The New England Journal of Statistics in Data Science

This contribution is a series of comments on Prof. Xiao-Li Meng’s article, “Double Your Variance, Dirtify Your Bayes, Devour Your Pufferfish, and Draw Your Kidstogram”. Prof. Meng’s article offers some radical proposals and not-so-radical proposals to improve the quality of statistical inference used in the sciences and also to extend distributional thinking to early education. Discussions and alternative proposals are presented.

Marginalization of latent variables or nuisance parameters is a fundamental aspect of Bayesian inference and uncertainty quantification. In this work, we focus on scalable marginalization of latent variables in modeling correlated data, such as spatio-temporal or functional observations. We first introduce Gaussian processes (GPs) for modeling correlated data and highlight the computational challenge, where the computational complexity increases cubically fast along with the number of observations. We then review the connection between the state space model and GPs with Matérn covariance for temporal inputs. The Kalman filter and Rauch-Tung-Striebel smoother were introduced as a scalable marginalization technique for computing the likelihood and making predictions of GPs without approximation. We introduce recent efforts on extending the scalable marginalization idea to the linear model of coregionalization for multivariate correlated output and spatio-temporal observations. In the final part of this work, we introduce a novel marginalization technique to estimate interaction kernels and forecast particle trajectories. The computational progress lies in the sparse representation of the inverse covariance matrix of the latent variables, then applying conjugate gradient for improving predictive accuracy with large data sets. The computational advances achieved in this work outline a wide range of applications in molecular dynamic simulation, cellular migration, and agent-based models.

Modern machine learning algorithms are capable of providing remarkably accurate point-predictions; however, questions remain about their statistical reliability. Unlike conventional machine learning methods, conformal prediction algorithms return confidence sets (i.e., set-valued predictions) that correspond to a given significance level. Moreover, these confidence sets are valid in the sense that they guarantee finite sample control over type 1 error probabilities, allowing the practitioner to choose an acceptable error rate. In our paper, we propose inductive conformal prediction (ICP) algorithms for the tasks of text infilling and part-of-speech (POS) prediction for natural language data. We construct new ICP-enhanced algorithms for POS tagging based on BERT (bidirectional encoder representations from transformers) and BiLSTM (bidirectional long short-term memory) models. For text infilling, we design a new ICP-enhanced BERT algorithm. We analyze the performance of the algorithms in simulations using the Brown Corpus, which contains over 57,000 sentences. Our results demonstrate that the ICP algorithms are able to produce valid set-valued predictions that are small enough to be applicable in real-world applications. We also provide a real data example for how our proposed set-valued predictions can improve machine generated audio transcriptions.

This article expands upon my presentation to the panel on “The Radical Prescription for Change” at the 2017 ASA (American Statistical Association) symposium on A World Beyond $p<0.05$. It emphasizes that, to greatly enhance the reliability of—and hence public trust in—statistical and data scientific findings, we need to take a holistic approach. We need to lead by example, incentivize study quality, and inoculate future generations with profound appreciations for the world of uncertainty and the uncertainty world. The four “radical” proposals in the title—with all their inherent defects and trade-offs—are designed to provoke reactions and actions. First, research methodologies are trustworthy only if they deliver what they promise, even if this means that they have to be overly protective, a necessary trade-off for practicing quality-guaranteed statistics. This guiding principle may compel us to doubling variance in some situations, a strategy that also coincides with the call to raise the bar from $p<0.05$ to $p<0.005$ [3]. Second, teaching principled practicality or corner-cutting is a promising strategy to enhance the scientific community’s as well as the general public’s ability to spot—and hence to deter—flawed arguments or findings. A remarkable quick-and-dirty Bayes formula for rare events, which simply divides the prevalence by the sum of the prevalence and the false positive rate (or the total error rate), as featured by the popular radio show Car Talk, illustrates the effectiveness of this strategy. Third, it should be a routine mental exercise to put ourselves in the shoes of those who would be affected by our research finding, in order to combat the tendency of rushing to conclusions or overstating confidence in our findings. A pufferfish/selfish test can serve as an effective reminder, and can help to institute the mantra “Thou shalt not sell what thou refuseth to buy” as the most basic professional decency. Considering personal stakes in our statistical endeavors also points to the concept of behavioral statistics, in the spirit of behavioral economics. Fourth, the current mathematical education paradigm that puts “deterministic first, stochastic second” is likely responsible for the general difficulties with reasoning under uncertainty, a situation that can be improved by introducing the concept of histogram, or rather kidstogram, as early as the concept of counting.

Phase I trials investigate the toxicity profile of a new treatment and identify the maximum tolerated dose for further evaluation. Most phase I trials use a binary dose-limiting toxicity endpoint to summarize the toxicity profile of a dose. In reality, reported toxicity information is much more abundant, including various types and grades of adverse events. Building upon the i3+3 design (Liu et al., 2020), we propose the Ti3+3 design, in which the letter “T” represents “total” toxicity. The proposed design takes into account multiple toxicity types and grades by computing the toxicity burden at each dose. The Ti3+3 design aims to achieve desirable operating characteristics using a simple statistics framework that utilizes“toxicity burden interval” (TBI). Simulation results show that Ti3+3 demonstrates comparable performance with existing more complex designs.

Random forests are a powerful machine learning tool that capture complex relationships between independent variables and an outcome of interest. Trees built in a random forest are dependent on several hyperparameters, one of the more critical being the node size. The original algorithm of Breiman, controls for node size by limiting the size of the parent node, so that a node cannot be split if it has less than a specified number of observations. We propose that this hyperparameter should instead be defined as the minimum number of observations in each terminal node. The two existing random forest approaches are compared in the regression context based on estimated generalization error, bias-squared, and variance of resulting predictions in a number of simulated datasets. Additionally the two approaches are applied to type 2 diabetes data obtained from the National Health and Nutrition Examination Survey. We have developed a straightforward method for incorporating weights into the random forest analysis of survey data. Our results demonstrate that generalization error under the proposed approach is competitive to that attained from the original random forest approach when data have large random error variability. The R code created from this work is available and includes an illustration.

There are many cases in which one has continuous flows over networks, and there is interest in predicting and monitoring such flows. This paper provides Bayesian models for two types of networks—those in which flow can be bidirectional, and those in which flow is unidirectional. The former is illustrated by an application to electrical transmission over the power grid, and the latter is examined with data on volumetric water flow in a river system. Both applications yield good predictive accuracy over short time horizons. Predictive accuracy is important in these applications—it improves the efficiency of the energy market and enables flood warnings and water management.

In this paper, we build a mechanistic system to understand the relation between a reduction in human mobility and Covid-19 spread dynamics within New York City. To this end, we propose a multivariate compartmental system that jointly models smartphone mobility data and case counts during the first 90 days of the epidemic. Parameter calibration is achieved through the formulation of a general statistical-mechanistic Bayesian hierarchical model. The open-source probabilistic programming language Stan is used for the requisite computation. Through sensitivity analysis and out-of-sample forecasting, we find our simple and interpretable model provides quantifiable evidence for how reductions in human mobility altered early case dynamics in New York City.