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Inspired by the row and column action methods for solving large-scale linear systems, in this work, we explore the use of frontal slices for solving tensor linear systems. In particular, this paper presents a novel approach for using frontal slices of a tensor $\mathcal{A}$ to solve tensor linear systems $\mathcal{A} * \mathcal{X} = \mathcal{B}$ where $*$ denotes the t-product. In addition, we consider variations of this method, including cyclic, block, and randomized approaches, each designed to optimize performance in different operational contexts. Our primary contribution lies in the development and convergence analysis of these methods. Experimental results on synthetically generated and real-world data, including applications such as image and video deblurring, demonstrate the efficacy of our proposed approaches and validate our theoretical findings., Comment: 41 pages, 10 figures

We proposed the tensor-input tree (TT) method for scalar-on-tensor and tensor-on-tensor regression problems. We first address scalar-on-tensor problem by proposing scalar-output regression tree models whose input variable are tensors (i.e., multi-way arrays). We devised and implemented fast randomized and deterministic algorithms for efficient fitting of scalar-on-tensor trees, making TT competitive against tensor-input GP models. Based on scalar-on-tensor tree models, we extend our method to tensor-on-tensor problems using additive tree ensemble approaches. Theoretical justification and extensive experiments on real and synthetic datasets are provided to illustrate the performance of TT., Comment: 36 pages, 9 Figures

Topology can extract the structural information in a dataset efficiently. In this paper, we attempt to incorporate topological information into a multiple output Gaussian process model for transfer learning purposes. To achieve this goal, we extend the framework of circular coordinates into a novel framework of mixed valued coordinates to take linear trends in the time series into consideration. One of the major challenges to learn from multiple time series effectively via a multiple output Gaussian process model is constructing a functional kernel. We propose to use topologically induced clustering to construct a cluster based kernel in a multiple output Gaussian process model. This kernel not only incorporates the topological structural information, but also allows us to put forward a unified framework using topological information in time and motion series., Comment: 7 pages, 4 figures

The Gaussian process (GP) is a popular statistical technique for stochastic function approximation and uncertainty quantification from data. GPs have been adopted into the realm of machine learning in the last two decades because of their superior prediction abilities, especially in data-sparse scenarios, and their inherent ability to provide robust uncertainty estimates. Even so, their performance highly depends on intricate customizations of the core methodology, which often leads to dissatisfaction among practitioners when standard setups and off-the-shelf software tools are being deployed. Arguably the most important building block of a GP is the kernel function which assumes the role of a covariance operator. Stationary kernels of the Mat\'ern class are used in the vast majority of applied studies; poor prediction performance and unrealistic uncertainty quantification are often the consequences. Non-stationary kernels show improved performance but are rarely used due to their more complicated functional form and the associated effort and expertise needed to define and tune them optimally. In this perspective, we want to help ML practitioners make sense of some of the most common forms of non-stationarity for Gaussian processes. We show a variety of kernels in action using representative datasets, carefully study their properties, and compare their performances. Based on our findings, we propose a new kernel that combines some of the identified advantages of existing kernels.

Algorithms from Randomized Numerical Linear Algebra (RandNLA) are known to be effective in handling high-dimensional computational problems, providing high-quality empirical performance as well as strong probabilistic guarantees. However, their practical application is complicated by the fact that the user needs to set various algorithm-specific tuning parameters which are different than those used in traditional NLA. This paper demonstrates how a surrogate-based autotuning approach can be used to address fundamental problems of parameter selection in RandNLA algorithms. In particular, we provide a detailed investigation of surrogate-based autotuning for sketch-and-precondition (SAP) based randomized least squares methods, which have been one of the great success stories in modern RandNLA. Empirical results show that our surrogate-based autotuning approach can achieve near-optimal performance with much less tuning cost than a random search (up to about 4x fewer trials of different parameter configurations). Moreover, while our experiments focus on least squares, our results demonstrate a general-purpose autotuning pipeline applicable to any kind of RandNLA algorithm.

