large-scale randomized control trial with a stratified cluster sampling design, and compare traditional and nonparametric treatment effect estimation methods with MRP methodology. Using MRP-style estimators, treatment effect estimates for areas as small as 1.3$\%$ of the population have lower bias and variance than standard causal inference methods, even in the presence of treatment effect heterogeneity. The design of our simulation studies also requires us to build upon a MRP variant that allows for non-census covariates to be incorporated into poststratification.

The additive hazards model specifies the effect of covariates on the hazard in an additive way, in contrast to the popular Cox model, in which it is multiplicative. As non-parametric model, it offers a very flexible way of modeling time-varying covariate effects. It is most commonly estimated by ordinary least squares. In this paper we consider the case where covariates are bounded, and derive the maximum likelihood estimator under the constraint that the hazard is non-negative for all covariate values in their domain. We describe an efficient algorithm to find the maximum likelihood estimator. The method is contrasted with the ordinary least squares approach in a simulation study, and the method is illustrated on a realistic data set.

We propose two generic methods for improving semi-supervised learning (SSL). The first integrates weight perturbation (WP) into existing "consistency regularization" (CR) based methods. We implement WP by leveraging variational Bayesian inference (VBI). The second method proposes a novel consistency loss called "maximum uncertainty regularization" (MUR). While most consistency losses act on perturbations in the vicinity of each data point, MUR actively searches for "virtual" points situated beyond this region that cause the most uncertain class predictions. This allows MUR to impose smoothness on a wider area in the input-output manifold. Our experiments show clear improvements in classification errors of various CR based methods when they are combined with VBI or MUR or both.

From only positive (P) and unlabeled (U) data, a binary classifier could be trained with PU learning, in which the state of the art is unbiased PU learning. However, if its model is very flexible, empirical risks on training data will go negative, and we will suffer from serious overfitting. In this paper, we propose a non-negative risk estimator for PU learning: when getting minimized, it is more robust against overfitting, and thus we are able to use very flexible models (such as deep neural networks) given limited P data. Moreover, we analyze the bias, consistency, and mean-squared-error reduction of the proposed risk estimator, and bound the estimation error of the resulting empirical risk minimizer. Experiments demonstrate that our risk estimator fixes the overfitting problem of its unbiased counterparts.