Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees. - Yufeng Wu 001; Jiayin Wang 002 (ISBRA, 2010)

Identifying interacting SNPs with parallel fish-agent based logic regression. - Jiayin Wang 002; Jin Zhang 038; Yufeng Wu 001 (ICCABS, 2011)

Rate-adaptive admission control for bandwidth assurance in multirate wireless mesh networks. - Peng Zhao 001; Xinyu Yang 001; Chaoxin Hu; Jiayin Wang 002; Benyuan Liu; Jie Wang 002 (ICC, 2012)

BOR/AC: Bandwidth-aware opportunistic routing with admission control in wireless mesh networks. - Peng Zhao 001; Xinyu Yang 001; Jiayin Wang 002; Benyuan Liu; Jie Wang 002 (INFOCOM, 2012)

An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data. - Jin Zhang 038; Jiayin Wang 002; Yufeng Wu 001 (BMC Bioinform., 2012)

Admission control on multipath routing in 802.11-based wireless mesh networks. - Peng Zhao 001; Xinyu Yang 001; Jiayin Wang 002; Benyuan Liu; Jie Wang 002 (Ad Hoc Networks, 2013)

A probabilistic method for identifying rare variants underlying complex traits. - Jiayin Wang 002; Zhongmeng Zhao; Zhi Cao; Aiyuan Yang; Jin Zhang 038 (BMC Genom., 2013)

Chaotic image encryption based on circular substitution box and key stream buffer. - Xuanping Zhang; Zhongmeng Zhao; Jiayin Wang 002 (Signal Process. Image Commun., 2014)

An Artificial Fish Swarm Algorithm for Identifying Associations between Multiple Variants and Multiple Phenotypes. - Ruoyu Liu; Xin Lai 003; Xiao Xiao; Xuanping Zhang; Xiaoyan Zhu 003; Jiayin Wang 002 (BIBM, 2019)

GSDcreator: An Efficient and Comprehensive Simulator for Genarating NGS Data with Population Genetic Information. - Shenjie Wang; Jiayin Wang 002; Xiao Xiao; Xuanping Zhang; Xuwen Wang; Xiaoyan Zhu 003; Xin Lai 003 (BIBM, 2019)

FilterLAP: Filtering False-positive Mutation Calls via a Label Propagation Framework. - Xuwen Wang; Xiaoyan Zhu 003; Xiao Xiao; Shenjie Wang; Xuanping Zhang; Xin Lai 003; Jiayin Wang 002 (BIBM, 2019)

SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles. - Yong Zhang 036; Yongsheng Chen; Huixin Xu; Junbin Fang; Zijian Zhao; Weipeng Hu; Xiaoqin Yang; Jia Ye; Yun Cheng; Jiayin Wang 002; Weiqiang Sun; Jian Wang 065; et al. (BMC Bioinform., 2020)

A hybrid correcting method considering heterozygous variations by a comprehensive probabilistic model. - Jiaqi Liu; Jiayin Wang 002; Xiao Xiao; Xin Lai 003; Daocheng Dai; Xuanping Zhang; Xiaoyan Zhu 003; Zhongmeng Zhao; Juan Wang; Zhimin Li (BMC Genom., 2020)

SETE: Sequence-based Ensemble learning approach for TCR Epitope binding prediction. - Yao Tong; Jiayin Wang 002; Tian Zheng; Xuanping Zhang; Xiao Xiao; Xiaoyan Zhu 003; Xin Lai 003; Xiang Liu (Comput. Biol. Chem., 2020)

A machine learning framework for accurately recognizing circular RNAs for clinical decision-supporting. - Yidan Wang; Xuanping Zhang; Tao Wang; Jinchun Xing; Zhun Wu; Wei Li; Jiayin Wang 002 (BMC Medical Informatics Decis. Mak., 2020)

A prognostic index based on a fourteen long non-coding RNA signature to predict the recurrence-free survival for muscle-invasive bladder cancer patients. - Xiaolong Zhang; Meng Zhang; Xuanping Zhang; Xiaoyan Zhu 003; Jiayin Wang 002 (BMC Medical Informatics Decis. Mak., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

Accurately estimating the length distributions of genomic micro-satellites by tumor purity deconvolution. - Yixuan Wang; Xuanping Zhang; Xiao Xiao; Fei-Ran Zhang; Xinxing Yan; Xuan Feng; Zhongmeng Zhao; Yanfang Guan; Jiayin Wang 002 (BMC Bioinform., 2020)

A new multiple instance algorithm using structural information. - Xiaoyan Zhu 003; Ting Wang; Jiayin Wang 002; Ying Xu; Yuqian Liu (ICDM, 2021)

