Shan He

78 papers A* 1A 2B 7C 3Journal 54Unranked 11
YearRankTypeTitle / Venue / Authors
2026 J jnl
Knowledge-guided hyper-heuristic evolutionary algorithm for large-scale Boolean network inference.
Expert Syst. Appl.
Xiang Liu, Yan Wang, Xiayu Jiang, Zhicheng Ji, Shan He
2026 J jnl
Prodrug-ML: prodrug-likeness prediction via machine learning on sampled negative decoys.
J. Comput. Aided Mol. Des.
Sadettin Y. Ugurlu, Shan He
2025 J jnl
A Survey on Evolutionary Computation-Based Drug Discovery.
IEEE Trans. Evol. Comput.
Qiyuan Yu, Qiuzhen Lin, Junkai Ji, Wei Zhou, Shan He, Zexuan Zhu, Kay Chen Tan
2025 J jnl
MDTL-ACP: Anticancer Peptides Prediction Based on Multi-Domain Transfer Learning.
IEEE J. Biomed. Health Informatics
Junhang Cao, Wei Zhou, Qiyuan Yu, Junkai Ji, Jun Zhang, Shan He, Zexuan Zhu
2025 J jnl
TG-CDDPM: text-guided antimicrobial peptides generation based on conditional denoising diffusion probabilistic model.
Briefings Bioinform.
Junhang Cao, Jun Zhang, Qiyuan Yu, Junkai Ji, Jianqiang Li, Shan He, Zexuan Zhu
2024 J jnl
Cobdock: an accurate and practical machine learning-based consensus blind docking method.
J. Cheminformatics
Sadettin Y. Ugurlu, David W. McDonald, Huangshu Lei, Alan M. Jones, Shu Li, Henry H. Y. Tong, Mark S. Butler, Shan He
2024 J jnl
Dockformer: A transformer-based molecular docking paradigm for large-scale virtual screening.
CoRR
Zhangfan Yang, Junkai Ji, Shan He, Jianqiang Li, Tiantian He, Ruibin Bai, Zexuan Zhu, Yew Soon Ong
2024 J jnl
MEF-AlloSite: an accurate and robust Multimodel Ensemble Feature selection for the Allosteric Site identification model.
J. Cheminformatics
Sadettin Y. Ugurlu, David W. McDonald, Shan He
2024 J jnl
MIFuGP: Boolean network inference from multivariate time series using fuzzy genetic programming.
Inf. Sci.
Xiang Liu, Yan Wang, Shan Liu, Zhicheng Ji, Shan He
2023 J jnl
Improving therapeutic synergy score predictions with adverse effects using multi-task heterogeneous network learning.
Briefings Bioinform.
Yang Yue, Yongxuan Liu, Luoying Hao, Huangshu Lei, Shan He
2023 J jnl
MIX-TPI: a flexible prediction framework for TCR-pMHC interactions based on multimodal representations.
Bioinform.
Minghao Yang, Zhi-An Huang, Wei Zhou, Junkai Ji, Jun Zhang, Shan He, Zexuan Zhu
2023 J jnl
MpbPPI: a multi-task pre-training-based equivariant approach for the prediction of the effect of amino acid mutations on protein-protein interactions.
Briefings Bioinform.
Yang Yue, Shu Li, Lingling Wang, Huanxiang Liu, Henry H. Y. Tong, Shan He
2023 J jnl
Multi-Domain Active Learning: Literature Review and Comparative Study.
IEEE Trans. Emerg. Top. Comput. Intell.
Rui He, Shengcai Liu, Shan He, Ke Tang
2023 J jnl
Multi-Domain Learning From Insufficient Annotations.
CoRR
Rui He, Shengcai Liu, Jiahao Wu, Shan He, Ke Tang
2023 A conf
Multi-Domain Learning from Insufficient Annotations.
ECAI
Rui He, Shengcai Liu, Jiahao Wu, Shan He, Ke Tang
2023 J jnl
Network Biomarker Detection From Gene Co-Expression Network Using Gaussian Mixture Model Clustering.
IEEE ACM Trans. Comput. Biol. Bioinform.
Han Zhang, Zexuan Zhu, Hui Li, Shan He
2023 A conf
Perturbation-Based Two-Stage Multi-Domain Active Learning.
