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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 real-time analysis of infectious disease surveillance data, e.g. time-series of reported cases or fatalities, can help to provide situational awareness about the current state of a pandemic. This task is challenged by reporting delays that give rise to occurred-but-not-yet-reported events. If these events are not taken into consideration, this can lead to an under-estimation of the counts-to-be-reported and, hence, introduces misconceptions by the interpreter, the media or the general public -- as has been seen for example for reported fatalities during the COVID-19 pandemic. Nowcasting methods provide close to real-time estimates of the complete number of events using the incomplete time-series of currently reported events by using information about the reporting delays from the past. In this report, we consider nowcasting the number of COVID-19 related fatalities in Sweden. We propose a flexible Bayesian approach that considers temporal changes in the reporting delay distribution and, as an extension to existing nowcasting methods, incorporates a regression component for the (lagged) time-series of the number of ICU admissions. This results in a model considering both the past behavior of the time-series of fatalities as well as additional data streams that are in a time-lagged association with the number of fatalities.

We are concerned with the problem of decomposing the parameter space of a parametric system of polynomial equations, and possibly some polynomial inequality constraints, with respect to the number of real solutions that the system attains. Previous studies apply a two step approach to this problem, where first the discriminant variety of the system is computed via a Groebner Basis (GB), and then a Cylindrical Algebraic Decomposition (CAD) of this is produced to give the desired computation. However, even on some reasonably small applied examples this process is too expensive, with computation of the discriminant variety alone infeasible. In this paper we develop new approaches to build the discriminant variety using resultant methods (the Dixon resultant and a new method using iterated univariate resultants). This reduces the complexity compared to GB and allows for a previous infeasible example to be tackled. We demonstrate the benefit by giving a symbolic solution to a problem from population dynamics -- the analysis of the steady states of three connected populations which exhibit Allee effects - which previously could only be tackled numerically.

We demonstrate from first principles a core fallacy employed by a coterie of authors who claim that data from the Vaccine Adverse Reporting System (VAERS) show that hundreds of thousands of U.S. deaths are attributable to COVID vaccination.

Reliable probability estimation is of crucial importance in many real-world applications where there is inherent uncertainty, such as weather forecasting, medical prognosis, or collision avoidance in autonomous vehicles. Probability-estimation models are trained on observed outcomes (e.g. whether it has rained or not, or whether a patient has died or not), because the ground-truth probabilities of the events of interest are typically unknown. The problem is therefore analogous to binary classification, with the important difference that the objective is to estimate probabilities rather than predicting the specific outcome. The goal of this work is to investigate probability estimation from high-dimensional data using deep neural networks. There exist several methods to improve the probabilities generated by these models but they mostly focus on classification problems where the probabilities are related to model uncertainty. In the case of problems with inherent uncertainty, it is challenging to evaluate performance without access to ground-truth probabilities. To address this, we build a synthetic dataset to study and compare different computable metrics. We evaluate existing methods on the synthetic data as well as on three real-world probability estimation tasks, all of which involve inherent uncertainty. We also give a theoretical analysis of a model for high-dimensional probability estimation which reproduces several of the phenomena evinced in our experiments. Finally, we propose a new method for probability estimation using neural networks, which modifies the training process to promote output probabilities that are consistent with empirical probabilities computed from the data. The method outperforms existing approaches on most metrics on the simulated as well as real-world data.

A solution to control for nonresponse bias consists of multiplying the design weights of respondents by the inverse of estimated response probabilities to compensate for the nonrespondents. Maximum likelihood and calibration are two approaches that can be applied to obtain estimated response probabilities. The paper develops asymptotic properties of the resulting estimator when calibration is applied. A logistic regression model for the response probabilities is postulated and missing at random data is supposed. The author shows that the estimators with the response probabilities estimated via calibration are asymptotically equivalent to unbiased estimators and that a gain in efficiency is obtained when estimating the response probabilities via calibration as compared to the estimator with the true response probabilities.

