Aki Vehtari, Janne Ojanen.

Source: Statistics Surveys, Volume 8, , 1--1.

Abstract:
Errata for “A survey of Bayesian predictive methods for model assessment, selection and comparison” by A. Vehtari and J. Ojanen, Statistics Surveys , 6 (2012), 142–228. doi:10.1214/12-SS102.

Aki Vehtari, Janne Ojanen

Source: Statist. Surv., Volume 6, 142--228.

Abstract:
To date, several methods exist in the statistical literature for model assessment, which purport themselves specifically as Bayesian predictive methods. The decision theoretic assumptions on which these methods are based are not always clearly stated in the original articles, however. The aim of this survey is to provide a unified review of Bayesian predictive model assessment and selection methods, and of methods closely related to them. We review the various assumptions that are made in this context and discuss the connections between different approaches, with an emphasis on how each method approximates the expected utility of using a Bayesian model for the purpose of predicting future data.

Gregory J. Matthews, Ofer Harel

Source: Statist. Surv., Volume 5, 1--29.

Abstract:
There is an ever increasing demand from researchers for access to useful microdata files. However, there are also growing concerns regarding the privacy of the individuals contained in the microdata. Ideally, microdata could be released in such a way that a balance between usefulness of the data and privacy is struck. This paper presents a review of proposed methods of statistical disclosure control and techniques for assessing the privacy of such methods under different definitions of disclosure.

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Scott H. Holan, Robert Lund, Ginger Davis

Source: Statist. Surv., Volume 4, 232--274.

Abstract:
Autoregressive moving-average (ARMA) difference equations are ubiquitous models for short memory time series and have parsimoniously described many stationary series. Variants of ARMA models have been proposed to describe more exotic series features such as long memory autocovariances, periodic autocovariances, and count support set structures. This review paper enumerates, compares, and contrasts the common variants of ARMA models in today’s literature. After the basic properties of ARMA models are reviewed, we tour ARMA variants that describe seasonal features, long memory behavior, multivariate series, changing variances (stochastic volatility) and integer counts. A list of ARMA variant acronyms is provided.

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Sophie Achard, Jean-François Coeurjolly

Source: Statist. Surv., Volume 4, 117--147.

Abstract:
This paper gives an overview of the problem of estimating the Hurst parameter of a fractional Brownian motion when the data are observed with outliers and/or with an additive noise by using methods based on discrete variations. We show that the classical estimation procedure based on the log-linearity of the variogram of dilated series is made more robust to outliers and/or an additive noise by considering sample quantiles and trimmed means of the squared series or differences of empirical variances. These different procedures are compared and discussed through a large simulation study and are implemented in the R package dvfBm.

Methods for generating synthetic data have become of increasing importance to build large datasets required for Convolution Neural Networks (CNN) based deep learning techniques for a wide range of computer vision applications. In this work, we extend existing methodologies to show how 2D thermal facial data can be mapped to provide 3D facial models. For the proposed research work we have used tufts datasets for generating 3D varying face poses by using a single frontal face pose. The system works by refining the existing image quality by performing fusion based image preprocessing operations. The refined outputs have better contrast adjustments, decreased noise level and higher exposedness of the dark regions. It makes the facial landmarks and temperature patterns on the human face more discernible and visible when compared to original raw data. Different image quality metrics are used to compare the refined version of images with original images. In the next phase of the proposed study, the refined version of images is used to create 3D facial geometry structures by using Convolution Neural Networks (CNN). The generated outputs are then imported in blender software to finally extract the 3D thermal facial outputs of both males and females. The same technique is also used on our thermal face data acquired using prototype thermal camera (developed under Heliaus EU project) in an indoor lab environment which is then used for generating synthetic 3D face data along with varying yaw face angles and lastly facial depth map is generated.

