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Common tasks encountered in epidemiology, including disease incidence estimation and causal inference, rely on predictive modeling. Constructing a predictive model can be thought of as learning a prediction function, i.e., a function that takes as input covariate data and outputs a predicted value. Many strategies for learning these functions from data are available, from parametric regressions to machine learning algorithms. It can be challenging to choose an approach, as it is impossible to know in advance which one is the most suitable for a particular dataset and prediction task at hand. The super learner (SL) is an algorithm that alleviates concerns over selecting the one "right" strategy while providing the freedom to consider many of them, such as those recommended by collaborators, used in related research, or specified by subject-matter experts. It is an entirely pre-specified and data-adaptive strategy for predictive modeling. To ensure the SL is well-specified for learning the prediction function, the analyst does need to make a few important choices. In this Education Corner article, we provide step-by-step guidelines for making these choices, walking the reader through each of them and providing intuition along the way. In doing so, we aim to empower the analyst to tailor the SL specification to their prediction task, thereby ensuring their SL performs as well as possible. A flowchart provides a concise, easy-to-follow summary of key suggestions and heuristics, based on our accumulated experience, and guided by theory.

The naive importance sampling (IS) estimator generally does not work well in examples involving simultaneous inference on several targets, as the importance weights can take arbitrarily large values, making the estimator highly unstable. In such situations, alternative multiple IS estimators involving samples from multiple proposal distributions are preferred. Just like the naive IS, the success of these multiple IS estimators crucially depends on the choice of the proposal distributions. The selection of these proposal distributions is the focus of this article. We propose three methods: (i) a geometric space filling approach, (ii) a minimax variance approach, and (iii) a maximum entropy approach. The first two methods are applicable to any IS estimator, whereas the third approach is described in the context of Doss's (2010) two-stage IS estimator. For the first method, we propose a suitable measure of 'closeness' based on the symmetric Kullback-Leibler divergence, while the second and third approaches use estimates of asymptotic variances of Doss's (2010) IS estimator and Geyer's (1994) reverse logistic regression estimator, respectively. Thus, when samples from the proposal distributions are obtained by running Markov chains, we provide consistent spectral variance estimators for these asymptotic variances. The proposed methods for selecting proposal densities are illustrated using various detailed examples.

The shift towards end-to-end deep learning has brought unprecedented advances in many areas of computer vision. However, deep neural networks are trained on images with resolutions that rarely exceed $1,000 \times 1,000$ pixels. The growing use of scanners that create images with extremely high resolutions (average can be $100,000 \times 100,000$ pixels) thereby presents novel challenges to the field. Most of the published methods preprocess high-resolution images into a set of smaller patches, imposing an a priori belief on the best properties of the extracted patches (magnification, field of view, location, etc.). Herein, we introduce Magnifying Networks (MagNets) as an alternative deep learning solution for gigapixel image analysis that does not rely on a preprocessing stage nor requires the processing of billions of pixels. MagNets can learn to dynamically retrieve any part of a gigapixel image, at any magnification level and field of view, in an end-to-end fashion with minimal ground truth (a single global, slide-level label). Our results on the publicly available Camelyon16 and Camelyon17 datasets corroborate to the effectiveness and efficiency of MagNets and the proposed optimization framework for whole slide image classification. Importantly, MagNets process far less patches from each slide than any of the existing approaches ($10$ to $300$ times less).

We review the scholarly contributions that utilise Natural Language Processing (NLP) techniques to support the design process. Using a heuristic approach, we gathered 223 articles that are published in 32 journals within the period 1991-present. We present state-of-the-art NLP in-and-for design research by reviewing these articles according to the type of natural language text sources: internal reports, design concepts, discourse transcripts, technical publications, consumer opinions, and others. Upon summarizing and identifying the gaps in these contributions, we utilise an existing design innovation framework to identify the applications that are currently being supported by NLP. We then propose a few methodological and theoretical directions for future NLP in-and-for design research.

We introduce Universal Solution Manifold Network (USM-Net), a novel surrogate model, based on Artificial Neural Networks (ANNs), which applies to differential problems whose solution depends on physical and geometrical parameters. Our method employs a mesh-less architecture, thus overcoming the limitations associated with image segmentation and mesh generation required by traditional discretization methods. Indeed, we encode geometrical variability through scalar landmarks, such as coordinates of points of interest. In biomedical applications, these landmarks can be inexpensively processed from clinical images. Our approach is non-intrusive and modular, as we select a data-driven loss function. The latter can also be modified by considering additional constraints, thus leveraging available physical knowledge. Our approach can also accommodate a universal coordinate system, which supports the USM-Net in learning the correspondence between points belonging to different geometries, boosting prediction accuracy on unobserved geometries. Finally, we present two numerical test cases in computational fluid dynamics involving variable Reynolds numbers as well as computational domains of variable shape. The results show that our method allows for inexpensive but accurate approximations of velocity and pressure, avoiding computationally expensive image segmentation, mesh generation, or re-training for every new instance of physical parameters and shape of the domain.