In this paper we develop the randomized Sharded Bayesian Additive Regression Trees (SBT) model. We introduce a randomization auxiliary variable and a sharding tree to decide partitioning of data, and fit each partition component to a sub-model using Bayesian Additive Regression Tree (BART). By observing that the optimal design of a sharding tree can determine optimal sharding for sub-models on a product space, we introduce an intersection tree structure to completely specify both the sharding and modeling using only tree structures. In addition to experiments, we also derive the theoretical optimal weights for minimizing posterior contractions and prove the worst-case complexity of SBT., Comment: 46 pages, 10 figures (Appendix included)

We introduce an efficient and robust auto-tuning framework for hyperparameter selection in dimension reduction (DR) algorithms, focusing on large-scale datasets and arbitrary performance metrics. By leveraging Bayesian optimization (BO) with a surrogate model, our approach enables efficient hyperparameter selection with multi-objective trade-offs and allows us to perform data-driven sensitivity analysis. By incorporating normalization and subsampling, the proposed framework demonstrates versatility and efficiency, as shown in applications to visualization techniques such as t-SNE and UMAP. We evaluate our results on various synthetic and real-world datasets using multiple quality metrics, providing a robust and efficient solution for hyperparameter selection in DR algorithms., Comment: 20 pages, 16 figures

Supervised dimension reduction (SDR) has been a topic of growing interest in data science, as it enables the reduction of high-dimensional covariates while preserving the functional relation with certain response variables of interest. However, existing SDR methods are not suitable for analyzing datasets collected from case-control studies. In this setting, the goal is to learn and exploit the low-dimensional structure unique to or enriched by the case group, also known as the foreground group. While some unsupervised techniques such as the contrastive latent variable model and its variants have been developed for this purpose, they fail to preserve the functional relationship between the dimension-reduced covariates and the response variable. In this paper, we propose a supervised dimension reduction method called contrastive inverse regression (CIR) specifically designed for the contrastive setting. CIR introduces an optimization problem defined on the Stiefel manifold with a non-standard loss function. We prove the convergence of CIR to a local optimum using a gradient descent-based algorithm, and our numerical study empirically demonstrates the improved performance over competing methods for high-dimensional data.

This paper presents a computationally efficient framework for identifying resonance modes of 3D radio-frequency (RF) cavities with damping waveguide ports. The proposed framework relies on surface integral equation (IE) formulations to convert the task of resonance detection to the task of finding resonance frequencies at which the lowest few eigenvalues of the system matrix is close to zero. For the linear eigenvalue problem \rev{with a fixed frequency}, we propose leveraging fast direct solvers to efficiently invert the system matrix; for the frequency search problem, we develop a hybrid optimization algorithm that combines Bayesian optimization with down-hill simplex optimization. The proposed IE-based resonance detection framework (IERD) has been applied to detection of high-order resonance modes (HOMs) of realistic accelerator RF cavities to demonstrate its efficiency and accuracy.

Randomized numerical linear algebra - RandNLA, for short - concerns the use of randomization as a resource to develop improved algorithms for large-scale linear algebra computations. The origins of contemporary RandNLA lay in theoretical computer science, where it blossomed from a simple idea: randomization provides an avenue for computing approximate solutions to linear algebra problems more efficiently than deterministic algorithms. This idea proved fruitful in the development of scalable algorithms for machine learning and statistical data analysis applications. However, RandNLA's true potential only came into focus upon integration with the fields of numerical analysis and "classical" numerical linear algebra. Through the efforts of many individuals, randomized algorithms have been developed that provide full control over the accuracy of their solutions and that can be every bit as reliable as algorithms that might be found in libraries such as LAPACK. Recent years have even seen the incorporation of certain RandNLA methods into MATLAB, the NAG Library, NVIDIA's cuSOLVER, and SciKit-Learn. For all its success, we believe that RandNLA has yet to realize its full potential. In particular, we believe the scientific community stands to benefit significantly from suitably defined "RandBLAS" and "RandLAPACK" libraries, to serve as standards conceptually analogous to BLAS and LAPACK. This 200-page monograph represents a step toward defining such standards. In it, we cover topics spanning basic sketching, least squares and optimization, low-rank approximation, full matrix decompositions, leverage score sampling, and sketching data with tensor product structures (among others). Much of the provided pseudo-code has been tested via publicly available MATLAB and Python implementations., Comment: v1: this is the first arXiv release of LAPACK Working Note 299. v2: complete rewrite of the subsection on trace estimation, among other changes. See frontmatter page ii (pdf page 5) for revision history

The modeling and uncertainty quantification of closed curves is an important problem in the field of shape analysis, and can have significant ramifications for subsequent statistical tasks. Many of these tasks involve collections of closed curves, which often exhibit structural similarities at multiple levels. Modeling multiple closed curves in a way that efficiently incorporates such between-curve dependence remains a challenging problem. In this work, we propose and investigate a multiple-output (a.k.a. multi-output), multi-dimensional Gaussian process modeling framework. We illustrate the proposed methodological advances, and demonstrate the utility of meaningful uncertainty quantification, on several curve and shape-related tasks. This model-based approach not only addresses the problem of inference on closed curves (and their shapes) with kernel constructions, but also opens doors to nonparametric modeling of multi-level dependence for functional objects in general., Comment: 66 pages, 20 figures