Building a scalable machine learning system for unsupervised anomaly detection via representation learning is highly desirable. One of the prevalent methods is using a reconstruction error from variational autoencoder (VAE) via maximizing the evidence lower bound. We revisit VAE from the perspective of information theory to provide some theoretical foundations on using the reconstruction error, and finally arrive at a simpler and more effective model for anomaly detection. In addition, to enhance the effectiveness of detecting anomalies, we incorporate a practical model uncertainty measure into the metric. We show empirically the competitive performance of our approach on benchmark datasets.

We show, by an explicit construction, that a mixture of univariate Gaussians with variance 1 and means in $[-A,A]$ can have $Omega(A^2)$ modes. This disproves a recent conjecture of Dytso, Yagli, Poor and Shamai [IEEE Trans. Inform. Theory, Apr. 2020], who showed that such a mixture can have at most $O(A^2)$ modes and surmised that the upper bound could be improved to $O(A)$. Our result holds even if an additional variance constraint is imposed on the mixing distribution. Extending the result to higher dimensions, we exhibit a mixture of Gaussians in $mathbb{R}^d$, with identity covariances and means inside $[-A,A]^d$, that has $Omega(A^{2d})$ modes.

The very first case of corona-virus illness was recorded on 30 January 2020, in India and the number of infected cases, including the death toll, continues to rise. In this paper, we present short-term forecasts of COVID-19 for 28 Indian states and five union territories using real-time data from 30 January to 21 April 2020. Applying Holt's second-order exponential smoothing method and autoregressive integrated moving average (ARIMA) model, we generate 10-day ahead forecasts of the likely number of infected cases and deaths in India for 22 April to 1 May 2020. Our results show that the number of cumulative cases in India will rise to 36335.63 [PI 95% (30884.56, 42918.87)], concurrently the number of deaths may increase to 1099.38 [PI 95% (959.77, 1553.76)] by 1 May 2020. Further, we have divided the country into severity zones based on the cumulative cases. According to this analysis, Maharashtra is likely to be the most affected states with around 9787.24 [PI 95% (6949.81, 13757.06)] cumulative cases by 1 May 2020. However, Kerala and Karnataka are likely to shift from the red zone (i.e. highly affected) to the lesser affected region. On the other hand, Gujarat and Madhya Pradesh will move to the red zone. These results mark the states where lockdown by 3 May 2020, can be loosened.

Segmentation of cardiac images, particularly late gadolinium-enhanced magnetic resonance imaging (LGE-MRI) widely used for visualizing diseased cardiac structures, is a crucial first step for clinical diagnosis and treatment. However, direct segmentation of LGE-MRIs is challenging due to its attenuated contrast. Since most clinical studies have relied on manual and labor-intensive approaches, automatic methods are of high interest, particularly optimized machine learning approaches. To address this, we organized the "2018 Left Atrium Segmentation Challenge" using 154 3D LGE-MRIs, currently the world's largest cardiac LGE-MRI dataset, and associated labels of the left atrium segmented by three medical experts, ultimately attracting the participation of 27 international teams. In this paper, extensive analysis of the submitted algorithms using technical and biological metrics was performed by undergoing subgroup analysis and conducting hyper-parameter analysis, offering an overall picture of the major design choices of convolutional neural networks (CNNs) and practical considerations for achieving state-of-the-art left atrium segmentation. Results show the top method achieved a dice score of 93.2% and a mean surface to a surface distance of 0.7 mm, significantly outperforming prior state-of-the-art. Particularly, our analysis demonstrated that double, sequentially used CNNs, in which a first CNN is used for automatic region-of-interest localization and a subsequent CNN is used for refined regional segmentation, achieved far superior results than traditional methods and pipelines containing single CNNs. This large-scale benchmarking study makes a significant step towards much-improved segmentation methods for cardiac LGE-MRIs, and will serve as an important benchmark for evaluating and comparing the future works in the field.

