Hengrui Luo

Younghyun Cho, James W. Demmel, Michał Dereziński et al.

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.

Hengrui Luo, Younghyun Cho, James W. Demmel et al.

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.

Marcus M. Noack, Hengrui Luo, Mark D. Risser

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 Matérn 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.

Hengrui Luo, Matthew T. Pratola

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.

Hengrui Luo, Jisu Kim, Alice Patania et al.

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.

Hengrui Luo, Jeremy E. Purvis, Didong Li

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.

Yin-Ting Liao, Hengrui Luo, Anna Ma

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.

James Demmel, Hengrui Luo, Ryan Schneider et al.

We analyze several versions of Jacobi's method for the symmetric eigenvalue problem. Our goal is to reduce the asymptotic cost of the algorithm as much as possible, as measured by the number of arithmetic operations performed and associated (serial or parallel) communication, i.e., the amount of data moved between slow and fast memory or between processors in a network. The first half of this effort, which considers the serial setting, is presented here; this paper contains rigorous complexity bounds for a variety of serial Jacobi algorithms, built on both classic $O(n^3)$ matrix multiplication and fast, Strassen-like $O(n^{ω_0})$ alternatives. In the classical case, we show that a blocked implementation of Jacobi's method attains the communication lower bound for $O(n^3)$ matrix multiplication (and is therefore expected to be communication optimal among $O(n^3)$ eigensolvers). In the fast setting, we demonstrate that a recursive version of blocked Jacobi can go further, reaching essentially optimal complexity in both measures. We also derive analogous complexity bounds for (one-sided) Jacobi SVD algorithms. A forthcoming sequel to this paper will extend our complexity analysis to the parallel case.

Hengrui Luo, Akira Horiguchi, Li Ma

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.

Hengrui Luo, Justin D. Strait

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.

Jason Han, Nicholas S. DiBrita, Younghyun Cho et al.

Amplitude embedding (AE) is essential in quantum machine learning (QML) for encoding classical data onto quantum circuits. However, conventional AE methods suffer from deep, variable-length circuits that introduce high output error due to extensive gate usage and variable error rates across samples, resulting in noise-driven inconsistencies that degrade model accuracy. We introduce EnQode, a fast AE technique based on symbolic representation that addresses these limitations by clustering dataset samples and solving for cluster mean states through a low-depth, machine-specific ansatz. Optimized to reduce physical gates and SWAP operations, EnQode ensures all samples face consistent, low noise levels by standardizing circuit depth and composition. With over 90% fidelity in data mapping, EnQode enables robust, high-performance QML on noisy intermediate-scale quantum (NISQ) devices. Our open-source solution provides a scalable and efficient alternative for integrating classical data with quantum models.

Haoming Shi, Eric C. Chi, Hengrui Luo

We study rank selection for low-rank tensor regression under random covariates design. Under a Gaussian random-design model and some mild conditions, we derive population expressions for the expected training-testing discrepancy (optimism) for both CP and Tucker decomposition. We further demonstrate that the optimism is minimized at the true tensor rank for both CP and Tucker regression. This yields a prediction-oriented rank-selection rule that aligns with cross-validation and extends naturally to tensor-model averaging. We also discuss conditions under which under- or over-ranked models may appear preferable, thereby clarifying the scope of the method. Finally, we showcase its practical utility on a real-world image regression task and extend its application to tensor-based compression of neural network, highlighting its potential for model selection in deep learning.

Hengrui Luo, Anna Ma, Ludovic Stephan et al.

We introduce Wedge Sampling, a new non-adaptive sampling scheme for low-rank tensor completion. We study recovery of an order-$k$ low-rank tensor of dimension $n \times \cdots \times n$ from a subset of its entries. Unlike the standard uniform entry model (i.e., i.i.d. samples from $[n]^k$), wedge sampling allocates observations to structured length-two patterns (wedges) in an associated bipartite sampling graph. By directly promoting these length-two connections, the sampling design strengthens the spectral signal that underlies efficient initialization, in regimes where uniform sampling is too sparse to generate enough informative correlations. Our main result shows that this change in sampling paradigm enables polynomial-time algorithms to achieve both weak and exact recovery with nearly linear sample complexity in $n$. The approach is also plug-and-play: wedge-sampling-based spectral initialization can be combined with existing refinement procedures (e.g., spectral or gradient-based methods) using only an additional $\tilde{O}(n)$ uniformly sampled entries, substantially improving over the $\tilde{O}(n^{k/2})$ sample complexity typically required under uniform entry sampling for efficient methods. Overall, our results suggest that the statistical-to-computational gap highlighted in Barak and Moitra (2022) is, to a large extent, a consequence of the uniform entry sampling model for tensor completion, and that alternative non-adaptive measurement designs that guarantee a strong initialization can overcome this barrier.

Vardaan Tekriwal, Mark D. Risser, Hengrui Luo et al.

Conditional density estimation is complicated by multimodality, heteroscedasticity, and strong non-Gaussianity. Gaussian processes (GPs) provide a principled nonparametric framework with calibrated uncertainty, but standard GP regression is limited by its unimodal Gaussian predictive form. We introduce the Generalized Gaussian Mixture Process (GGMP), a GP-based method for multimodal conditional density estimation in settings where each input may be associated with a complex output distribution rather than a single scalar response. GGMP combines local Gaussian mixture fitting, cross-input component alignment and per-component heteroscedastic GP training to produce a closed-form Gaussian mixture predictive density. The method is tractable, compatible with standard GP solvers and scalable methods, and avoids the exponentially large latent-assignment structure of naive multimodal GP formulations. Empirically, GGMPs improve distributional approximation on synthetic and real-world datasets with pronounced non-Gaussianity and multimodality.

