Shi-Hua Zhang

According to our database1, Shi-Hua Zhang authored at least 94 papers between 2006 and 2024.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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Bibliography

2024
Tessellating the Latent Space for Non-Adversarial Generative Auto-Encoders.
IEEE Trans. Pattern Anal. Mach. Intell., February, 2024

Adversarial Information Bottleneck.
IEEE Trans. Neural Networks Learn. Syst., January, 2024

2023
A Python Package <i>itca</i> for Information-Theoretic Classification Accuracy: A Criterion That Guides Data-Driven Combination of Ambiguous Outcome Labels in Multiclass Classification.
J. Comput. Biol., November, 2023

Improving sparse graph attention for feature matching by informative keypoints exploration.
Comput. Vis. Image Underst., October, 2023

SmartGate is a spatial metabolomics tool for resolving tissue structures.
Briefings Bioinform., May, 2023

Learnable Graph-Regularization for Matrix Decomposition.
ACM Trans. Knowl. Discov. Data, April, 2023

Monte Carlo Neural Operator for Learning PDEs via Probabilistic Representation.
CoRR, 2023

U-Match: Two-view Correspondence Learning with Hierarchy-aware Local Context Aggregation.
Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence, 2023

ConvMatch: Rethinking Network Design for Two-View Correspondence Learning.
Proceedings of the Thirty-Seventh AAAI Conference on Artificial Intelligence, 2023

2022
A Novel Sparse Graph-Regularized Singular Value Decomposition Model and Its Application to Genomic Data Analysis.
IEEE Trans. Neural Networks Learn. Syst., 2022

Distributed Bayesian Matrix Decomposition for Big Data Mining and Clustering.
IEEE Trans. Knowl. Data Eng., 2022

Predicting Cancer Lymph-Node Metastasis From LncRNA Expression Profiles Using Local Linear Reconstruction Guided Distance Metric Learning.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Prediction of Transcription Factor Binding Sites With an Attention Augmented Convolutional Neural Network.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022.
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Nucleic Acids Res., 2022

Information-theoretic Classification Accuracy: A Criterion that Guides Data-driven Combination of Ambiguous Outcome Labels in Multi-class Classification.
J. Mach. Learn. Res., 2022

Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data.
J. Comput. Biol., 2022

VP-Detector: A 3D multi-scale dense convolutional neural network for macromolecule localization and classification in cryo-electron tomograms.
Comput. Methods Programs Biomed., 2022

GCN-GENE: A novel method for prediction of coronary heart disease-related genes.
Comput. Biol. Medicine, 2022

Disease category-specific annotation of variants using an ensemble learning framework.
Briefings Bioinform., 2022

Investigation of Potential FEC Schemes for 800G-ZR Forward Error Correction.
Proceedings of the Optical Fiber Communications Conference and Exhibition, 2022

Rethinking Influence Functions of Neural Networks in the Over-Parameterized Regime.
Proceedings of the Thirty-Sixth AAAI Conference on Artificial Intelligence, 2022

2021
Group-Sparse SVD Models via $L_1$L1- and $L_0$L0-norm Penalties and their Applications in Biological Data.
IEEE Trans. Knowl. Data Eng., 2021

An Integrative Framework for Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Approximate distance correlation for selecting highly interrelated genes across datasets.
PLoS Comput. Biol., 2021

TSCCA: A tensor sparse CCA method for detecting microRNA-gene patterns from multiple cancers.
PLoS Comput. Biol., 2021

Bayesian Joint Matrix Decomposition for Data Integration with Heterogeneous Noise.
IEEE Trans. Pattern Anal. Mach. Intell., 2021

Robust Bayesian matrix decomposition with mixture of Gaussian noise.
Neurocomputing, 2021

A Mathematical Principle of Deep Learning: Learn the Geodesic Curve in the Wasserstein Space.
CoRR, 2021

Leveraging partially overlapping channels for intra- and inter-coalition communication in cooperative UAV swarms.
Sci. China Inf. Sci., 2021

LncR2metasta: a manually curated database for experimentally supported lncRNAs during various cancer metastatic events.
Briefings Bioinform., 2021

Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data.
Briefings Bioinform., 2021

2020
A General Joint Matrix Factorization Framework for Data Integration and Its Systematic Algorithmic Exploration.
IEEE Trans. Fuzzy Syst., 2020

Comparison of Computational Methods for Imputing Single-Cell RNA-Sequencing Data.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020

Probe Efficient Feature Representation of Gapped K-mer Frequency Vectors from Sequences Using Deep Neural Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020

Tessellated Wasserstein Auto-Encoders.
CoRR, 2020

Distributed Bayesian Matrix Decomposition for Big Data Mining and Clustering.
CoRR, 2020

Prediction of enhancer-promoter interactions using the cross-cell type information and domain adversarial neural network.
BMC Bioinform., 2020

Sparse deep nonnegative matrix factorization.
Big Data Min. Anal., 2020

2019
Towards Understanding Residual and Dilated Dense Neural Networks via Convolutional Sparse Coding.
CoRR, 2019

Matrix Normal PCA for Interpretable Dimension Reduction and Graphical Noise Modeling.
CoRR, 2019

Simple tricks of convolutional neural network architectures improve DNA-protein binding prediction.
Bioinform., 2019

2018
The Discovery of Mutated Driver Pathways in Cancer: Models and Algorithms.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Network-Regularized Sparse Logistic Regression Models for Clinical Risk Prediction and Biomarker Discovery.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

