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Bayesian Joint Matrix Decomposition for Data Integration with Heterogeneous Noise 期刊论文
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 2021, 卷号: 43, 期号: 4, 页码: 1184-1196
作者:  Zhang, Chihao;  Zhang, Shihua
收藏  |  浏览/下载：183/0  |  提交时间：2021/04/26
Matrix decomposition  Bayes methods  Data integration  Inference algorithms  Data models  Data mining  Gaussian distribution  Bayesian methods  matrix decomposition  data integration  variational Bayesian inference  maximum a posterior  
Group-Sparse SVD Models via L-1- and L-0-norm Penalties and their Applications in Biological Data 期刊论文
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING, 2021, 卷号: 33, 期号: 2, 页码: 536-550
作者:  Min, Wenwen;  Liu, Juan;  Zhang, Shihua
收藏  |  浏览/下载：157/0  |  提交时间：2021/04/26
Sparse SVD  low-rank matrix decomposition  group-sparse penalty  overlapping group-sparse penalty  coordinate descent method  alternating direction method of multipliers (ADMM)  data mining  
A General Joint Matrix Factorization Framework for Data Integration and Its Systematic Algorithmic Exploration 期刊论文
IEEE TRANSACTIONS ON FUZZY SYSTEMS, 2020, 卷号: 28, 期号: 9, 页码: 1971-1983
作者:  Zhang, Lihua;  Zhang, Shihua
收藏  |  浏览/下载：146/0  |  提交时间：2021/01/14
Sparse matrices  Pattern recognition  Data integration  Prediction algorithms  Data models  Matrix decomposition  Signal processing algorithms  Bioinformatics  data integration  network-regularized constraint  nonnegative matrix factorization (NMF)  pattern recognition  
Circular Trajectory Reconstruction Uncovers Cell-Cycle Progression and Regulatory Dynamics from Single-Cell Hi-C Maps 期刊论文
ADVANCED SCIENCE, 2019, 页码: 13
作者:  Ye, Yusen;  Gao, Lin;  Zhang, Shihua
收藏  |  浏览/下载：272/0  |  提交时间：2020/01/10
cell cycle  chromosomal architectures  circular trajectory  dynamic structures  single-cell Hi-C maps  
Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization 期刊论文
NUCLEIC ACIDS RESEARCH, 2019, 卷号: 47, 期号: 13, 页码: 6606-6617
作者:  Zhang, Lihua;  Zhang, Shihua
收藏  |  浏览/下载：191/0  |  提交时间：2020/01/10
MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps 期刊论文
NUCLEIC ACIDS RESEARCH, 2019, 卷号: 47, 期号: 11, 页码: 11
作者:  Ye, Yusen;  Gao, Lin;  Zhang, Shihua
收藏  |  浏览/下载：159/0  |  提交时间：2020/01/10
Simple tricks of convolutional neural network architectures improve DNA-protein binding prediction 期刊论文
BIOINFORMATICS, 2019, 卷号: 35, 期号: 11, 页码: 1837-1843
作者:  Cao, Zhen;  Zhang, Shihua
收藏  |  浏览/下载：189/0  |  提交时间：2020/01/10
Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model 期刊论文
BMC GENOMICS, 2018, 卷号: 19, 页码: 13
作者:  Wang, Can;  Zhang, Shihua
收藏  |  浏览/下载：247/0  |  提交时间：2019/01/11
Epigenomics  Cell type-specific regulatory elements  Hidden Markov model  Histone modification  
Edge-group sparse PCA for network-guided high dimensional data analysis 期刊论文
BIOINFORMATICS, 2018, 卷号: 34, 期号: 20, 页码: 3479-3487
作者:  Min, Wenwen;  Liu, Juan;  Zhang, Shihua
收藏  |  浏览/下载：187/0  |  提交时间：2019/01/11
Matrix Integrative Analysis (MIA) of Multiple Genomic Data for Modular Patterns 期刊论文
FRONTIERS IN GENETICS, 2018, 卷号: 9, 页码: 12
作者:  Chen, Jinyu;  Zhang, Shihua
收藏  |  浏览/下载：176/0  |  提交时间：2018/07/30
bioinformatics  multi-dimensional genomics  matrix integrative analysis  data integration  module discovery  non-negative matrix factorization (NMF)  partial least squares (PLS)