Hengrui Luo, Xiaoye S. Li, Yang Liu et al.

Gaussian process (GP) regression is widely used for uncertainty quantification, yet the standard formulation assumes noise-free covariates. When inputs are measured with error, this errors-in-variables (EIV) setting can lead to optimistically narrow posterior intervals and biased decisions. We study GP regression under input measurement uncertainty by representing each noisy input as a probability measure and defining covariance through Wasserstein distances between these measures. Building on this perspective, we instantiate a deterministic projected Wasserstein ARD (PWA) kernel whose one-dimensional components admit closed-form expressions and whose product structure yields a scalable, positive-definite kernel on distributions. Unlike latent-input GP models, PWA-based GPs (\PWAGPs) handle input noise without introducing unobserved covariates or Monte Carlo projections, making uncertainty quantification more transparent and robust.

Marcus M. Noack, Mark D. Risser, Hengrui Luo et al.

Despite a large corpus of recent work on scaling up Gaussian processes, a stubborn trade-off between computational speed, prediction and uncertainty quantification accuracy, and customizability persists. This is because the vast majority of existing methodologies exploit various levels of approximations that lower accuracy and limit the flexibility of kernel and noise-model designs -- an unacceptable drawback at a time when expressive non-stationary kernels are on the rise in many fields. Here, we propose a methodology we term \emph{gp2Scale} that scales exact Gaussian processes to more than 10 million data points without relying on inducing points, kernel interpolation, or neighborhood-based approximations, and instead leveraging the existing capabilities of a GP: its kernel design. Highly flexible, compactly supported, and non-stationary kernels lead to the identification of naturally occurring sparse structure in the covariance matrix, which is then exploited for the calculations of the linear system solution and the log-determinant for training. We demonstrate our method's functionality on several real-world datasets and compare it with state-of-the-art approximation algorithms. Although we show superior approximation performance in many cases, the method's real power lies in its agnosticism toward arbitrary GP customizations -- core kernel design, noise, and mean functions -- and the type of input space, making it optimally suited for modern Gaussian process applications.

Yordan P. Raykov, Hengrui Luo, Justin D. Strait et al.

We propose causal effect estimators based on empirical Fréchet means and operator-valued kernels, tailored to functional data spaces. These methods address the challenges of high-dimensionality, sequential ordering, and model complexity while preserving robustness to treatment misspecification. Using structural assumptions, we obtain compact representations of potential outcomes, enabling scalable estimation of causal effects over time and across covariates. We provide both theoretical, regarding the consistency of functional causal effects, as well as empirical comparison of a range of proposed causal effect estimators. Applications to binary treatment settings with functional outcomes illustrate the framework's utility in biomedical monitoring, where outcomes exhibit complex temporal dynamics. Our estimators accommodate scenarios with registered covariates and outcomes, aligning them to the Fréchet means, as well as cases requiring higher-order representations to capture intricate covariate-outcome interactions. These advancements extend causal inference to dynamic and non-linear domains, offering new tools for understanding complex treatment effects in functional data settings.

Hengrui Luo, Yunzhang Zhu

We derived the closed-form asymptotic optimism of linear regression models under random designs, and generalizes it to kernel ridge regression. Using scaled asymptotic optimism as a generic predictive model complexity measure, we studied the fundamental different behaviors of linear regression model, tangent kernel (NTK) regression model and three-layer fully connected neural networks (NN). Our contribution is two-fold: we provided theoretical ground for using scaled optimism as a model predictive complexity measure; and we show empirically that NN with ReLUs behaves differently from kernel models under this measure. With resampling techniques, we can also compute the optimism for regression models with real data.

Mark D. Risser, Marcus M. Noack, Hengrui Luo et al.

The Gaussian process (GP) is a widely used probabilistic machine learning method with implicit uncertainty characterization for stochastic function approximation, stochastic modeling, and analyzing real-world measurements of nonlinear processes. Traditional implementations of GPs involve stationary kernels (also termed covariance functions) that limit their flexibility, and exact methods for inference that prevent application to data sets with more than about ten thousand points. Modern approaches to address stationarity assumptions generally fail to accommodate large data sets, while all attempts to address scalability focus on approximating the Gaussian likelihood, which can involve subjectivity and lead to inaccuracies. In this work, we explicitly derive an alternative kernel that can discover and encode both sparsity and nonstationarity. We embed the kernel within a fully Bayesian GP model and leverage high-performance computing resources to enable the analysis of massive data sets. We demonstrate the favorable performance of our novel kernel relative to existing exact and approximate GP methods across a variety of synthetic data examples. Furthermore, we conduct space-time prediction based on more than one million measurements of daily maximum temperature and verify that our results outperform state-of-the-art methods in the Earth sciences. More broadly, having access to exact GPs that use ultra-scalable, sparsity-discovering, nonstationary kernels allows GP methods to truly compete with a wide variety of machine learning methods.

Sam Hawke, Hengrui Luo, Didong Li

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.

Hengrui Luo, James W. Demmel, Younghyun Cho et al.

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.

Leland Wilkinson, Hengrui Luo

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.

Hengrui Luo, Alice Patania, Jisu Kim et al.

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.

Hengrui Luo, Justin Strait

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.