CIKM
Rui He, Zeyu Dai, Shan He, Ke Tang
2023 J jnl
Perturbation-Based Two-Stage Multi-Domain Active Learning.
CoRR
Rui He, Zeyu Dai, Shan He, Ke Tang
2022 J jnl
CURC: a CUDA-based reference-free read compressor.
Bioinform.
Shaohui Xie, Xiaotian He, Shan He, Zexuan Zhu
2022 J jnl
Data-Driven Boolean Network Inference Using a Genetic Algorithm With Marker-Based Encoding.
IEEE ACM Trans. Comput. Biol. Bioinform.
Xiang Liu, Ning Shi, Yan Wang, Zhicheng Ji, Shan He
2022 A* conf
GloDyNE: Global Topology Preserving Dynamic Network Embedding (Extended Abstract).
ICDE
Chengbin Hou, Han Zhang, Shan He, Ke Tang
2022 J jnl
GloDyNE: Global Topology Preserving Dynamic Network Embedding.
IEEE Trans. Knowl. Data Eng.
Chengbin Hou, Han Zhang, Shan He, Ke Tang
2022 J jnl
MPVNN: Mutated Pathway Visible Neural Network Architecture for Interpretable Prediction of Cancer-specific Survival Risk.
CoRR
Gourab Ghosh Roy, Nicholas Geard, Karin Verspoor, Shan He
2022 J jnl
MPVNN: Mutated Pathway Visible Neural Network architecture for interpretable prediction of cancer-specific survival risk.
Bioinform.
Gourab Ghosh Roy, Nicholas Geard, Karin Verspoor, Shan He
2021 — conf
A Network Embedding Based Approach to Drug-Target Interaction Prediction Using Additional Implicit Networks.
ICANN (1)
Han Zhang, Chengbin Hou, David W. McDonald, Shan He
2021 J jnl
Active Module Identification From Multilayer Weighted Gene Co-Expression Networks: A Continuous Optimization Approach.
IEEE ACM Trans. Comput. Biol. Bioinform.
Dong Li, Zhisong Pan, Guyu Hu, Graham Anderson, Shan He
2021 J jnl
DTI-HeNE: a novel method for drug-target interaction prediction based on heterogeneous network embedding.
BMC Bioinform.
Yang Yue, Shan He
2021 J jnl
GAPORE: Boolean network inference using a genetic algorithm with novel polynomial representation and encoding scheme.
Knowl. Based Syst.
Xiang Liu, Yan Wang, Ning Shi, Zhicheng Ji, Shan He
2021 J jnl
Multi-Domain Active Learning: A Comparative Study.
CoRR
Rui He, Shan He, Ke Tang
2021 J jnl
PoLoBag: Polynomial Lasso Bagging for signed gene regulatory network inference from expression data.
Bioinform.
Gourab Ghosh Roy, Nicholas Geard, Karin Verspoor, Shan He
2021 J jnl
Robust Dynamic Network Embedding via Ensembles.
CoRR
Chengbin Hou, Guoji Fu, Peng Yang, Shan He, Ke Tang
2020 J jnl
ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics.
Bioinform.
Ning Shi, Zexuan Zhu, Ke Tang, David Parker, Shan He
2020 J jnl
GloDyNE: Global Topology Preserving Dynamic Network Embedding.
CoRR
Chengbin Hou, Han Zhang, Shan He, Ke Tang
2020 — conf
HEAT: Hyperbolic Embedding of Attributed Networks.
IDEAL (1)
David W. McDonald, Shan He
2020 J jnl
MUMI: Multitask Module Identification for Biological Networks.
IEEE Trans. Evol. Comput.
Weiqi Chen, Zexuan Zhu, Shan He
2020 J jnl
RoSANE: Robust and scalable attributed network embedding for sparse networks.
Neurocomputing
Chengbin Hou, Shan He, Ke Tang
2019 J jnl
DynWalks: Global Topology and Recent Changes Awareness Dynamic Network Embedding.
CoRR
Chengbin Hou, Han Zhang, Ke Tang, Shan He
2019 J jnl
Ensemble multi-objective evolutionary algorithm for gene regulatory network reconstruction based on fuzzy cognitive maps.
CAAI Trans. Intell. Technol.
Jing Liu, Yaxiong Chi, Zongdong Liu, Shan He
2019 J jnl
HEAT: Hyperbolic Embedding of Attributed Networks.