This paper presents a new type of hybrid model for Bayesian optimization (BO) adept at managing mixed variables, encompassing both quantitative (continuous and integer) and qualitative (categorical) types. Our proposed new hybrid models (named hybridM) merge the Monte Carlo Tree Search structure (MCTS) for categorical variables with Gaussian Processes (GP) for continuous ones. hybridM leverages the upper confidence bound tree search (UCTS) for MCTS strategy, showcasing the tree architecture's integration into Bayesian optimization. Our innovations, including dynamic online kernel selection in the surrogate modeling phase and a unique UCTS search strategy, position our hybrid models as an advancement in mixed-variable surrogate models. Numerical experiments underscore the superiority of hybrid models, highlighting their potential in Bayesian optimization., Comment: 33 pages, 8 Figures

Modern datasets often exhibit high dimensionality, yet the data reside in low-dimensional manifolds that can reveal underlying geometric structures critical for data analysis. A prime example of such a dataset is a collection of cell cycle measurements, where the inherently cyclical nature of the process can be represented as a circle or sphere. Motivated by the need to analyze these types of datasets, we propose a nonlinear dimension reduction method, Spherical Rotation Component Analysis (SRCA), that incorporates geometric information to better approximate low-dimensional manifolds. SRCA is a versatile method designed to work in both high-dimensional and small sample size settings. By employing spheres or ellipsoids, SRCA provides a low-rank spherical representation of the data with general theoretic guarantees, effectively retaining the geometric structure of the dataset during dimensionality reduction. A comprehensive simulation study, along with a successful application to human cell cycle data, further highlights the advantages of SRCA compared to state-of-the-art alternatives, demonstrating its superior performance in approximating the manifold while preserving inherent geometric structures., Comment: 60 pages

The statistical methods used to analyze medical data are becoming increasingly complex. Novel statistical methods increasingly rely on simulation studies to assess their validity. Such assessments typically appear in statistical or computational journals, and the methodology is later introduced to the medical community through tutorials. This can be problematic if applied researchers use the methodologies in settings that have not been evaluated. In this paper, we explore a case study of one such method that has become popular in the analysis of coronavirus disease 2019 (COVID-19) data. The integrated nested Laplace approximations (INLA), as implemented in the R-INLA package, approximates the marginal posterior distributions of target parameters that would have been obtained from a fully Bayesian analysis. We seek to answer an important question: Does existing research on the accuracy of INLA's approximations support how researchers are currently using it to analyze COVID-19 data? We identify three limitations to work assessing INLA's accuracy: 1) inconsistent definitions of accuracy, 2) a lack of studies validating how researchers are actually using INLA, and 3) a lack of research into the reproducibility of INLA's output. We explore the practical impact of each limitation with simulation studies based on models and data used in COVID-19 research. Our results suggest existing methods of assessing the accuracy of the INLA technique may not support how COVID-19 researchers are using it. Guided in part by our results, we offer a proposed set of minimum guidelines for researchers using statistical methodologies primarily validated through simulation studies.

Building surrogate models is one common approach when we attempt to learn unknown black-box functions. Bayesian optimization provides a framework which allows us to build surrogate models based on sequential samples drawn from the function and find the optimum. Tuning algorithmic parameters to optimize the performance of large, complicated "black-box" application codes is a specific important application, which aims at finding the optima of black-box functions. Within the Bayesian optimization framework, the Gaussian process model produces smooth or continuous sample paths. However, the black-box function in the tuning problem is often non-smooth. This difficult tuning problem is worsened by the fact that we usually have limited sequential samples from the black-box function. Motivated by these issues encountered in tuning, we propose a novel additive Gaussian process model called clustered Gaussian process (cGP), where the additive components are induced by clustering. In the examples we studied, the performance can be improved by as much as 90% among repetitive experiments. By using this surrogate model, we want to capture the non-smoothness of the black-box function. In addition to an algorithm for constructing this model, we also apply the model to several artificial and real applications to evaluate it., Comment: 61 pages

