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In many real-world deployments of machine learning, we use a prediction algorithm to choose what data to test next. For example, in the protein design problem, we have a regression model that predicts some real-valued property of a protein sequence, which we use to propose new sequences believed to exhibit higher property values than observed in the training data. Since validating designed sequences in the wet lab is typically costly, it is important to know how much we can trust the model's predictions. In such settings, however, there is a distinct type of distribution shift between the training and test data: one where the training and test data are statistically dependent, as the latter is chosen based on the former. Consequently, the model's error on the test data -- that is, the designed sequences -- has some non-trivial relationship with its error on the training data. Herein, we introduce a method to quantify predictive uncertainty in such settings. We do so by constructing confidence sets for predictions that account for the dependence between the training and test data. The confidence sets we construct have finite-sample guarantees that hold for any prediction algorithm, even when a trained model chooses the test-time input distribution. As a motivating use case, we demonstrate how our method quantifies uncertainty for the predicted fitness of designed protein using several real data sets.

Longitudinal modified treatment policies (LMTP) have been recently developed as a novel method to define and estimate causal parameters that depend on the natural value of treatment. LMTPs represent an important advancement in causal inference for longitudinal studies as they allow the non-parametric definition and estimation of the joint effect of multiple categorical, numerical, or continuous exposures measured at several time points. We extend the LMTP methodology to problems in which the outcome is a time-to-event variable subject to right-censoring and competing risks. We present identification results and non-parametric locally efficient estimators that use flexible data-adaptive regression techniques to alleviate model misspecification bias, while retaining important asymptotic properties such as $\sqrt{n}$-consistency. We present an application to the estimation of the effect of the time-to-intubation on acute kidney injury amongst COVID-19 hospitalized patients, where death by other causes is taken to be the competing event.

Randomized controlled trials (RCT's) allow researchers to estimate causal effects in an experimental sample with minimal identifying assumptions. However, to generalize or transport a causal effect from an RCT to a target population, researchers must adjust for a set of treatment effect moderators. In practice, it is impossible to know whether the set of moderators has been properly accounted for. In the following paper, I propose a three parameter sensitivity analysis for generalizing or transporting experimental results using weighted estimators, with several advantages over existing methods. First, the framework does not require assumptions on the underlying data generating process for either the experimental sample selection mechanism or treatment effect heterogeneity. Second, I show that the sensitivity parameters are guaranteed to be bounded and propose several tools researchers can use to perform sensitivity analysis: (1) graphical and numerical summaries for researchers to assess how robust a point estimate is to killer confounders; (2) an extreme scenario analysis; and (3) a formal benchmarking approach for researchers to estimate potential sensitivity parameter values using existing data. Finally, I demonstrate that the proposed framework can be easily extended to the class of doubly robust, augmented weighted estimators. The sensitivity analysis framework is applied to a set of Jobs Training Program experiments.

We propose some extensions to semi-parametric models based on Bayesian additive regression trees (BART). In the semi-parametric BART paradigm, the response variable is approximated by a linear predictor and a BART model, where the linear component is responsible for estimating the main effects and BART accounts for non-specified interactions and non-linearities. Previous semi-parametric models based on BART have assumed that the set of covariates in the linear predictor and the BART model are mutually exclusive in an attempt to avoid bias and poor coverage properties. The main novelty in our approach lies in the way we change the tree-generation moves in BART to deal with bias/confounding between the parametric and non-parametric components, even when they have covariates in common. This allows us to model complex interactions involving the covariates of primary interest, both among themselves and with those in the BART component. Through synthetic and real-world examples, we demonstrate that the performance of our novel semi-parametric BART is competitive when compared to regression models, alternative formulations of semi-parametric BART, and other tree-based methods. The implementation of the proposed method is available at //github.com/ebprado/CSP-BART.

The vast majority of literature on evaluating the significance of a treatment effect based on observational data has been confined to discrete treatments. These methods are not applicable to drawing inference for a continuous treatment, which arises in many important applications. To adjust for confounders when evaluating a continuous treatment, existing inference methods often rely on discretizing the treatment or using (possibly misspecified) parametric models for the effect curve. Recently, Kennedy et al. (2017) proposed nonparametric doubly robust estimation for a continuous treatment effect in observational studies. However, inference for the continuous treatment effect is a significantly harder problem. To the best of our knowledge, a completely nonparametric doubly robust approach for inference in this setting is not yet available. We develop such a nonparametric doubly robust procedure in this paper for making inference on the continuous treatment effect curve. Using empirical process techniques for local U- and V-processes, we establish the test statistic's asymptotic distribution. Furthermore, we propose a wild bootstrap procedure for implementing the test in practice. We illustrate the new method via simulations and a study of a constructed dataset relating the effect of nurse staffing hours on hospital performance. We implement and share code for our doubly robust dose response test in the R package DRDRtest on CRAN.

