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Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data 期刊论文
JOURNAL OF COMPUTATIONAL BIOLOGY, 2022, 页码: 14
作者:  Shan, Xu;  Chen, Jinyu;  Dong, Kangning;  Zhou, Wei;  Zhang, Shihua
收藏  |  浏览/下载：83/0  |  提交时间：2023/02/07
data integration  single-cell transcriptomics  spatial modular patterns  spatial transcriptomics  
VP-Detector: A 3D multi-scale dense convolutional neural network for macromolecule localization and classification in cryo-electron tomograms 期刊论文
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, 2022, 卷号: 221, 页码: 14
作者:  Hao, Yu;  Wan, Xiaohua;  Yan, Rui;  Liu, Zhiyong;  Li, Jintao;  Zhang, Shihua;  Cui, Xuefeng;  Zhang, Fa
收藏  |  浏览/下载：121/0  |  提交时间：2023/02/07
Cryo-ET  Sub-tomogram averaging  Particle localization  Particle classification  Convolutional neural networks  
Adversarial Information Bottleneck 期刊论文
IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS, 2022, 页码: 10
作者:  Zhai, Penglong;  Zhang, Shihua
收藏  |  浏览/下载：57/0  |  提交时间：2023/02/07
Robustness  Optimization  Mutual information  Deep learning  Perturbation methods  Training  Task analysis  Adversarial robustness  deep learning  hyperparameter selection  information bottleneck (IB)  
Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data 期刊论文
BRIEFINGS IN BIOINFORMATICS, 2021, 卷号: 22, 期号: 3, 页码: 15
作者:  Dong, Kangning;  Zhang, Shihua
收藏  |  浏览/下载：117/0  |  提交时间：2022/04/02
cis-regulatory interaction networks  single-cell ATAC-seq  Gaussian graphical LASSO  
Towards understanding residual and dilated dense neural networks via convolutional sparse coding 期刊论文
NATIONAL SCIENCE REVIEW, 2021, 卷号: 8, 期号: 3, 页码: 13
作者:  Zhang, Zhiyang;  Zhang, Shihua
收藏  |  浏览/下载：153/0  |  提交时间：2021/10/26
convolutional neural network  convolutional sparse coding  residual neural network  mixed-scale dense neural network  dilated convolution  dense connection  
A Novel Sparse Graph-Regularized Singular Value Decomposition Model and Its Application to Genomic Data Analysis 期刊论文
IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS, 2021, 页码: 15
作者:  Min, Wenwen;  Wan, Xiang;  Chang, Tsung-Hui;  Zhang, Shihua
收藏  |  浏览/下载：142/0  |  提交时间：2022/04/02
Gene expression  Biology  Biological system modeling  Principal component analysis  Mathematical model  Data models  Big Data  Absolute-valued graph regularization  graph regularization  sparse learning  structured sparse singular value decomposition (SVD)  
An Integrative Framework for Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2021, 卷号: 18, 期号: 1, 页码: 355-364
作者:  Jing, Fang;  Zhang, Shao-Wu;  Cao, Zhen;  Zhang, Shihua
收藏  |  浏览/下载：180/0  |  提交时间：2021/04/26
Bioinformatics  machine learning  transcription factors binding sites  convolutional neural networks  DNA accessibility  histone modification  
Probe Efficient Feature Representation of Gapped K-mer Frequency Vectors from Sequences Using Deep Neural Networks 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2020, 卷号: 17, 期号: 2, 页码: 657-667
作者:  Cao, Zhen;  Zhang, Shihua
收藏  |  浏览/下载：200/0  |  提交时间：2020/05/24
DNA  Bioinformatics  Kernel  Feature extraction  Support vector machines  Genomics  Task analysis  Bioinformatics  machine learning  gapped k-mer  deep neural network  transcription factor binding site prediction  
Brief Survey of Biological Network Alignment and a Variant with Incorporation of Functional Annotations 期刊论文
CURRENT BIOINFORMATICS, 2019, 卷号: 14, 期号: 1, 页码: 4-10
作者:  Jing, Fang;  Zhang, Shao-Wu;  Zhang, Shihua
收藏  |  浏览/下载：184/0  |  提交时间：2019/04/02
Biological network  network alignment  gene ontology  alignment graph  optimization  
Network-Regularized Sparse Logistic Regression Models for Clinical Risk Prediction and Biomarker Discovery 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2018, 卷号: 15, 期号: 3, 页码: 944-953
作者:  Min, Wenwen;  Liu, Juan;  Zhang, Shihua
收藏  |  浏览/下载：254/0  |  提交时间：2018/07/30
Sparse logistic regression  network-regularized penalty  survival risk prediction  feature selection