CoRR
David W. McDonald, Shan He
2018 J jnl
Attributed Network Embedding for Incomplete Structure Information.
CoRR
Chengbin Hou, Shan He, Ke Tang
2018 J jnl
RepLong: de novo repeat identification using long read sequencing data.
Bioinform.
Rui Guo, Yan-Ran Li, Shan He, Le Ou-Yang, Yiwen Sun, Zexuan Zhu
2017 J jnl
Active module identification in intracellular networks using a memetic algorithm with a new binary decoding scheme.
BMC Genom.
Dong Li, Zhisong Pan, Guyu Hu, Zexuan Zhu, Shan He
2017 J jnl
Nadir point estimation for many-objective optimization problems based on emphasized critical regions.
Soft Comput.
Handing Wang, Shan He, Xin Yao
2017 J jnl
Prior knowledge guided active modules identification: an integrated multi-objective approach.
BMC Syst. Biol.
Weiqi Chen, Jing Liu, Shan He
2016 J jnl
A multi-objective memetic algorithm based on locality-sensitive hashing for one-to-many-to-one dynamic pickup-and-delivery problem.
Inf. Sci.
Zexuan Zhu, Jun Xiao, Shan He, Zhen Ji, Yiwen Sun
2016 J jnl
Cooperative Co-Evolutionary Module Identification With Application to Cancer Disease Module Discovery.
IEEE Trans. Evol. Comput.
Shan He, Guanbo Jia, Zexuan Zhu, Dan A. Tennant, Qiang Huang, Ke Tang, Jing Liu, Mirco Musolesi, John K. Heath, Xin Yao
2016 B conf
Metabolomics biomarker discovery using multimodal memetic algorithm and multivariate mutual information based feature selection.
CEC
Jiarui Zhou, Zhen Ji, Zexuan Zhu, Shan He
2015 J jnl
A Memetic Optimization Strategy Based on Dimension Reduction in Decision Space.
Evol. Comput.
Handing Wang, Licheng Jiao, Ronghua Shang, Shan He, Fang Liu
2015 — conf
A Multimodal Optimization and Surprise Based Consensus Community Detection Algorithm.
GECCO (Companion)
Guanbo Jia, Shan He, Zexuan Zhu, Jing Liu, Ke Tang
2015 J jnl
Global path planning of mobile robots using a memetic algorithm.
Int. J. Syst. Sci.
Zexuan Zhu, Fangxiao Wang, Shan He, Yiwen Sun
2015 J jnl
High-throughput DNA sequence data compression.
Briefings Bioinform.
Zexuan Zhu, Yongpeng Zhang, Zhen Ji, Shan He, Xiao Yang
2015 J jnl
Light-weight reference-based compression of FASTQ data.
BMC Bioinform.
Yongpeng Zhang, Linsen Li, Yanli Yang, Xiao Yang, Shan He, Zexuan Zhu
2015 J jnl
MUSCLE: automated multi-objective evolutionary optimization of targeted LC-MS/MS analysis.
Bioinform.
James Bradbury, Grégory Genta-Jouve, James William Allwood, Warwick B. Dunn, Royston Goodacre, Joshua D. Knowles, Shan He, Mark R. Viant
2015 J jnl
Robust twin boosting for feature selection from high-dimensional omics data with label noise.
Inf. Sci.
Shan He, Huanhuan Chen, Zexuan Zhu, Douglas G. Ward, Helen J. Cooper, Mark R. Viant, John K. Heath, Xin Yao
2015 J jnl
Three-dimensional Gabor feature extraction for hyperspectral imagery classification using a memetic framework.
Inf. Sci.
Zexuan Zhu, Sen Jia, Shan He, Yiwen Sun, Zhen Ji, Linlin Shen
2014 J jnl
An Evolutionary Multiobjective Approach to Sparse Reconstruction.
IEEE Trans. Evol. Comput.
Lin Li, Xin Yao, Rustam Stolkin, Maoguo Gong, Shan He
2014 J jnl
Compression of next-generation sequencing quality scores using memetic algorithm.
BMC Bioinform.
Jiarui Zhou, Zhen Ji, Zexuan Zhu, Shan He
2014 J jnl
HAMMER: automated operation of mass frontier to construct
Bioinform.
