Knowledge-guided statistical learning methods for analysis of high-dimensional-omics data in precision oncology

Y Zhao, C Chang, Q Long - JCO Precision Oncology, 2019 - ascopubs.org
High-dimensional-omics data such as genomic, transcriptomic, and metabolomic data offer
great promise in advancing precision medicine. In particular, such data have enabled the …

[PDF][PDF] From controlled to undisciplined data: Estimating causal effects in the era of data science using a potential outcome framework

F Dominici, FJB Stoffi, F Mealli - 2021 - assets.pubpub.org
This article discusses the fundamental principles of causal inference–the area of statistics
that estimates the effect of specific occurrences, treatments, interventions, and exposures on …

Integrative analysis of multi-omics and imaging data with incorporation of biological information via structural Bayesian factor analysis

J Bao, C Chang, Q Zhang, AJ Saykin… - Briefings in …, 2023 - academic.oup.com
Motivation With the rapid development of modern technologies, massive data are available
for the systematic study of Alzheimer's disease (AD). Though many existing AD studies …

Integrative Bayesian analysis of brain functional networks incorporating anatomical knowledge

IA Higgins, S Kundu, Y Guo - Neuroimage, 2018 - Elsevier
Recently, there has been increased interest in fusing multimodal imaging to better
understand brain organization by integrating information on both brain structure and …

[HTML][HTML] Single-cell biclustering for cell-specific transcriptomic perturbation detection in AD progression

Y Gong, J Xu, M Wu, R Gao, J Sun, Z Yu, Y Zhang - Cell Reports Methods, 2024 - cell.com
The pathogenesis of Alzheimer disease (AD) involves complex gene regulatory changes
across different cell types. To help decipher this complexity, we introduce single-cell …

Incorporating graph information in Bayesian factor analysis with robust and adaptive shrinkage priors

Q Zhang, C Chang, L Shen, Q Long - Biometrics, 2024 - academic.oup.com
There has been an increasing interest in decomposing high-dimensional multi-omics data
into a product of low-rank and sparse matrices for the purpose of dimension reduction and …

Accounting for network noise in graph-guided Bayesian modeling of structured high-dimensional data

W Li, C Chang, S Kundu, Q Long - Biometrics, 2024 - academic.oup.com
There is a growing body of literature on knowledge-guided statistical learning methods for
analysis of structured high-dimensional data (such as genomic and transcriptomic data) that …

[HTML][HTML] Bayesian network marker selection via the thresholded graph Laplacian Gaussian prior

Q Cai, J Kang, T Yu - Bayesian analysis, 2020 - ncbi.nlm.nih.gov
Selecting informative nodes over large-scale networks becomes increasingly important in
many research areas. Most existing methods focus on the local network structure and incur …

[HTML][HTML] Integrative Bayesian tensor regression for imaging genetics applications

Y Liu, N Chakraborty, ZS Qin, S Kundu… - Frontiers in …, 2023 - frontiersin.org
Identifying biomarkers for Alzheimer's disease with a goal of early detection is a fundamental
problem in clinical research. Both medical imaging and genetics have contributed …

Iterative supervised principal components

J Piironen, A Vehtari - International Conference on Artificial …, 2018 - proceedings.mlr.press
In high-dimensional prediction problems, where the number of features may greatly exceed
the number of training instances, fully Bayesian approach with a sparsifying prior is known to …