We focus on the challenge of finding a diverse collection of quality solutions on complex continuous domains. While quality diver-sity (QD) algorithms like Novelty Search with Local Competition (NSLC) and MAP-Elites are designed to generate a diverse range of solutions, these algorithms require a large number of evaluations for exploration of continuous spaces. Meanwhile, variants of the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) are among the best-performing derivative-free optimizers in single-objective continuous domains. This paper proposes a new QD algorithm called Covariance Matrix Adaptation MAP-Elites (CMA-ME). Our new algorithm combines the self-adaptation techniques of CMA-ES with archiving and mapping techniques for maintaining diversity in QD. Results from experiments based on standard continuous optimization benchmarks show that CMA-ME finds better-quality solutions than MAP-Elites; similarly, results on the strategic game Hearthstone show that CMA-ME finds both a higher overall quality and broader diversity of strategies than both CMA-ES and MAP-Elites. Overall, CMA-ME more than doubles the performance of MAP-Elites using standard QD performance metrics. These results suggest that QD algorithms augmented by operators from state-of-the-art optimization algorithms can yield high-performing methods for simultaneously exploring and optimizing continuous search spaces, with significant applications to design, testing, and reinforcement learning among other domains.

This paper develops a general framework for analyzing asymptotics of $V$-statistics. Previous literature on limiting distribution mainly focuses on the cases when $n o infty$ with fixed kernel size $k$. Under some regularity conditions, we demonstrate asymptotic normality when $k$ grows with $n$ by utilizing existing results for $U$-statistics. The key in our approach lies in a mathematical reduction to $U$-statistics by designing an equivalent kernel for $V$-statistics. We also provide a unified treatment on variance estimation for both $U$- and $V$-statistics by observing connections to existing methods and proposing an empirically more accurate estimator. Ensemble methods such as random forests, where multiple base learners are trained and aggregated for prediction purposes, serve as a running example throughout the paper because they are a natural and flexible application of $V$-statistics.

Factor analysis is a flexible technique for assessment of multivariate dependence and codependence. Besides being an exploratory tool used to reduce the dimensionality of multivariate data, it allows estimation of common factors that often have an interesting theoretical interpretation in real problems. However, standard factor analysis is only applicable when the variables are scaled, which is often inappropriate, for example, in data obtained from questionnaires in the field of psychology,where the variables are often categorical. In this framework, we propose a factor model for the analysis of multivariate ordered and non-ordered polychotomous data. The inference procedure is done under the Bayesian approach via Markov chain Monte Carlo methods. Two Monte-Carlo simulation studies are presented to investigate the performance of this approach in terms of estimation bias, precision and assessment of the number of factors. We also illustrate the proposed method to analyze participants' responses to the Motivational State Questionnaire dataset, developed to study emotions in laboratory and field settings.

A deep neural network has relieved the burden of feature engineering by human experts, but comparable efforts are instead required to determine an effective architecture. On the other hands, as the size of a network has over-grown, a lot of resources are also invested to reduce its size. These problems can be addressed by sparsification of an over-complete model, which removes redundant parameters or connections by pruning them away after training or encouraging them to become zero during training. In general, however, these approaches are not fully differentiable and interrupt an end-to-end training process with the stochastic gradient descent in that they require either a parameter selection or a soft-thresholding step. In this paper, we propose a fully differentiable sparsification method for deep neural networks, which allows parameters to be exactly zero during training, and thus can learn the sparsified structure and the weights of networks simultaneously using the stochastic gradient descent. We apply the proposed method to various popular models in order to show its effectiveness.

A major difficulty of solving continuous POMDPs is to infer the multi-modal distribution of the unobserved true states and to make the planning algorithm dependent on the perceived uncertainty. We cast POMDP filtering and planning problems as two closely related Sequential Monte Carlo (SMC) processes, one over the real states and the other over the future optimal trajectories, and combine the merits of these two parts in a new model named the DualSMC network. In particular, we first introduce an adversarial particle filter that leverages the adversarial relationship between its internal components. Based on the filtering results, we then propose a planning algorithm that extends the previous SMC planning approach [Piche et al., 2018] to continuous POMDPs with an uncertainty-dependent policy. Crucially, not only can DualSMC handle complex observations such as image input but also it remains highly interpretable. It is shown to be effective in three continuous POMDP domains: the floor positioning domain, the 3D light-dark navigation domain, and a modified Reacher domain.