Present-day atomistic simulations generate long trajectories of ever more complex systems. Analyzing these data, discovering metastable states, and uncovering their nature is becoming increasingly challenging. In this paper, we first use the variational approach to conformation dynamics to discover the slowest dynamical modes of the simulations. This allows the different metastable states of the system to be located and organized hierarchically. The physical descriptors that characterize metastable states are discovered by means of a machine learning method. We show in the cases of two proteins, Chignolin and Bovine Pancreatic Trypsin Inhibitor, how such analysis can be effortlessly performed in a matter of seconds. Another strength of our approach is that it can be applied to the analysis of both unbiased and biased simulations.

Holonomic functions play an essential role in Computer Algebra since they allow the application of many symbolic algorithms. Among all algorithmic attempts to find formulas for power series, the holonomic property remains the most important requirement to be satisfied by the function under consideration. The targeted functions mainly summarize that of meromorphic functions. However, expressions like $\tan(z)$, $z/(\exp(z)-1)$, $\sec(z)$, etc., particularly, reciprocals, quotients and compositions of holonomic functions, are generally not holonomic. Therefore their power series are inaccessible by the holonomic framework. From the mathematical dictionaries, one can observe that most of the known closed-form formulas of non-holonomic power series involve another sequence whose evaluation depends on some finite summations. In the case of $\tan(z)$ and $\sec(z)$ the corresponding sequences are the Bernoulli and Euler numbers, respectively. Thus providing a symbolic approach that yields complete representations when linear summations for power series coefficients of non-holonomic functions appear, might be seen as a step forward towards the representation of non-holonomic power series. By adapting the method of ansatz with undetermined coefficients, we build an algorithm that computes least-order quadratic differential equations with polynomial coefficients for a large class of non-holonomic functions. A differential equation resulting from this procedure is converted into a recurrence equation by applying the Cauchy product formula and rewriting powers into polynomials and derivatives into shifts. Finally, using enough initial values we are able to give normal form representations to characterize several non-holonomic power series and prove non-trivial identities. We discuss this algorithm and its implementation for Maple 2022.

Models for dependent data are distinguished by their targets of inference. Marginal models are useful when interest lies in quantifying associations averaged across a population of clusters. When the functional form of a covariate-outcome association is unknown, flexible regression methods are needed to allow for potentially non-linear relationships. We propose a novel marginal additive model (MAM) for modelling cluster-correlated data with non-linear population-averaged associations. The proposed MAM is a unified framework for estimation and uncertainty quantification of a marginal mean model, combined with inference for between-cluster variability and cluster-specific prediction. We propose a fitting algorithm that enables efficient computation of standard errors and corrects for estimation of penalty terms. We demonstrate the proposed methods in simulations and in application to (i) a longitudinal study of beaver foraging behaviour, and (ii) a spatial analysis of Loaloa infection in West Africa. R code for implementing the proposed methodology is available at //github.com/awstringer1/mam.

This book develops an effective theory approach to understanding deep neural networks of practical relevance. Beginning from a first-principles component-level picture of networks, we explain how to determine an accurate description of the output of trained networks by solving layer-to-layer iteration equations and nonlinear learning dynamics. A main result is that the predictions of networks are described by nearly-Gaussian distributions, with the depth-to-width aspect ratio of the network controlling the deviations from the infinite-width Gaussian description. We explain how these effectively-deep networks learn nontrivial representations from training and more broadly analyze the mechanism of representation learning for nonlinear models. From a nearly-kernel-methods perspective, we find that the dependence of such models' predictions on the underlying learning algorithm can be expressed in a simple and universal way. To obtain these results, we develop the notion of representation group flow (RG flow) to characterize the propagation of signals through the network. By tuning networks to criticality, we give a practical solution to the exploding and vanishing gradient problem. We further explain how RG flow leads to near-universal behavior and lets us categorize networks built from different activation functions into universality classes. Altogether, we show that the depth-to-width ratio governs the effective model complexity of the ensemble of trained networks. By using information-theoretic techniques, we estimate the optimal aspect ratio at which we expect the network to be practically most useful and show how residual connections can be used to push this scale to arbitrary depths. With these tools, we can learn in detail about the inductive bias of architectures, hyperparameters, and optimizers.

This paper focuses on the expected difference in borrower's repayment when there is a change in the lender's credit decisions. Classical estimators overlook the confounding effects and hence the estimation error can be magnificent. As such, we propose another approach to construct the estimators such that the error can be greatly reduced. The proposed estimators are shown to be unbiased, consistent, and robust through a combination of theoretical analysis and numerical testing. Moreover, we compare the power of estimating the causal quantities between the classical estimators and the proposed estimators. The comparison is tested across a wide range of models, including linear regression models, tree-based models, and neural network-based models, under different simulated datasets that exhibit different levels of causality, different degrees of nonlinearity, and different distributional properties. Most importantly, we apply our approaches to a large observational dataset provided by a global technology firm that operates in both the e-commerce and the lending business. We find that the relative reduction of estimation error is strikingly substantial if the causal effects are accounted for correctly.