A risk-adjusted approach to monitoring surgery for survival outcomes based on a weighted score test. - Xin Lai 003; Xiao Li 034; Liu Liu 002; Fugee Tsung; Paul B. S. Lai; Jiayin Wang 002; Xuanping Zhang; Xiaoyan Zhu 003; Jiaqi Liu (Comput. Ind. Eng., 2021)

Ensemble of ML-KNN for classification algorithm recommendation. - Xiaoyan Zhu 003; Chenzhen Ying; Jiayin Wang 002; Jiaxuan Li 001; Xin Lai 003; Guangtao Wang (Knowl. Based Syst., 2021)

A non-linear ensemble model-based surgical risk calculator for mixed data from multiple surgical fields. - Ruoyu Liu; Xin Lai 003; Jiayin Wang 002; Xuanping Zhang; Xiaoyan Zhu 003; Paul B. S. Lai; Ci-ren Guo (BMC Medical Informatics Decis. Mak., 2021)

Risk-adjusted zero-inflated Poisson CUSUM charts for monitoring influenza surveillance data. - Yueying Tan; Xin Lai 003; Jiayin Wang 002; Xuanping Zhang; Xiaoyan Zhu 003; Ka Chun Chong; Paul K. S. Chan; Jing Tang (BMC Medical Informatics Decis. Mak., 2021)

Automatic Recommendation of a Distance Measure for Clustering Algorithms. - Xiaoyan Zhu 003; Yingbin Li; Jiayin Wang 002; Tian Zheng; Jingwen Fu (ACM Trans. Knowl. Discov. Data, 2021)

PEcnv: accurate and efficient detection of copy number variations of various lengths. - Xuwen Wang; Ying Xu; Ruoyu Liu; Xin Lai 003; Yuqian Liu; Shenjie Wang; Xuanping Zhang; Jiayin Wang 002 (Briefings Bioinform., 2022)

Residuals based EWMA control charts with risk adjustments for zero-inflated Poisson models. - Xin Lai 003; Ruoyu Liu; Liu Liu 002; Jiayin Wang 002; Xuanping Zhang; Xiaoyan Zhu 003; Ka Chun Chong (Qual. Reliab. Eng. Int., 2022)

AdaBoost.C2: Boosting Classifiers Chains for Multi-Label Classification. - Jiaxuan Li 001; Xiaoyan Zhu 003; Jiayin Wang 002 (AAAI, 2023)

A Control Chart Method for Simultaneously Monitoring the Average Level and Stability of Surgical Quality. - Ruoyu Liu; Xin Lai 003; Jiayin Wang 002; Paul B. S. Lai; Ka Chun Chong (BIBM, 2023)

A Statistical Explainable Learning Model Optimizing Co-localization of Multidimensional Positivity Thresholds in Immunotherapy Decision-Supporting. - Yixuan Wang; Jingjing Liu; Jian Zhao 034; Jiayin Wang 002; Quan Wang 004; Xiaofeng Song (BIBM, 2023)

Generalized likelihood ratio based risk-adjusted control chart for zero-inflated Poisson process. - Xin Lai 003; Xin Lian; Liu Liu 002; Jiayin Wang 002; Yuqian Liu; Ka Chun Chong (Qual. Reliab. Eng. Int., 2023)

Dynamic ensemble learning for multi-label classification. - Xiaoyan Zhu 003; Jiaxuan Li 001; Jingtao Ren; Jiayin Wang 002; Guangtao Wang (Inf. Sci., 2023)

Scheduling on proportionate flow shop with job rejection and common due date assignment. - Xin-Na Geng; Xinyu Sun; Jiayin Wang 002; Lei Pan (Comput. Ind. Eng., 2023)

DELFMUT: duplex sequencing-oriented depth estimation model for stable detection of low-frequency mutations. - Guiying Wu; Mengmeng Song; Ke Wang; Tianyu Cui; Zicong Jiao; Liyan Ji; Xuan Gao; Jiayin Wang 002; Tao Liu; Xuefeng Xia; Huan Fang 005; Yanfang Guan; et al. (Briefings Bioinform., 2023)

Automated machine learning with dynamic ensemble selection. - Xiaoyan Zhu 003; Jingtao Ren; Jiayin Wang 002; Jiaxuan Li 001 (Appl. Intell., 2023)

SCR-CUSUM: An illness-death semi-Markov model-based risk-adjusted CUSUM for semi-competing risk data monitoring. - Ruoyu Liu; Xin Lai 003; Jiayin Wang 002; Xiaoyan Zhu 003; Yuqian Liu (Comput. Ind. Eng., 2023)

Multi-Objective Policy Monitoring Method for Epidemic Control. - Xin Lai 003; Rundong Fan; Ruoyu Liu; Jiayin Wang 002; Xiaoyan Zhu 003; Yuqian Liu; Xuwen Wang; Shenjie Wang (BIBM, 2024)