We consider continuous-time survival or more general event-history settings, where the aim is to infer the causal effect of a time-dependent treatment process. This is formalised as the effect on the outcome event of a (possibly hypothetical) intervention on the intensity of the treatment process, i.e. a stochastic intervention. To establish whether valid inference about the interventional situation can be drawn from typical observational, i.e. non-experimental, data we propose graphical rules indicating whether the observed information is sufficient to identify the desired causal effect by suitable re-weighting. In analogy to the well-known causal directed acyclic graphs, the corresponding dynamic graphs combine causal semantics with local independence models for multivariate counting processes. Importantly, we highlight that causal inference from censored data requires structural assumptions on the censoring process beyond the usual independent censoring assumption, which can be represented and verified graphically. Our results establish general non-parametric identifiability and do not rely on particular survival models. We illustrate our proposal with a data example on HPV-testing for cervical cancer screening, where the desired effect is estimated by re-weighted cumulative incidence curves.

We consider hyper-differential sensitivity analysis (HDSA) of nonlinear Bayesian inverse problems governed by PDEs with infinite-dimensional parameters. In previous works, HDSA has been used to assess the sensitivity of the solution of deterministic inverse problems to additional model uncertainties and also different types of measurement data. In the present work, we extend HDSA to the class of Bayesian inverse problems governed by PDEs. The focus is on assessing the sensitivity of certain key quantities derived from the posterior distribution. Specifically, we focus on analyzing the sensitivity of the MAP point and the Bayes risk and make full use of the information embedded in the Bayesian inverse problem. After establishing our mathematical framework for HDSA of Bayesian inverse problems, we present a detailed computational approach for computing the proposed HDSA indices. We examine the effectiveness of the proposed approach on a model inverse problem governed by a PDE for heat conduction.

Causal inference is essential for data-driven decision making across domains such as business engagement, medical treatment or policy making. However, research on causal discovery and inference has evolved separately, and the combination of the two domains is not trivial. In this work, we develop Deep End-to-end Causal Inference (DECI), a single flow-based method that takes in observational data and can perform both causal discovery and inference, including conditional average treatment effect (CATE) estimation. We provide a theoretical guarantee that DECI can recover the ground truth causal graph under mild assumptions. In addition, our method can handle heterogeneous, real-world, mixed-type data with missing values, allowing for both continuous and discrete treatment decisions. Moreover, the design principle of our method can generalize beyond DECI, providing a general End-to-end Causal Inference (ECI) recipe, which enables different ECI frameworks to be built using existing methods. Our results show the superior performance of DECI when compared to relevant baselines for both causal discovery and (C)ATE estimation in over a thousand experiments on both synthetic datasets and other causal machine learning benchmark datasets.

We present a method for assessing the sensitivity of the true causal effect to unmeasured confounding. The method requires the analyst to set two intuitive parameters. Otherwise, the method is assumption-free. The method returns an interval that contains the true causal effect, and whose bounds are arbitrarily sharp, i.e. practically attainable. We show experimentally that our bounds can be tighter than those obtained by the method of Ding and VanderWeele (2016a) which, moreover, requires to set one more parameter than our method. Finally, we extend our method to bound the natural direct and indirect effects when there are measured mediators and unmeasured exposure-outcome confounding.

"Program sensitivity" measures the distance between the outputs of a program when it is run on two related inputs. This notion, which plays an important role in areas such as data privacy and optimization, has been the focus of several program analysis techniques introduced in recent years. One approach that has proved particularly fruitful for this domain is the use of type systems inspired by linear logic, as pioneered by Reed and Pierce in the Fuzz programming language. In Fuzz, each type is equipped with its own notion of distance, and the typing rules explain how those distances can be treated soundly when analyzing the sensitivity of a program. In particular, Fuzz features two products types, corresponding to two different sensitivity analyses: the "tensor product" combines the distances of each component by adding them, while the "with product" takes their maximum. In this work, we show that products in Fuzz can be generalized to arbitrary $L^p$ distances, metrics that are often used in privacy and optimization. The original Fuzz products, tensor and with, correspond to the special cases $L^1$ and $L^\infty$. To simplify the handling of such products, we extend the Fuzz type system with bunches -- as in the logic of bunched implications -- where the distances of different groups of variables can be combined using different $L^p$ distances. We show that our extension can be used to reason about important examples of metrics between probability distributions in a natural way.