Author name cluster

Didong Li

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

11 papers

2 author rows

JMLR Journal 2025 Journal Article

Bayesian Multi-Group Gaussian Process Models for Heterogeneous Group-Structured Data

Didong Li
Andrew Jones
Sudipto Banerjee
Barbara E. Engelhardt

Gaussian processes are pervasive in functional data analysis, machine learning, and spatial statistics for modeling complex dependencies. Scientific data are often heterogeneous in their inputs and contain multiple known discrete groups of samples; thus, it is desirable to leverage the similarity among groups while accounting for heterogeneity across groups. We propose multi-group Gaussian processes (MGGPs) defined over $\mathbb{R}^p\times \mathscr{C}$, where $\mathscr{C}$ is a finite set representing the group label, by developing general classes of valid (positive definite) covariance functions on such domains. MGGPs are able to accurately recover relationships between the groups and efficiently share strength across samples from all groups during inference, while capturing distinct group-specific behaviors in the conditional posterior distributions. We demonstrate inference in MGGPs through simulation experiments, and we apply our proposed MGGP regression framework to gene expression data to illustrate the behavior and enhanced inferential capabilities of multi-group Gaussian processes by jointly modeling continuous and categorical variables. [abs] [ pdf ][ bib ] [ code ] &copy JMLR 2025. ( edit, beta )

PDF Details

AAAI Conference 2025 Conference Paper

Contrastive Functional Principal Component Analysis

Eric Zhang
Didong Li

As functional data assumes a central role in contemporary data analysis, the search for meaningful dimension reduction becomes critical due to its inherent infinite-dimensional structure. Traditional methods, such as Functional Principal Component Analysis (FPCA), adeptly explore the overarching structures within the functional data. However, these methods may not sufficiently identify low-dimensional representations that are specific or enriched in a foreground dataset (case or treatment group) relative to a background dataset (control group). This limitation becomes critical in scenarios where the foreground dataset, such as a specific treatment group in biomedical applications, contains unique patterns or trends that are not as pronounced in the background dataset. Addressing this gap, we propose Contrastive Functional Principal Component Analysis (CFPCA), a method designed to spotlight low-dimensional structures unique to or enriched in the foreground dataset relative to the background counterpart. We supplement our method with theoretical guarantees on CFPCA estimates supported by multiple simulations. Through a series of applications, CFPCA successfully identifies these foreground-specific structures, thereby revealing distinct patterns and trends that traditional FPCA overlooks.

PDF Details DOI

JMLR Journal 2025 Journal Article

Deep Generative Models: Complexity, Dimensionality, and Approximation

Kevin Wang
Hongqian Niu
Yixin Wang
Didong Li

Generative networks have shown remarkable success in learning complex data distributions, particularly in generating high-dimensional data from lower-dimensional inputs. While this capability is well-documented empirically, its theoretical underpinning remains unclear. One common theoretical explanation appeals to the widely accepted manifold hypothesis, which suggests that many real-world datasets, such as images and signals, often possess intrinsic low-dimensional geometric structures. Under this manifold hypothesis, it is widely believed that to approximate a distribution on a $d$-dimensional Riemannian manifold, the latent dimension needs to be at least $d$ or $d+1$. In this work, we show that this requirement on the latent dimension is not necessary by demonstrating that generative networks can approximate distributions on $d$-dimensional Riemannian manifolds from inputs of any arbitrary dimension, even lower than $d$, taking inspiration from the concept of space-filling curves. This approach, in turn, leads to a super-exponential complexity bound of the deep neural networks through expanded neurons. Our findings thus challenge the conventional belief on the relationship between input dimensionality and the ability of generative networks to model data distributions. This novel insight not only corroborates the practical effectiveness of generative networks in handling complex data structures, but also underscores a critical trade-off between approximation error, dimensionality, and model complexity. [abs] [ pdf ][ bib ] [ code ] &copy JMLR 2025. ( edit, beta )