An Enhanced Multiple Correction Method with Limited Independent Effective SNPs. - Xin Lai 003; Xiaohai Yang; Jiayin Wang 002; Xiaoyan Zhu 003; Yuqian Liu; Ruoyu Liu; Xuwen Wang; Shenjie Wang (BIBM, 2024)

Enhancing Dental Implant Risk Prediction with an Interpretable Multi-Instance Learning Model. - Yuqian Liu; Almonzer Salah Nooraldaim; Zhengfa Xue; Jiayin Wang 002 (BIBM, 2024)

LMR-EWMA: A LASSO-based Multivariate Residual Control Chart for Monitoring Rare Health-Related Events. - Ruoyu Liu; Jiayin Wang 002; Xiaoyan Zhu 003; Yuqian Liu; Yixuan Wang; Shuanying Yang; Xin Lai 003 (BIBM, 2024)

RMComBat: A Batch Effect Correction Algorithm for Repeated Measurement Sequencing Data to Prevent Overcorrection. - Yuqian Liu; Zhaoxing Wei; Jiayin Wang 002; Xiaoyan Zhu 003; Ruoyu Liu; Xuwen Wang; Shenjie Wang; Xin Lai 003 (BIBM, 2024)

Enabling Adaptive CNV Detection through A Novel Predictive Control Framework. - Yuqian Liu; Jiajing Yuan; Xiaoyan Zhu 003; Xin Lai 003; Ruoyu Liu; Xuwen Wang; Jiayin Wang 002 (BIBM, 2024)

Correction of Read Biases Induced by Complex Reference Genome Regions for Improving Copy Number Variation Detection Using a Gaussian Mixture Model. - Xuwen Wang; Zhili Chang; Shenjie Wang; Ruoyu Liu; Yuqian Liu; Xiaoyan Zhu 003; Yang Shao; Xin Lai 003; Shuanying Yang; Jiayin Wang 002 (BIBM, 2024)

An Enhanced Batch Query Architecture in Real-time Recommendation. - Qiang Zhang 055; Zhipeng Teng; Disheng Wu; Jiayin Wang 002 (CIKM, 2024)

Label-Specific Multi-label Classification with Entropy Guided Clustering. - Jiaxuan Li 001; Tong Zhu; Xiaoyan Zhu 003; Jiayin Wang 002 (ICPR (2), 2024)

Enhancing MET Copy Number Estimation by Factoring in Tumor Purity and Variant Types. - Minchao Zhao; Jiayin Wang 002; Zhili Chang; Yuqian Liu (IWBBIO (2), 2024)

Classifier chain-based monitoring method for multivariate surgical outcomes. - Xin Lai 003; Xin Lian; Jiayin Wang 002; Liu Liu 002; Xuanping Zhang; Xiaoyan Zhu 003; Yuqian Liu; Xin Chen; Paul B. S. Lai (Comput. Ind. Eng., 2024)

Stacked co-training for semi-supervised multi-label learning. - Jiaxuan Li 001; Xiaoyan Zhu 003; Hongrui Wang; Yu Zhang 203; Jiayin Wang 002 (Inf. Sci., 2024)

Graph-enhanced and collaborative attention networks for session-based recommendation. - Xiaoyan Zhu 003; Yu Zhang 203; Jiayin Wang 002; Guangtao Wang (Knowl. Based Syst., 2024)

scMSI: Accurately inferring the sub-clonal Micro-Satellite status by an integrated deconvolution model on length spectrum. - Yuqian Liu; Yan Chen; Huanwen Wu; Xuanping Zhang; Yuqi Wang; Xin Yi; Zhiyong Liang; Jiayin Wang 002 (PLoS Comput. Biol., 2024)

A ranking-based problem transformation method for weakly supervised multi-label learning. - Jiaxuan Li 001; Xiaoyan Zhu 003; Weichu Zhang; Jiayin Wang 002 (Pattern Recognit., 2024)

A novel instance-based method for cross-project just-in-time defect prediction. - Xiaoyan Zhu 003; Tian Qiu; Jiayin Wang 002; Xin Lai 003 (Softw. Pract. Exp., 2024)

A risk-adjusted exponentially weighted moving average control chart for detection of the scale parameter in surgical quality monitoring. - Xin Lai 003; Xiao Li 034; Liu Liu 002; Jiayin Wang 002; Xuanping Zhang; Xiaoyan Zhu 003; Paul B. S. Lai (Qual. Reliab. Eng. Int., 2024)

TMBstable: a variant caller controls performance variation across heterogeneous sequencing samples. - Shenjie Wang; Xiaoyan Zhu 003; Xuwen Wang; Yuqian Liu; Minchao Zhao; Zhili Chang; Xiaonan Wang; Yang Shao; Jiayin Wang 002 (Briefings Bioinform., 2024)