In the presence of prognostic covariates, inference about the treatment effect with time-to-event endpoints is mostly conducted via the stratified log-rank test or the score test based on the Cox proportional hazards model. In their ground-breaking work Ye and Shao (2020) have demonstrated theoretically that when the model is misspecified, the robust score test (Wei and Lin, 1989) as well as the unstratified log-rank test are conservative in trials with stratified randomization. This fact, however, was not established for the Pocock and Simon covariate-adaptive allocation other than through simulations. In this paper, we expand the results of Ye and Shao to a more general class of randomization procedures and show, in part theoretically, in part through simulations, that the Pocock and Simon covariate-adaptive allocation belongs to this class. We also advance the search for the correlation structure of the normalized within-stratum imbalances with minimization by describing the asymptotic correlation matrix for the case of equal prevalence of all strata. We expand the robust tests proposed by Ye and Shao for stratified randomization to minimization and examine their performance trough simulations.

Statistical wisdom suggests that very complex models, interpolating training data, will be poor at prediction on unseen examples. Yet, this aphorism has been recently challenged by the identification of benign overfitting regimes, specially studied in the case of parametric models: generalization capabilities may be preserved despite model high complexity. While it is widely known that fully-grown decision trees interpolate and, in turn, have bad predictive performances, the same behavior is yet to be analyzed for random forests. In this paper, we study the trade-off between interpolation and consistency for several types of random forest algorithms. Theoretically, we prove that interpolation regimes and consistency cannot be achieved for non-adaptive random forests. Since adaptivity seems to be the cornerstone to bring together interpolation and consistency, we introduce and study interpolating Adaptive Centered Forests, which are proved to be consistent in a noiseless scenario. Numerical experiments show that Breiman's random forests are consistent while exactly interpolating, when no bootstrap step is involved. We theoretically control the size of the interpolation area, which converges fast enough to zero, so that exact interpolation and consistency occur in conjunction.

The COVID-19 pandemic continues to affect the conduct of clinical trials globally. Complications may arise from pandemic-related operational challenges such as site closures, travel limitations and interruptions to the supply chain for the investigational product, or from health-related challenges such as COVID-19 infections. Some of these complications lead to unforeseen intercurrent events in the sense that they affect either the interpretation or the existence of the measurements associated with the clinical question of interest. In this article, we demonstrate how the ICH E9(R1) Addendum on estimands and sensitivity analyses provides a rigorous basis to discuss potential pandemic-related trial disruptions and to embed these disruptions in the context of study objectives and design elements. We introduce several hypothetical estimand strategies and review various causal inference and missing data methods, as well as a statistical method that combines unbiased and possibly biased estimators for estimation. To illustrate, we describe the features of a stylized trial, and how it may have been impacted by the pandemic. This stylized trial will then be re-visited by discussing the changes to the estimand and the estimator to account for pandemic disruptions. Finally, we outline considerations for designing future trials in the context of unforeseen disruptions.

This paper proposes a recommender system to alleviate the cold-start problem that can estimate user preferences based on only a small number of items. To identify a user's preference in the cold state, existing recommender systems, such as Netflix, initially provide items to a user; we call those items evidence candidates. Recommendations are then made based on the items selected by the user. Previous recommendation studies have two limitations: (1) the users who consumed a few items have poor recommendations and (2) inadequate evidence candidates are used to identify user preferences. We propose a meta-learning-based recommender system called MeLU to overcome these two limitations. From meta-learning, which can rapidly adopt new task with a few examples, MeLU can estimate new user's preferences with a few consumed items. In addition, we provide an evidence candidate selection strategy that determines distinguishing items for customized preference estimation. We validate MeLU with two benchmark datasets, and the proposed model reduces at least 5.92% mean absolute error than two comparative models on the datasets. We also conduct a user study experiment to verify the evidence selection strategy.