arXiv subjects

Jun Young Park

Publications and source records attributed to Jun Young Park.

8 recordsLinked to original sources

arXiv2026

Group-regularized matrix factorization for fast and reliable module discovery in pan-omics pan-cancer studies

In pan-omics pan-cancer studies, it is critical to identify latent sources of variation that are shared across particular subsets. This task often requires bidimensionally linked data matrices to be decomposed into a sum of block-sparse, low-rank modules. Existing approaches often rely on pre-specified module numbers, ranks, or post-hoc thresholding and can be sensitive to model specification when the underlying sharing structure is complex. To address these issues, we propose GL-BIDIFAC+, a group-regularized matrix factorization framework for discovering partially shared modules. It requires only an upper bound on the latent dimension and encourages module selection through group regularization with theoretically-motivated tuning parameter selection and local support recovery analysis, providing both scalability and principled guidance for module discovery. It also admits a probabilistic interpretation that enables model-based imputation of missing data. Simulation studies demonstrate accurate module recovery and favorable computational performance relative to existing approaches. We further apply GL-BIDIFAC+ to analyze the Cancer Genome Atlas data, where well-established molecular structure provides interpretable biological references. Our analysis distinguishes broad pan-cancer variation, cancer-specific subtype structure, and variation shared across cancers with related tissue origins or histologic features.

stat.AP↗

arXiv2026

The Second LoViF 2026 Challenge on Real-World All-in-One Image Restoration: Methods and Results

This paper presents a review of the second LoViF Challenge on Real-World All-in-One Image Restoration. The challenge aims to advance unified image restoration under diverse real-world degradation conditions, including blur, low-light, haze, rain, and snow. It provides a common benchmark for evaluating the restoration accuracy, robustness, and generalization capability of models across multiple degradation categories within a unified framework. The competition attracted 158 registered participants, and 20 teams were included in the final ranking after their submitted results were successfully reproduced and verified. This report provides a comprehensive analysis of the submitted solutions and corresponding results, highlighting recent advances in real-world all-in-one image restoration. The summarized methods and empirical findings reveal effective design strategies and establish an updated benchmark for future research in real-world low-level vision.

cs.CV↗

arXiv2026

Sparse covariate-driven factorization of high-dimensional brain connectivity with application to site effect correction

Large-scale neuroimaging studies often collect data from multiple scanners across different sites, where variations in scanners, scanning procedures, and other conditions across sites can introduce artificial site effects. These effects may bias brain connectivity measures, such as functional connectivity (FC), which quantify functional network organization derived from functional magnetic resonance imaging (fMRI). How to leverage high-dimensional network structures to effectively mitigate site effects has yet to be addressed. In this paper, we propose SLACC (Sparse LAtent Covariate-driven Connectome) factorization, a multivariate method that explicitly parameterizes covariate effects in latent subject scores corresponding to sparse rank-1 latent patterns derived from brain connectivity. The proposed method identifies localized site-driven variability within and across brain networks, enabling targeted correction. We develop a penalized Expectation-Maximization (EM) algorithm for parameter estimation, incorporating the Bayesian Information Criterion (BIC) to guide optimization. Extensive simulations validate SLACC's robustness in recovering the true parameters and underlying connectivity patterns. Applied to the Autism Brain Imaging Data Exchange (ABIDE) dataset, SLACC demonstrates its ability to reduce site effects.

stat.ME↗

arXiv2026

The Fourth Challenge on Image Super-Resolution ($\times$4) at NTIRE 2026: Benchmark Results and Method Overview

This paper presents the NTIRE 2026 image super-resolution ($\times$4) challenge, one of the associated competitions of the NTIRE 2026 Workshop at CVPR 2026. The challenge aims to reconstruct high-resolution (HR) images from low-resolution (LR) inputs generated through bicubic downsampling with a $\times$4 scaling factor. The objective is to develop effective super-resolution solutions and analyze recent advances in the field. To reflect the evolving objectives of image super-resolution, the challenge includes two tracks: (1) a restoration track, which emphasizes pixel-wise fidelity and ranks submissions based on PSNR; and (2) a perceptual track, which focuses on visual realism and evaluates results using a perceptual score. A total of 194 participants registered for the challenge, with 31 teams submitting valid entries. This report summarizes the challenge design, datasets, evaluation protocol, main results, and methods of participating teams. The challenge provides a unified benchmark and offers insights into current progress and future directions in image super-resolution.