We study the problem of parameter estimation for a non-ergodic Gaussian Vasicek-type model defined as $dX_t=(mu+ heta X_t)dt+dG_t, tgeq0$ with unknown parameters $ heta>0$ and $muinR$, where $G$ is a Gaussian process. We provide least square-type estimators $widetilde{ heta}_T$ and $widetilde{mu}_T$ respectively for the drift parameters $ heta$ and $mu$ based on continuous-time observations ${X_t, tin[0,T]}$ as $T ightarrowinfty$.

Our aim is to derive some sufficient conditions on the driving Gaussian process $G$ in order to ensure that $widetilde{ heta}_T$ and $widetilde{mu}_T$ are strongly consistent, the limit distribution of $widetilde{ heta}_T$ is a Cauchy-type distribution and $widetilde{mu}_T$ is asymptotically normal. We apply our result to fractional Vasicek, subfractional Vasicek and bifractional Vasicek processes. In addition, this work extends the result of cite{EEO} studied in the case where $mu=0$.

We study the interplay of two important issues on Bayesian model selection (BMS): censoring and model misspecification. We consider additive accelerated failure time (AAFT), Cox proportional hazards and probit models, and a more general concave log-likelihood structure. A fundamental question is what solution can one hope BMS to provide, when (inevitably) models are misspecified. We show that asymptotically BMS keeps any covariate with predictive power for either the outcome or censoring times, and discards other covariates. Misspecification refers to assuming the wrong model or functional effect on the response, including using a finite basis for a truly non-parametric effect, or omitting truly relevant covariates. We argue for using simple models that are computationally practical yet attain good power to detect potentially complex effects, despite misspecification. Misspecification and censoring both have an asymptotically negligible effect on (suitably-defined) false positives, but their impact on power is exponential. We portray these issues via simple descriptions of early/late censoring and the drop in predictive accuracy due to misspecification. From a methods point of view, we consider local priors and a novel structure that combines local and non-local priors to enforce sparsity. We develop algorithms to capitalize on the AAFT tractability, approximations to AAFT and probit likelihoods giving significant computational gains, a simple augmented Gibbs sampler to hierarchically explore linear and non-linear effects, and an implementation in the R package mombf. We illustrate the proposed methods and others based on likelihood penalties via extensive simulations under misspecification and censoring. We present two applications concerning the effect of gene expression on colon and breast cancer.

We propose a novel estimation procedure for scale-by-scale lead-lag relationships of financial assets observed at high-frequency in a non-synchronous manner. The proposed estimation procedure does not require any interpolation processing of original datasets and is applicable to those with highest time resolution available. Consistency of the proposed estimators is shown under the continuous-time framework that has been developed in our previous work Hayashi and Koike (2018). An empirical application to a quote dataset of the NASDAQ-100 assets identifies two types of lead-lag relationships at different time scales.

Heat waves resulting from prolonged extreme temperatures pose a significant risk to human health globally. Given the limitations of observations of extreme temperature, climate models are often used to characterize extreme temperature globally, from which one can derive quantities like return values to summarize the magnitude of a low probability event for an arbitrary geographic location. However, while these derived quantities are useful on their own, it is also often important to apply a spatial statistical model to such data in order to, e.g., understand how the spatial dependence properties of the return values vary over space and emulate the climate model for generating additional spatial fields with corresponding statistical properties. For these objectives, when modeling global data it is critical to use a nonstationary covariance function. Furthermore, given that the output of modern global climate models can be on the order of $mathcal{O}(10^4)$, it is important to utilize approximate Gaussian process methods to enable inference. In this paper, we demonstrate the application of methodology introduced in Risser and Turek (2020) to conduct a nonstationary and fully Bayesian analysis of a large data set of 20-year return values derived from an ensemble of global climate model runs with over 50,000 spatial locations. This analysis uses the freely available BayesNSGP software package for R.