Jiarui Zhou, Ralf J. M. Weber, James William Allwood, Robert Mistrik, Zexuan Zhu, Zhen Ji, Siping Chen, Warwick B. Dunn, Shan He, Mark R. Viant
2014 B conf
Protein folding estimation using Paired-Bacteria Optimizer.
IEEE Congress on Evolutionary Computation
Mengshi Li, Tianyao Ji, Peter Wu, Shan He, Qing-Hua Wu
2013 — conf
A coevolving memetic algorithm for simultaneous partitional clustering and feature weighting.
Memetic Computing
Yiwen Sun, Zexuan Zhu, Shan He, Zhen Ji
2013 C conf
Minimal-redundancy-maximal-relevance feature selection using different relevance measures for omics data classification.
CIBCB
Junshan Yang, Zexuan Zhu, Shan He, Zhen Ji
2013 J jnl
Towards energy-efficient parallel analysis of neural signals.
Clust. Comput.
Dan Chen, Dongchuan Lu, Mingwei Tian, Shan He, Shuaiting Wang, Jian Tian, Chang Cai, Xiaoli Li
2012 B conf
A crown jewel defense strategy based particle swarm optimization.
IEEE Congress on Evolutionary Computation
Ling Lin, Zhen Ji, Shan He, Zexuan Zhu
2012 B conf
A memory binary particle swarm optimization.
IEEE Congress on Evolutionary Computation
Zhen Ji, Tao Tian, Shan He, Zexuan Zhu
2012 — conf
An Empirical Comparison of Several Recent Multi-objective Evolutionary Algorithms.
AIAI (1)
Thomas White, Shan He
2012 — conf
Community Detection Using Cooperative Co-evolutionary Differential Evolution.
PPSN (2)
Qiang Huang, Thomas White, Guanbo Jia, Mirco Musolesi, Nil Turan, Ke Tang, Shan He, John K. Heath, Xin Yao
2012 — conf
Community Detection in Social and Biological Networks Using Differential Evolution.
LION
Guanbo Jia, Zixing Cai, Mirco Musolesi, Yong Wang, Dan A. Tennant, Ralf J. M. Weber, John K. Heath, Shan He
2012 J jnl
MaConDa: a publicly accessible mass spectrometry contaminants database.
Bioinform.
Ralf J. M. Weber, Eva Li, Jonathan Bruty, Shan He, Mark R. Viant
2012 — conf
Memetic Three-Dimensional Gabor Feature Extraction for Hyperspectral Imagery Classification.
ICSI (1)
Zexuan Zhu, Linlin Shen, Yiwen Sun, Shan He, Zhen Ji
2012 B conf
Memetic clustering based on particle swarm optimizer and K-means.
IEEE Congress on Evolutionary Computation
Zexuan Zhu, Wenmin Liu, Shan He, Zhen Ji
2012 B conf
Survival analysis of gene expression data using PSO based radial basis function networks.
IEEE Congress on Evolutionary Computation
Wenmin Liu, Zhen Ji, Shan He, Zexuan Zhu
2009 J jnl
Group Search Optimizer: An Optimization Algorithm Inspired by Animal Searching Behavior.
IEEE Trans. Evol. Comput.
Shan He, Q. Henry Wu, Jon R. Saunders
2009 — conf
Profiling of Mass Spectrometry Data for Ovarian Cancer Detection Using Negative Correlation Learning.
ICANN (2)
Shan He, Huanhuan Chen, Xiaoli Li, Xin Yao
2008 C conf
Application of a group search optimization based Artificial Neural Network to machine condition monitoring.
ETFA
Shan He, Xiaoli Li
2008 — conf
Mixing bounded Laplace and Gaussian fingerprints.
ACSCC
Shan He, Darko Kirovski
2007 C conf
Profiling of High-Throughput Mass Spectrometry Data for Ovarian Cancer Detection.
IDEAL
Shan He, Xiaoli Li
2006 — conf
A Group Search Optimizer for Neural Network Training.
ICCSA (3)
Shan He, Q. H. Wu, Jon R. Saunders
2005 B conf
A particle swarm optimiser with passive congregation approach to thermal modelling for power transformers.
Congress on Evolutionary Computation
Wenhu Tang, Shan He, Emmanuel Prempain, Q. H. Wu, J. Fitch