BMTK: a toolkit for determining modules in biological bipartite networks.
Quant. Biol., 2018

Group-sparse SVD Models and Their Applications in Biological Data.
CoRR, 2018

Edge-group sparse PCA for network-guided high dimensional data analysis.
Bioinform., 2018

FPGA Investigation on Error-Floor Performance of a Concatenated Staircase and Hamming Code for 400G-ZR Forward Error Correction.
Proceedings of the Optical Fiber Communications Conference and Exposition, 2018

Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning.
Proceedings of the Bioinformatics Research and Applications - 14th International Symposium, 2018

2017
When to offload in two-tier smallcell networks: a Stackelberg game approach with pre-offloading-decision.
Wirel. Networks, 2017

Integrative cancer genomics: models, algorithms and analysis.
Frontiers Comput. Sci., 2017

Sparse Weighted Canonical Correlation Analysis.
CoRR, 2017

A Unified Joint Matrix Factorization Framework for Data Integration.
CoRR, 2017

TBC2health: a database of experimentally validated health-beneficial effects of tea bioactive compounds.
Briefings Bioinform., 2017

Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns.
Briefings Bioinform., 2017

2016
A Probabilistic Method for Estimating the Sharing of Identity by Descent for Populations with Migration.
IEEE ACM Trans. Comput. Biol. Bioinform., 2016

Quantitative function and algorithm for community detection in bipartite networks.
Inf. Sci., 2016

L0-norm Sparse Graph-regularized SVD for Biclustering.
CoRR, 2016

DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank.
Bioinform., 2016

Integrative analysis for identifying joint modular patterns of gene-expression and drug-response data.
Bioinform., 2016

An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data.
Algorithms Mol. Biol., 2016

2015
Guest Editorial for Special Section on ISB/TBC 2014.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

A neurodynamic framework for local community extraction in networks.
CoRR, 2015

Local community extraction in directed networks.
CoRR, 2015

IIIDB: a database for isoform-isoform interactions and isoform network modules.
BMC Genom., 2015

A novel two-stage method for identifying microRNA-gene regulatory modules in breast cancer.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

2014
Discovery of co-occurring driver pathways in cancer.
BMC Bioinform., 2014

2013
Promote Connections of Young Computational Biologists in China.
Genom. Proteom. Bioinform., 2013

Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data.
BMC Syst. Biol., 2013

Travelling waves and global attractivity of an SIRS disease model with spatial diffusion and temporary immunity.
Appl. Math. Comput., 2013

Modelling and analysis of a delayed predator-prey model with disease in the predator.
Appl. Math. Comput., 2013

2012
Efficient methods for identifying mutated driver pathways in cancer.
Bioinform., 2012

Identifying multi-layer gene regulatory modules from multi-dimensional genomic data.
Bioinform., 2012

Identifying mutated core modules in glioblastoma by integrative network analysis.
Proceedings of the 6th IEEE International Conference on Systems Biology, 2012

2011
Co-community Structure in Multiple Evolving Networks
CoRR, 2011

A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules.
Bioinform., 2011

A Querying Method with Feedback Mechanism for Protein Interaction Network.
Proceedings of the 2011 IEEE International Conference on Healthcare Informatics, 2011

2010
Determining modular organization of protein interaction networks by maximizing modularity density.
BMC Syst. Biol., 2010

Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test.
BMC Syst. Biol., 2010

Detecting disease associated modules and prioritizing active genes based on high throughput data.
BMC Bioinform., 2010

A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps.
Bioinform., 2010

2009
Fuzzy System Methods in Modeling Gene Expression and Analyzing Protein Networks.
Proceedings of the Fuzzy Systems in Bioinformatics and Computational Biology, 2009

Disease-Aging Network Reveals Significant Roles of Aging Genes in Connecting Genetic Diseases.
PLoS Comput. Biol., 2009

A hybrid graph-theoretic method for mining overlapping functional modules in large sparse protein interaction networks.
Int. J. Data Min. Bioinform., 2009

A Method for Querying Conserved Subnetwork in a Large-Scale Biomolecular Network.
Proceedings of the High Performance Computing and Applications, 2009

3D Rotation Invariant Features for the Characterization of Molecular Density Maps.
Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine, 2009

2008
Clustering complex networks and biological networks by nonnegative matrix factorization with various similarity measures.
Neurocomputing, 2008

Biomolecular network querying: a promising approach in systems biology.
BMC Syst. Biol., 2008

2007
Alignment of molecular networks by integer quadratic programming.
Bioinform., 2007

Identifying Modules in Complex Networks by a Graph-Theoretical Method and Its Application in Protein Interaction Networks.
Proceedings of the Advanced Intelligent Computing Theories and Applications. With Aspects of Artificial Intelligence, 2007

2006
Identification of functional modules in a PPI network by clique percolation clustering.
Comput. Biol. Chem., 2006

Prediction of Protein Complexes Based on Protein Interaction Data and Functional Annotation Data Using Kernel Methods.
Proceedings of the Computational Intelligence and Bioinformatics, 2006

A Graph-Theoretic Method for Mining Functional Modules in Large Sparse Protein Interaction Networks.
Proceedings of the Workshops Proceedings of the 6th IEEE International Conference on Data Mining (ICDM 2006), 2006

Alignment of Protein Interaction Networks by Integer Quadratic Programming.
Proceedings of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, 2006


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