PDF Details

ICLR Conference 2025 Conference Paper

Identifiability for Gaussian Processes with Holomorphic Kernels

Ameer Qaqish
Didong Li

Gaussian processes (GPs) are widely recognized for their robustness and flexibility across various domains, including machine learning, time series, spatial statistics, and biomedicine. In addition to their common usage in regression tasks, GP kernel parameters are frequently interpreted in various applications. For example, in spatial transcriptomics, estimated kernel parameters are used to identify spatial variable genes, which exhibit significant expression patterns across different tissue locations. However, before these parameters can be meaningfully interpreted, it is essential to establish their identifiability. Existing studies of GP parameter identifiability have focused primarily on Mat\'ern-type kernels, as their spectral densities allow for more established mathematical tools. In many real-world applications, particuarly in time series analysis, other kernels such as the squared exponential, periodic, and rational quadratic kernels, as well as their combinations, are also widely used. These kernels share the property of being holomorphic around zero, and their parameter identifiability remains underexplored. In this paper, we bridge this gap by developing a novel theoretical framework for determining kernel parameter identifiability for kernels holomorphic near zero. Our findings enable practitioners to determine which parameters are identifiable in both existing and newly constructed kernels, supporting application-specific interpretation of the identifiable parameters, and highlighting non-identifiable parameters that require careful interpretation.

Details

TMLR Journal 2025 Journal Article

Lower Ricci Curvature for Efficient Community Detection

Yun Jin Park
Didong Li

This study introduces the Lower Ricci Curvature (LRC), a novel, scalable, and scale-free discrete curvature designed to enhance community detection in networks. Addressing the computational challenges posed by existing curvature-based methods, LRC offers a streamlined approach with linear computational complexity, which makes it well suited for large-scale network analysis. We further develop an LRC-based preprocessing method that effectively augments popular community detection algorithms. Through applications on multiple real-world datasets, including the NCAA football league network, the DBLP collaboration network, the Amazon product co-purchasing network, and the YouTube social network, we demonstrate the efficacy of our method in significantly improving the performance of various community detection algorithms.

PDF Details

NeurIPS Conference 2024 Conference Paper

Contrastive dimension reduction: when and how?

Sam Hawke
Yueen Ma
Didong Li

Dimension reduction (DR) is an important and widely studied technique in exploratory data analysis. However, traditional DR methods are not applicable to datasets with with a contrastive structure, where data are split into a foreground group of interest (case or treatment group), and a background group (control group). This type of data, common in biomedical studies, necessitates contrastive dimension reduction (CDR) methods to effectively capture information unique to or enriched in the foreground group relative to the background group. Despite the development of various CDR methods, two critical questions remain underexplored: when should these methods be applied, and how can the information unique to the foreground group be quantified? In this work, we address these gaps by proposing a hypothesis test to determine the existence of contrastive information, and introducing a contrastive dimension estimator (CDE) to quantify the unique components in the foreground group. We provide theoretical support for our methods and validate their effectiveness through extensive simulated, semi-simulated, and real experiments involving images, gene expressions, protein expressions, and medical sensors, demonstrating their ability to identify the unique information in the foreground group.

PDF Details DOI

TMLR Journal 2024 Journal Article

KD-BIRL: Kernel Density Bayesian Inverse Reinforcement Learning

Aishwarya Mandyam
Didong Li
Andrew Jones
Diana Cai
Barbara E Engelhardt

Inverse reinforcement learning (IRL) methods infer an agent's reward function using demonstrations of expert behavior. A Bayesian IRL approach models a distribution over candidate reward functions, capturing a degree of uncertainty in the inferred reward function. This is critical in some applications, such as those involving clinical data. Typically, Bayesian IRL algorithms require large demonstration datasets to ensure posterior concentration, which may not be available in practice. In this work, we incorporate existing domain-specific data to achieve better posterior concentration rates. We study a common setting in clinical and biological applications where we have access to expert demonstrations and known reward functions for a set of training tasks. Our aim is to learn the reward function of a new test task given limited expert demonstrations. Existing Bayesian IRL methods impose restrictions on the form of input data, thus limiting the incorporation of training task data. To better leverage information from training tasks, we introduce kernel density Bayesian inverse reinforcement learning (KD-BIRL). Our approach employs a conditional kernel density estimator, which uses the known reward functions of the training tasks to improve the likelihood estimation across a range of reward functions and demonstration samples. Our empirical results highlight KD-BIRL's faster concentration rate in comparison to baselines, particularly in low test task expert demonstration data regimes. Additionally, we are the first to provide theoretical guarantees of posterior concentration for a Bayesian IRL algorithm. Taken together, this work introduces a principled and theoretically grounded framework that enables Bayesian IRL to be applied across a variety of domains, especially those with limited expert demonstration datasets.