We present LCE, a Local Cascade Ensemble for traditional (tabular) multivariate data classification, and its extension LCEM for Multivariate Time Series (MTS) classification. LCE is a new hybrid ensemble method that combines an explicit boosting-bagging approach to handle the usual bias-variance tradeoff faced by machine learning models and an implicit divide-and-conquer approach to individualize classifier errors on different parts of the training data. Our evaluation firstly shows that the hybrid ensemble method LCE outperforms the state-of-the-art classifiers on the UCI datasets and that LCEM outperforms the state-of-the-art MTS classifiers on the UEA datasets. Furthermore, LCEM provides explainability by design and manifests robust performance when faced with challenges arising from continuous data collection (different MTS length, missing data and noise).

In Canada, financial advisors and dealers by provincial securities commissions, and those self-regulatory organizations charged with direct regulation over investment dealers and mutual fund dealers, respectively to collect and maintain Know Your Client (KYC) information, such as their age or risk tolerance, for investor accounts. With this information, investors, under their advisor's guidance, make decisions on their investments which are presumed to be beneficial to their investment goals. Our unique dataset is provided by a financial investment dealer with over 50,000 accounts for over 23,000 clients. We use a modified behavioural finance recency, frequency, monetary model for engineering features that quantify investor behaviours, and machine learning clustering algorithms to find groups of investors that behave similarly. We show that the KYC information collected does not explain client behaviours, whereas trade and transaction frequency and volume are most informative. We believe the results shown herein encourage financial regulators and advisors to use more advanced metrics to better understand and predict investor behaviours.

Disaggregation regression has become an important tool in spatial disease mapping for making fine-scale predictions of disease risk from aggregated response data. By including high resolution covariate information and modelling the data generating process on a fine scale, it is hoped that these models can accurately learn the relationships between covariates and response at a fine spatial scale. However, validating these high resolution predictions can be a challenge, as often there is no data observed at this spatial scale. In this study, disaggregation regression was performed on simulated data in various settings and the resulting fine-scale predictions are compared to the simulated ground truth. Performance was investigated with varying numbers of data points, sizes of aggregated areas and levels of model misspecification. The effectiveness of cross validation on the aggregate level as a measure of fine-scale predictive performance was also investigated. Predictive performance improved as the number of observations increased and as the size of the aggregated areas decreased. When the model was well-specified, fine-scale predictions were accurate even with small numbers of observations and large aggregated areas. Under model misspecification predictive performance was significantly worse for large aggregated areas but remained high when response data was aggregated over smaller regions. Cross-validation correlation on the aggregate level was a moderately good predictor of fine-scale predictive performance. While the simulations are unlikely to capture the nuances of real-life response data, this study gives insight into the effectiveness of disaggregation regression in different contexts.

Early detection of patients vulnerable to infections acquired in the hospital environment is a challenge in current health systems given the impact that such infections have on patient mortality and healthcare costs. This work is focused on both the identification of risk factors and the prediction of healthcare-associated infections in intensive-care units by means of machine-learning methods. The aim is to support decision making addressed at reducing the incidence rate of infections. In this field, it is necessary to deal with the problem of building reliable classifiers from imbalanced datasets. We propose a clustering-based undersampling strategy to be used in combination with ensemble classifiers. A comparative study with data from 4616 patients was conducted in order to validate our proposal. We applied several single and ensemble classifiers both to the original dataset and to data preprocessed by means of different resampling methods. The results were analyzed by means of classic and recent metrics specifically designed for imbalanced data classification. They revealed that the proposal is more efficient in comparison with other approaches.