cs.CV↗

arXiv2026

Boosting multi-view association testing via devariation

Understanding the interplay between high-dimensional data from different views is essential in biomedical research, particularly in fields such as genomics, neuroimaging and biobank-scale studies involving high-dimensional features. Existing statistical tests for the association between two random vectors often do not fully capture dependencies between views due to limitations in modeling within-view dependencies, particularly in high-dimensional data without clear dependency patterns, which can lead to a potential loss of statistical power. In this work, we propose a novel approach termed devariation which is considered a simple yet effective preprocessing method to address the limitations by adopting a penalized low-rank factor model to flexibly capture within-view dependencies. Theoretical analysis of asymptotic power shows that devariation increases statistical power, especially when within-view correlations impact signal-to-noise ratios, while maintaining robustness in scenarios without strong internal correlations. Simulation studies demonstrate devariation's superior performance over existing methods in various scenarios. We further validate devariation in multimodal neuroimaging data from the UK Biobank study, examining the associations between imaging-derived phenotypes (IDPs) from functional, structural, and diffusion magnetic resonance imaging (MRI).

stat.ME↗

arXiv2025

Rank-adaptive covariance testing with applications to genomics and neuroimaging

In biomedical studies, testing for differences in covariance offers scientific insights beyond mean differences, especially when differences are driven by complex joint behavior between features. However, when differences in joint behavior are weakly dispersed across many dimensions and arise from differences in low-rank structures within the data, as is often the case in genomics and neuroimaging, existing two-sample covariance testing methods may suffer from power loss. The Ky-Fan(k) norm, defined by the sum of the top Ky-Fan(k) singular values, is a simple and intuitive matrix norm able to capture signals caused by differences in low-rank structures between matrices, but its statistical properties in hypothesis testing have not been studied well. In this paper, we investigate the behavior of the Ky-Fan(k) norm in two-sample covariance testing. Ultimately, we propose a novel methodology, Rank-Adaptive Covariance Testing (RACT), which is able to leverage differences in low-rank structures found in the covariance matrices of two groups in order to maximize power. RACT uses permutation for statistical inference, ensuring an exact Type I error control. We validate RACT in simulation studies and evaluate its performance when testing for differences in gene expression networks between two types of lung cancer, as well as testing for covariance heterogeneity in diffusion tensor imaging (DTI) data taken on two different scanner types.

stat.ME↗

arXiv2022

Bidimensional linked matrix factorization for pan-omics pan-cancer analysis

Several modern applications require the integration of multiple large data matrices that have shared rows and/or columns. For example, cancer studies that integrate multiple omics platforms across multiple types of cancer, pan-omics pan-cancer analysis, have extended our knowledge of molecular heterogenity beyond what was observed in single tumor and single platform studies. However, these studies have been limited by available statistical methodology. We propose a flexible approach to the simultaneous factorization and decomposition of variation across such bidimensionally linked matrices, BIDIFAC+. This decomposes variation into a series of low-rank components that may be shared across any number of row sets (e.g., omics platforms) or column sets (e.g., cancer types). This builds on a growing literature for the factorization and decomposition of linked matrices, which has primarily focused on multiple matrices that are linked in one dimension (rows or columns) only. Our objective function extends nuclear norm penalization, is motivated by random matrix theory, gives an identifiable decomposition under relatively mild conditions, and can be shown to give the mode of a Bayesian posterior distribution. We apply BIDIFAC+ to pan-omics pan-cancer data from TCGA, identifying shared and specific modes of variability across 4 different omics platforms and 29 different cancer types.

stat.ML↗

arXiv2019

Integrative Factorization of Bidimensionally Linked Matrices

Advances in molecular "omics'" technologies have motivated new methodology for the integration of multiple sources of high-content biomedical data. However, most statistical methods for integrating multiple data matrices only consider data shared vertically (one cohort on multiple platforms) or horizontally (different cohorts on a single platform). This is limiting for data that take the form of bidimensionally linked matrices (e.g., multiple cohorts measured on multiple platforms), which are increasingly common in large-scale biomedical studies. In this paper, we propose BIDIFAC (Bidimensional Integrative Factorization) for integrative dimension reduction and signal approximation of bidimensionally linked data matrices. Our method factorizes the data into (i) globally shared, (ii) row-shared, (iii) column-shared, and (iv) single-matrix structural components, facilitating the investigation of shared and unique patterns of variability. For estimation we use a penalized objective function that extends the nuclear norm penalization for a single matrix. As an alternative to the complicated rank selection problem, we use results from random matrix theory to choose tuning parameters. We apply our method to integrate two genomics platforms (mRNA and miRNA expression) across two sample cohorts (tumor samples and normal tissue samples) using the breast cancer data from TCGA. We provide R code for fitting BIDIFAC, imputing missing values, and generating simulated data.

stat.ML↗