PDF Details

JMLR Journal 2024 Journal Article

Spherical Rotation Dimension Reduction with Geometric Loss Functions

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. [abs] [ pdf ][ bib ] &copy JMLR 2024. ( edit, beta )

PDF Details

NeurIPS Conference 2024 Conference Paper

STimage-1K4M: A histopathology image-gene expression dataset for spatial transcriptomics

Jiawen Chen
Muqing Zhou
Wenrong Wu
Jinwei Zhang
Yun Li
Didong Li

Recent advances in multi-modal algorithms have driven and been driven by the increasing availability of large image-text datasets, leading to significant strides in various fields, including computational pathology. However, in most existing medical image-text datasets, the text typically provides high-level summaries that may not sufficiently describe sub-tile regions within a large pathology image. For example, an image might cover an extensive tissue area containing cancerous and healthy regions, but the accompanying text might only specify that this image is a cancer slide, lacking the nuanced details needed for in-depth analysis. In this study, we introduce STimage-1K4M, a novel dataset designed to bridge this gap by providing genomic features for sub-tile images. STimage-1K4M contains 1, 149 images derived from spatial transcriptomics data, which captures gene expression information at the level of individual spatial spots within a pathology image. Specifically, each image in the dataset is broken down into smaller sub-image tiles, with each tile paired with $15, 000-30, 000$ dimensional gene expressions. With $4, 293, 195$ pairs of sub-tile images and gene expressions, STimage-1K4M offers unprecedented granularity, paving the way for a wide range of advanced research in multi-modal data analysis an innovative applications in computational pathology, and beyond.

PDF Details DOI

JMLR Journal 2023 Journal Article

Inference for Gaussian Processes with Matern Covariogram on Compact Riemannian Manifolds

Didong Li
Wenpin Tang
Sudipto Banerjee

Gaussian processes are widely employed as versatile modelling and predictive tools in spatial statistics, functional data analysis, computer modelling and diverse applications of machine learning. They have been widely studied over Euclidean spaces, where they are specified using covariance functions or covariograms for modelling complex dependencies. There is a growing literature on Gaussian processes over Riemannian manifolds in order to develop richer and more flexible inferential frameworks for non-Euclidean data. While numerical approximations through graph representations have been well studied for the Matern covariogram and heat kernel, the behaviour of asymptotic inference on the parameters of the covariogram has received relatively scant attention. We focus on asymptotic behaviour for Gaussian processes constructed over compact Riemannian manifolds. Building upon a recently introduced Matern covariogram on a compact Riemannian manifold, we employ formal notions and conditions for the equivalence of two Matern Gaussian random measures on compact manifolds to derive the parameter that is identifiable, also known as the microergodic parameter, and formally establish the consistency of the maximum likelihood estimate and the asymptotic optimality of the best linear unbiased predictor. The circle is studied as a specific example of compact Riemannian manifolds with numerical experiments to illustrate and corroborate the theory. [abs] [ pdf ][ bib ] &copy JMLR 2023. ( edit, beta )

PDF Details

NeurIPS Conference 2023 Conference Paper

On the Identifiability and Interpretability of Gaussian Process Models

Jiawen Chen
Wancen Mu
Yun Li
Didong Li

In this paper, we critically examine the prevalent practice of using additive mixtures of Mat\'ern kernels in single-output Gaussian process (GP) models and explore the properties of multiplicative mixtures of Mat\'ern kernels for multi-output GP models. For the single-output case, we derive a series of theoretical results showing that the smoothness of a mixture of Mat\'ern kernels is determined by the least smooth component and that a GP with such a kernel is effectively equivalent to the least smooth kernel component. Furthermore, we demonstrate that none of the mixing weights or parameters within individual kernel components are identifiable. We then turn our attention to multi-output GP models and analyze the identifiability of the covariance matrix $A$ in the multiplicative kernel $K(x, y) = AK_0(x, y)$, where $K_0$ is a standard single output kernel such as Mat\'ern. We show that $A$ is identifiable up to a multiplicative constant, suggesting that multiplicative mixtures are well suited for multi-output tasks. Our findings are supported by extensive simulations and real applications for both single- and multi-output settings. This work provides insight into kernel selection and interpretation for GP models, emphasizing the importance of choosing appropriate kernel structures for different tasks.

PDF Details