Simplicity is the ultimate sophistication. Differentiable Architecture Search (DARTS) has now become one of the mainstream paradigms of neural architecture search. However, it largely suffers from several disturbing factors of optimization process whose results are unstable to reproduce. FairDARTS points out that skip connections natively have an unfair advantage in exclusive competition which primarily leads to dramatic performance collapse. While FairDARTS turns the unfair competition into a collaborative one, we instead impede such unfair advantage by injecting unbiased random noise into skip operations' output. In effect, the optimizer should perceive this difficulty at each training step and refrain from overshooting on skip connections, but in a long run it still converges to the right solution area since no bias is added to the gradient. We name this novel approach as NoisyDARTS. Our experiments on CIFAR-10 and ImageNet attest that it can effectively break the skip connection's unfair advantage and yield better performance. It generates a series of models that achieve state-of-the-art results on both datasets.

In the field of numerical weather prediction (NWP), the probabilistic distribution of the future state of the atmosphere is sampled with Monte-Carlo-like simulations, called ensembles. These ensembles have deficiencies (such as conditional biases) that can be corrected thanks to statistical post-processing methods. Several ensembles exist and may be corrected with different statistiscal methods. A further step is to combine these raw or post-processed ensembles. The theory of prediction with expert advice allows us to build combination algorithms with theoretical guarantees on the forecast performance. This article adapts this theory to the case of probabilistic forecasts issued as step-wise cumulative distribution functions (CDF). The theory is applied to wind speed forecasting, by combining several raw or post-processed ensembles, considered as CDFs. The second goal of this study is to explore the use of two forecast performance criteria: the Continous ranked probability score (CRPS) and the Jolliffe-Primo test. Comparing the results obtained with both criteria leads to reconsidering the usual way to build skillful probabilistic forecasts, based on the minimization of the CRPS. Minimizing the CRPS does not necessarily produce reliable forecasts according to the Jolliffe-Primo test. The Jolliffe-Primo test generally selects reliable forecasts, but could lead to issuing suboptimal forecasts in terms of CRPS. It is proposed to use both criterion to achieve reliable and skillful probabilistic forecasts.

This paper deals with robust marginal estimation under a general regression model when missing data occur in the response and also in some of covariates. The target is a marginal location parameter which is given through an $M-$functional. To obtain robust Fisher--consistent estimators, properly defined marginal distribution function estimators are considered. These estimators avoid the bias due to missing values by assuming a missing at random condition. Three methods are considered to estimate the marginal distribution function which allows to obtain the $M-$location of interest: the well-known inverse probability weighting, a convolution--based method that makes use of the regression model and an augmented inverse probability weighting procedure that prevents against misspecification. The robust proposed estimators and the classical ones are compared through a numerical study under different missing models including clean and contaminated samples. We illustrate the estimators behaviour under a nonlinear model. A real data set is also analysed.

This paper revisits the problem of computing empirical cumulative distribution functions (ECDF) efficiently on large, multivariate datasets. Computing an ECDF at one evaluation point requires $mathcal{O}(N)$ operations on a dataset composed of $N$ data points. Therefore, a direct evaluation of ECDFs at $N$ evaluation points requires a quadratic $mathcal{O}(N^2)$ operations, which is prohibitive for large-scale problems. Two fast and exact methods are proposed and compared. The first one is based on fast summation in lexicographical order, with a $mathcal{O}(N{log}N)$ complexity and requires the evaluation points to lie on a regular grid. The second one is based on the divide-and-conquer principle, with a $mathcal{O}(Nlog(N)^{(d-1){vee}1})$ complexity and requires the evaluation points to coincide with the input points. The two fast algorithms are described and detailed in the general $d$-dimensional case, and numerical experiments validate their speed and accuracy. Secondly, the paper establishes a direct connection between cumulative distribution functions and kernel density estimation (KDE) for a large class of kernels. This connection paves the way for fast exact algorithms for multivariate kernel density estimation and kernel regression. Numerical tests with the Laplacian kernel validate the speed and accuracy of the proposed algorithms. A broad range of large-scale multivariate density estimation, cumulative distribution estimation, survival function estimation and regression problems can benefit from the proposed numerical methods.

