Difference in proportions is frequently used to measure treatment effect for binary outcomes in randomized clinical trials. The estimation of difference in proportions can be assisted by adjusting for prognostic baseline covariates to enhance precision and bolster statistical power. Standardization or G-computation is a widely used method for covariate adjustment in estimating unconditional difference in proportions, because of its robustness to model misspecification. Various inference methods have been proposed to quantify the uncertainty and confidence intervals based on large-sample theories. However, their performances under small sample sizes and model misspecification have not been comprehensively evaluated. We propose an alternative approach to estimate the unconditional variance of the standardization estimator based on the robust sandwich estimator to further enhance the finite sample performance. Extensive simulations are provided to demonstrate the performances of the proposed method, spanning a wide range of sample sizes, randomization ratios, and model misspecification. We apply the proposed method in a real data example to illustrate the practical utility.
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In clinical trials of longitudinal continuous outcomes, reference based imputation (RBI) has commonly been applied to handle missing outcome data in settings where the estimand incorporates the effects of intercurrent events, e.g. treatment discontinuation. RBI was originally developed in the multiple imputation framework, however recently conditional mean imputation (CMI) combined with the jackknife estimator of the standard error was proposed as a way to obtain deterministic treatment effect estimates and correct frequentist inference. For both multiple and CMI, a mixed model for repeated measures (MMRM) is often used for the imputation model, but this can be computationally intensive to fit to multiple data sets (e.g. the jackknife samples) and lead to convergence issues with complex MMRM models with many parameters. Therefore, a step-wise approach based on sequential linear regression (SLR) of the outcomes at each visit was developed for the imputation model in the multiple imputation framework, but similar developments in the CMI framework are lacking. In this article, we fill this gap in the literature by proposing a SLR approach to implement RBI in the CMI framework, and justify its validity using theoretical results and simulations. We also illustrate our proposal on a real data application.
Optimum distance flag codes (ODFCs), as special flag codes, have received a lot of attention due to its application in random network coding. In 2021, Alonso-Gonz\'{a}lez et al. constructed optimal $(n,\mathcal{A})$-ODFC for $\mathcal {A}\subseteq \{1,2,\ldots,k,n-k,\ldots,n-1\}$ with $k\in \mathcal A$ and $k|n$. In this paper, we introduce a new construction of $(n,\mathcal A)_q$-ODFCs by maximum rank-metric codes. It is proved that there is an $(n,\mathcal{A})$-ODFC of size $\frac{q^n-q^{k+r}}{q^k-1}+1$ for any $\mathcal{A}\subseteq\{1,2,\ldots,k,n-k,\ldots,n-1\}$ with $\mathcal A\cap \{k,n-k\}\neq\emptyset$, where $r\equiv n\pmod k$ and $0\leq r<k$. Furthermore, when $k>\frac{q^r-1}{q-1}$, this $(n,\mathcal A)_q$-ODFC is optimal. Specially, when $r=0$, Alonso-Gonz\'{a}lez et al.'s result is also obtained.
Over the last decade, approximating functions in infinite dimensions from samples has gained increasing attention in computational science and engineering, especially in computational uncertainty quantification. This is primarily due to the relevance of functions that are solutions to parametric differential equations in various fields, e.g. chemistry, economics, engineering, and physics. While acquiring accurate and reliable approximations of such functions is inherently difficult, current benchmark methods exploit the fact that such functions often belong to certain classes of holomorphic functions to get algebraic convergence rates in infinite dimensions with respect to the number of (potentially adaptive) samples $m$. Our work focuses on providing theoretical approximation guarantees for the class of $(\boldsymbol{b},\varepsilon)$-holomorphic functions, demonstrating that these algebraic rates are the best possible for Banach-valued functions in infinite dimensions. We establish lower bounds using a reduction to a discrete problem in combination with the theory of $m$-widths, Gelfand widths and Kolmogorov widths. We study two cases, known and unknown anisotropy, in which the relative importance of the variables is known and unknown, respectively. A key conclusion of our paper is that in the latter setting, approximation from finite samples is impossible without some inherent ordering of the variables, even if the samples are chosen adaptively. Finally, in both cases, we demonstrate near-optimal, non-adaptive (random) sampling and recovery strategies which achieve close to same rates as the lower bounds.
Finding the optimal design of experiments in the Bayesian setting typically requires estimation and optimization of the expected information gain functional. This functional consists of one outer and one inner integral, separated by the logarithm function applied to the inner integral. When the mathematical model of the experiment contains uncertainty about the parameters of interest and nuisance uncertainty, (i.e., uncertainty about parameters that affect the model but are not themselves of interest to the experimenter), two inner integrals must be estimated. Thus, the already considerable computational effort required to determine good approximations of the expected information gain is increased further. The Laplace approximation has been applied successfully in the context of experimental design in various ways, and we propose two novel estimators featuring the Laplace approximation to alleviate the computational burden of both inner integrals considerably. The first estimator applies Laplace's method followed by a Laplace approximation, introducing a bias. The second estimator uses two Laplace approximations as importance sampling measures for Monte Carlo approximations of the inner integrals. Both estimators use Monte Carlo approximation for the remaining outer integral estimation. We provide three numerical examples demonstrating the applicability and effectiveness of our proposed estimators.