Visualizing very large matrices involves many formidable problems. Various popular solutions to these problems involve sampling, clustering, projection, or feature selection to reduce the size and complexity of the original task. An important aspect of these methods is how to preserve relative distances between points in the higher-dimensional space after reducing rows and columns to fit in a lower dimensional space. This aspect is important because conclusions based on faulty visual reasoning can be harmful. Judging dissimilar points as similar or similar points as dissimilar on the basis of a visualization can lead to false conclusions. To ameliorate this bias and to make visualizations of very large datasets feasible, we introduce two new algorithms that respectively select a subset of rows and columns of a rectangular matrix. This selection is designed to preserve relative distances as closely as possible. We compare our matrix sketch to more traditional alternatives on a variety of artificial and real datasets., Comment: 38 pages, 13 figures

Topological data analysis (TDA) allows us to explore the topological features of a dataset. Among topological features, lower dimensional ones have recently drawn the attention of practitioners in mathematics and statistics due to their potential to aid the discovery of low dimensional structure in a data set. However, lower dimensional features are usually challenging to detect based on finite samples and using TDA methods that ignore the probabilistic mechanism that generates the data. In this paper, lower dimensional topological features occurring as zero-density regions of density functions are introduced and thoroughly investigated. Specifically, we consider sequences of coverings for the support of a density function in which the coverings are comprised of balls with shrinking radii. We show that, when these coverings satisfy certain sufficient conditions as the sample size goes to infinity, we can detect lower dimensional, zero-density regions with increasingly higher probability while guarding against false detection. We supplement the theoretical developments with the discussion of simulated experiments that elucidate the behavior of the methodology for different choices of the tuning parameters that govern the construction of the covering sequences and characterize the asymptotic results., Comment: 32 pages

Topological Data Analysis (TDA) provides novel approaches that allow us to analyze the geometrical shapes and topological structures of a dataset. As one important application, TDA can be used for data visualization and dimension reduction. We follow the framework of circular coordinate representation, which allows us to perform dimension reduction and visualization for high-dimensional datasets on a torus using persistent cohomology. In this paper, we propose a method to adapt the circular coordinate framework to take into account the roughness of circular coordinates in change-point and high-dimensional applications. We use a generalized penalty function instead of an $L_{2}$ penalty in the traditional circular coordinate algorithm. We provide simulation experiments and real data analysis to support our claim that circular coordinates with generalized penalty will detect the change in high-dimensional datasets under different sampling schemes while preserving the topological structures., Comment: 39 pages

A fundamental problem in computer vision is boundary estimation, where the goal is to delineate the boundary of objects in an image. In this paper, we propose a method which jointly incorporates geometric and topological information within an image to simultaneously estimate boundaries for objects within images with more complex topologies. We use a topological clustering-based method to assist initialization of the Bayesian active contour model. This combines pixel clustering, boundary smoothness, and potential prior shape information to produce an estimated object boundary. Active contour methods are knownto be extremely sensitive to algorithm initialization, relying on the user to provide a reasonable starting curve to the algorithm. In the presence of images featuring objects with complex topological structures, such as objects with holes or multiple objects, the user must initialize separate curves for each boundary of interest. Our proposed topologically-guided method can provide an interpretable, smart initialization in these settings, freeing up the user from potential pitfalls associated with objects of complex topological structure. We provide a detailed simulation study comparing our initialization to boundary estimates obtained from standard segmentation algorithms. The method is demonstrated on artificial image datasets from computer vision, as well as real-world applications to skin lesion and neural cellular images, for which multiple topological features can be identified., Comment: 38 pages with appendices, 15 figures

In this paper we introduce a novel model for Gaussian process (GP) regression in the fully Bayesian setting. Motivated by the ideas of sparsification, localization and Bayesian additive modeling, our model is built around a recursive partitioning (RP) scheme. Within each RP partition, a sparse GP (SGP) regression model is fitted. A Bayesian additive framework then combines multiple layers of partitioned SGPs, capturing both global trends and local refinements with efficient computations. The model addresses both the problem of efficiency in fitting a full Gaussian process regression model and the problem of prediction performance associated with a single SGP. Our approach mitigates the issue of pseudo-input selection and avoids the need for complex inter-block correlations in existing methods. The crucial trade-off becomes choosing between many simpler local model components or fewer complex global model components, which the practitioner can sensibly tune. Implementation is via a Metropolis-Hasting Markov chain Monte-Carlo algorithm with Bayesian back-fitting. We compare our model against popular alternatives on simulated and real datasets, and find the performance is competitive, while the fully Bayesian procedure enables the quantification of model uncertainties.