An accurate and prompt diagnosis of pediatric pneumonia is imperative for successful treatment intervention. One approach to diagnose pneumonia cases is using radiographic data. In this article, we propose a novel parsimonious scalar-on-image classification model adopting the ideas of functional data analysis. Our main idea is to treat images as functional measurements and exploit underlying covariance structures to select basis functions; these bases are then used in approximating both image profiles and corresponding regression coefficient. We re-express the regression model into a standard generalized linear model where the functional principal component scores are treated as covariates. We apply the method to (1) classify pneumonia against healthy and viral against bacterial pneumonia patients, and (2) test the null effect about the association between images and responses. Extensive simulation studies show excellent numerical performance in terms of classification, hypothesis testing, and efficient computation.

Uncertainties in a structure is inevitable, which generally lead to variation in dynamic response predictions. For a complex structure, brute force Monte Carlo simulation for response variation analysis is infeasible since one single run may already be computationally costly. Data driven meta-modeling approaches have thus been explored to facilitate efficient emulation and statistical inference. The performance of a meta-model hinges upon both the quality and quantity of training dataset. In actual practice, however, high-fidelity data acquired from high-dimensional finite element simulation or experiment are generally scarce, which poses significant challenge to meta-model establishment. In this research, we take advantage of the multi-level response prediction opportunity in structural dynamic analysis, i.e., acquiring rapidly a large amount of low-fidelity data from reduced-order modeling, and acquiring accurately a small amount of high-fidelity data from full-scale finite element analysis. Specifically, we formulate a composite neural network fusion approach that can fully utilize the multi-level, heterogeneous datasets obtained. It implicitly identifies the correlation of the low- and high-fidelity datasets, which yields improved accuracy when compared with the state-of-the-art. Comprehensive investigations using frequency response variation characterization as case example are carried out to demonstrate the performance.

I study the minimax-optimal design for a two-arm controlled experiment where conditional mean outcomes may vary in a given set. When this set is permutation symmetric, the optimal design is complete randomization, and using a single partition (i.e., the design that only randomizes the treatment labels for each side of the partition) has minimax risk larger by a factor of $n-1$. More generally, the optimal design is shown to be the mixed-strategy optimal design (MSOD) of Kallus (2018). Notably, even when the set of conditional mean outcomes has structure (i.e., is not permutation symmetric), being minimax-optimal for variance still requires randomization beyond a single partition. Nonetheless, since this targets precision, it may still not ensure sufficient uniformity in randomization to enable randomization (i.e., design-based) inference by Fisher's exact test to appropriately detect violations of null. I therefore propose the inference-constrained MSOD, which is minimax-optimal among all designs subject to such uniformity constraints. On the way, I discuss Johansson et al. (2020) who recently compared rerandomization of Morgan and Rubin (2012) and the pure-strategy optimal design (PSOD) of Kallus (2018). I point out some errors therein and set straight that randomization is minimax-optimal and that the "no free lunch" theorem and example in Kallus (2018) are correct.

Effective property prediction methods can help accelerate the search for COVID-19 antivirals either through accurate in-silico screens or by effectively guiding on-going at-scale experimental efforts. However, existing prediction tools have limited ability to accommodate scarce or fragmented training data currently available. In this paper, we introduce a novel approach to learn predictors that can generalize or extrapolate beyond the heterogeneous data. Our method builds on and extends recently proposed invariant risk minimization, adaptively forcing the predictor to avoid nuisance variation. We achieve this by continually exercising and manipulating latent representations of molecules to highlight undesirable variation to the predictor. To test the method we use a combination of three data sources: SARS-CoV-2 antiviral screening data, molecular fragments that bind to SARS-CoV-2 main protease and large screening data for SARS-CoV-1. Our predictor outperforms state-of-the-art transfer learning methods by significant margin. We also report the top 20 predictions of our model on Broad drug repurposing hub.