Compliant mechanisms actuated by pneumatic loads are receiving increasing attention due to their direct applicability as soft robots that perform tasks using their flexible bodies. Using multiple materials to build them can further improve their performance and efficiency. Due to developments in additive manufacturing, the fabrication of multi-material soft robots is becoming a real possibility. To exploit this opportunity, there is a need for a dedicated design approach. This paper offers a systematic approach to developing such mechanisms using topology optimization. The extended SIMP scheme is employed for multi-material modeling. The design-dependent nature of the pressure load is modeled using the Darcy law with a volumetric drainage term. Flow coefficient of each element is interpolated using a smoothed Heaviside function. The obtained pressure field is converted to consistent nodal loads. The adjoint-variable approach is employed to determine the sensitivities. A robust formulation is employed, wherein a min-max optimization problem is formulated using the output displacements of the eroded and blueprint designs. Volume constraints are applied to the blueprint design, whereas the strain energy constraint is formulated with respect to the eroded design. The efficacy and success of the approach are demonstrated by designing pneumatically actuated multi-material gripper and contractor mechanisms. A numerical study confirms that multiple-material mechanisms perform relatively better than their single-material counterparts.
The accuracy of solving partial differential equations (PDEs) on coarse grids is greatly affected by the choice of discretization schemes. In this work, we propose to learn time integration schemes based on neural networks which satisfy three distinct sets of mathematical constraints, i.e., unconstrained, semi-constrained with the root condition, and fully-constrained with both root and consistency conditions. We focus on the learning of 3-step linear multistep methods, which we subsequently applied to solve three model PDEs, i.e., the one-dimensional heat equation, the one-dimensional wave equation, and the one-dimensional Burgers' equation. The results show that the prediction error of the learned fully-constrained scheme is close to that of the Runge-Kutta method and Adams-Bashforth method. Compared to the traditional methods, the learned unconstrained and semi-constrained schemes significantly reduce the prediction error on coarse grids. On a grid that is 4 times coarser than the reference grid, the mean square error shows a reduction of up to an order of magnitude for some of the heat equation cases, and a substantial improvement in phase prediction for the wave equation. On a 32 times coarser grid, the mean square error for the Burgers' equation can be reduced by up to 35% to 40%.
Identifying replicable signals across different studies provides stronger scientific evidence and more powerful inference. Existing literature on high dimensional applicability analysis either imposes strong modeling assumptions or has low power. We develop a powerful and robust empirical Bayes approach for high dimensional replicability analysis. Our method effectively borrows information from different features and studies while accounting for heterogeneity. We show that the proposed method has better power than competing methods while controlling the false discovery rate, both empirically and theoretically. Analyzing datasets from the genome-wide association studies reveals new biological insights that otherwise cannot be obtained by using existing methods.
Genomics methods have uncovered patterns in a range of biological systems, but obscure important aspects of cell behavior: the shape, relative locations of, movement of, and interactions between cells in space. Spatial technologies that collect genomic or epigenomic data while preserving spatial information have begun to overcome these limitations. These new data promise a deeper understanding of the factors that affect cellular behavior, and in particular the ability to directly test existing theories about cell state and variation in the context of morphology, location, motility, and signaling that could not be tested before. Rapid advancements in resolution, ease-of-use, and scale of spatial genomics technologies to address these questions also require an updated toolkit of statistical methods with which to interrogate these data. We present four open biological questions that can now be answered using spatial genomics data paired with methods for analysis. We outline spatial data modalities for each that may yield specific insight, discuss how conflicting theories may be tested by comparing the data to conceptual models of biological behavior, and highlight statistical and machine learning-based tools that may prove particularly helpful to recover biological insight.
Complexity is a fundamental concept underlying statistical learning theory that aims to inform generalization performance. Parameter count, while successful in low-dimensional settings, is not well-justified for overparameterized settings when the number of parameters is more than the number of training samples. We revisit complexity measures based on Rissanen's principle of minimum description length (MDL) and define a novel MDL-based complexity (MDL-COMP) that remains valid for overparameterized models. MDL-COMP is defined via an optimality criterion over the encodings induced by a good Ridge estimator class. We provide an extensive theoretical characterization of MDL-COMP for linear models and kernel methods and show that it is not just a function of parameter count, but rather a function of the singular values of the design or the kernel matrix and the signal-to-noise ratio. For a linear model with $n$ observations, $d$ parameters, and i.i.d. Gaussian predictors, MDL-COMP scales linearly with $d$ when $d<n$, but the scaling is exponentially smaller -- $\log d$ for $d>n$. For kernel methods, we show that MDL-COMP informs minimax in-sample error, and can decrease as the dimensionality of the input increases. We also prove that MDL-COMP upper bounds the in-sample mean squared error (MSE). Via an array of simulations and real-data experiments, we show that a data-driven Prac-MDL-COMP informs hyper-parameter tuning for optimizing test MSE with ridge regression in limited data settings, sometimes improving upon cross-validation and (always) saving computational costs. Finally, our findings also suggest that the recently observed double decent phenomenons in overparameterized models might be a consequence of the choice of non-ideal estimators.
A key challenge when trying to understand innovation is that it is a dynamic, ongoing process, which can be highly contingent on ephemeral factors such as culture, economics, or luck. This means that any analysis of the real-world process must necessarily be historical - and thus probably too late to be most useful - but also cannot be sure what the properties of the web of connections between innovations is or was. Here I try to address this by designing and generating a set of synthetic innovation web "dictionaries" that can be used to host sampled innovation timelines, probe the overall statistics and behaviours of these processes, and determine the degree of their reliance on the structure or generating algorithm. Thus, inspired by the work of Fink, Reeves, Palma and Farr (2017) on innovation in language, gastronomy, and technology, I study how new symbol discovery manifests itself in terms of additional "word" vocabulary being available from dictionaries generated from a finite number of symbols. Several distinct dictionary generation models are investigated using numerical simulation, with emphasis on the scaling of knowledge as dictionary generators and parameters are varied, and the role of which order the symbols are discovered in.
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