Sparse estimation via penalized likelihood (PL) is now a popular approach to learn the associations among a large set of variables. This paper describes an R package called lslx that implements PL methods for semi-confirmatory structural equation modeling (SEM). In this semi-confirmatory approach, each model parameter can be specified as free/fixed for theory testing, or penalized for exploration. By incorporating either a L1 or minimax concave penalty, the sparsity pattern of the parameter matrix can be efficiently explored. Package lslx minimizes the PL criterion through a quasi-Newton method. The algorithm conducts line search and checks the first-order condition in each iteration to ensure the optimality of the obtained solution. A numerical comparison between competing packages shows that lslx can reliably find PL estimates with the least time. The current package also supports other advanced functionalities, including a two-stage method with auxiliary variables for missing data handling and a reparameterized multi-group SEM to explore population heterogeneity.

The random-effects or normal-normal hierarchical model is commonly utilized in a wide range of meta-analysis applications. A Bayesian approach to inference is very attractive in this context, especially when a meta-analysis is based only on few studies. The bayesmeta R package provides readily accessible tools to perform Bayesian meta-analyses and generate plots and summaries, without having to worry about computational details. It allows for flexible prior specification and instant access to the resulting posterior distributions, including prediction and shrinkage estimation, and facilitating for example quick sensitivity checks. The present paper introduces the underlying theory and showcases its usage.

The R package mvord implements composite likelihood estimation in the class of multivariate ordinal regression models with a multivariate probit and a multivariate logit link. A flexible modeling framework for multiple ordinal measurements on the same subject is set up, which takes into consideration the dependence among the multiple observations by employing different error structures. Heterogeneity in the error structure across the subjects can be accounted for by the package, which allows for covariate dependent error structures. In addition, different regression coefficients and threshold parameters for each response are supported. If a reduction of the parameter space is desired, constraints on the threshold as well as on the regression coefficients can be specified by the user. The proposed multivariate framework is illustrated by means of a credit risk application.

An R package for computing the all-subsets regression problem is presented. The proposed algorithms are based on computational strategies recently developed. A novel algorithm for the best-subset regression problem selects subset models based on a predetermined criterion. The package user can choose from exact and from approximation algorithms. The core of the package is written in C++ and provides an efficient implementation of all the underlying numerical computations. A case study and benchmark results illustrate the usage and the computational efficiency of the package.

Manifold optimization appears in a wide variety of computational problems in the applied sciences. In recent statistical methodologies such as sufficient dimension reduction and regression envelopes, estimation relies on the optimization of likelihood functions over spaces of matrices such as the Stiefel or Grassmann manifolds. Recently, Huang, Absil, Gallivan, and Hand (2016) have introduced the library ROPTLIB, which provides a framework and state of the art algorithms to optimize real-valued objective functions over commonly used matrix-valued Riemannian manifolds. This article presents ManifoldOptim, an R package that wraps the C++ library ROPTLIB. ManifoldOptim enables users to access functionality in ROPTLIB through R so that optimization problems can easily be constructed, solved, and integrated into larger R codes. Computationally intensive problems can be programmed with Rcpp and RcppArmadillo, and otherwise accessed through R. We illustrate the practical use of ManifoldOptim through several motivating examples involving dimension reduction and envelope methods in regression.

The last seminar in the 2017–18 History of Pre-Modern Medicine seminar series takes place on Tuesday 27 February. Speaker: Dr Dror Weil (Max Planck Institute for the History of Science, Berlin) Bodies translated: the circulation of Arabo-Persian physiological theories in late… Continue reading