NIPT-PG: empowering non-invasive prenatal testing to learn from population genomics through an incremental pan-genomic approach. - Zhengfa Xue; Aifen Zhou; Xiaoyan Zhu 003; Linxuan Li; Huanhuan Zhu; Xin Jin; Jiayin Wang 002 (Briefings Bioinform., 2024)

Dual-channel graph contrastive learning for multi-label classification with label-specific features and label correlations. - Xiaoyan Zhu 003; Tong Zhu; Jiaxuan Li 001; Jiayin Wang 002 (Neural Comput. Appl., 2024)

TCSR: Self-attention with time and category for session-based recommendation. - Xiaoyan Zhu 003; Yu Zhang 203; Jiaxuan Li 001; Jiayin Wang 002; Xin Lai 003 (Comput. Intell., 2024)

Multi-Label Ranking Loss Minimization for Matrix Completion. - Jiaxuan Li 001; Xiaoyan Zhu 003; Hongrui Wang; Yu Zhang 203; Xin Lai 003; Jiayin Wang 002 (AAAI, 2025)

Cross-Project Defect Prediction Based on Feature Fusion and Local Domain Adaptation. - Xianglu Zhou; Xiaoyan Zhu 003; Yu Wang 069; Jiayin Wang 002; Xin Lai 003 (APSEC, 2025)

Efficient Integration of ASR with Large Language Models to Enhance Video Search at Scale. - Qiang Zhang 055; Fengshun Xiao; Tianjiao Li; Li Lin; Hanyin Fang; Huyang Sun; Ruoyu Liu; Xiaoyan Zhu 003; Jiayin Wang 002 (WWW (Companion Volume), 2025)

MRDadaptis: self-adaptive parameter configuration enhances minimal residual disease detection in heterogeneous ctDNA samples. - Tianci Wang; Xin Lai 003; Shenjie Wang; Zhengfa Xue; Yuqian Liu; Xiaoyan Zhu 003; Xiaonan Wang; Zhili Chang; Yang Shao; Xian Zhang; Jiayin Wang 002 (Briefings Bioinform., 2025)

PangenomeX: a graph convolutional network-based pangenome framework for unbiased population-scale genomic variation analysis. - Zhengfa Xue; Yu Wang 069; Xuwen Wang; Jiajing Yuan; Lin Wang; Jingyu Zeng; Xin Jin; Huanhuan Zhu; Jiayin Wang 002 (Briefings Bioinform., 2025)

MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples. - Tianci Wang; Xin Lai 003; Shenjie Wang; Yuqian Liu; Xiaoyan Zhu 003; Jiayin Wang 002 (Bioinform., 2025)

ZIPcnv: accurate and efficient inference of copy number variations from shallow whole-genome sequencing. - Zhengfa Xue; Jingyu Zeng; Xuwen Wang; Jiajing Yuan; Tianci Wang; Xin Lai 003; Lin Wang; Yu Wang 069; Huanhuan Zhu; Xin Jin; Jiayin Wang 002 (Bioinform., 2025)

Multi-agent large language models as evolutionary optimizers for scheduling optimization. - Yidan Wang; Jiayin Wang 002; Zhiwei Chu (Comput. Ind. Eng., 2025)

Learning multi-behavior user intent for session-based recommendation. - Yu Zhang 203; Xiaoyan Zhu 003; Guopeng He; Jiaxuan Li 001; Jiayin Wang 002 (Expert Syst. Appl., 2025)

MRDtarget: A heuristic Gaussian approach for optimizing targeted capture regions to enhance Minimal Residual Disease detection. - Xuwen Wang; Yanfang Guan; Wei Gao; Xin Lai 003; Wuqiang Cao; Xiaoyan Zhu 003; Xiaoling Zeng; Yuqian Liu; Shenjie Wang; Ruoyu Liu; Xin Yi; Shuanying Yang; et al. (PLoS Comput. Biol., 2025)

THOR: a TMB heterogeneity-adaptive optimization model predicts immunotherapy response using clonal genomic features in group-structured data. - Yixuan Wang; Yanfang Guan; Xin Lai 003; Yuqian Liu; Zhili Chang; Xiaonan Wang; Quan Wang 004; Jingjing Liu; Jian Zhao 034; Shuanying Yang; Jiayin Wang 002; Xiaofeng Song (Briefings Bioinform., 2025)

EMcnv: enhancing CNV detection performance through ensemble strategies with heterogeneous meta-graph neural networks. - Xuwen Wang; Zhili Chang; Yuqian Liu; Shenjie Wang; Xiaoyan Zhu 003; Yang Shao; Jiayin Wang 002 (Briefings Bioinform., 2025)

TMBquant: an explainable AI-powered caller advancing tumor mutation burden quantification across heterogeneous samples. - Shenjie Wang; Xiaonan Wang; Xiaoyan Zhu 003; Xuwen Wang; Yuqian Liu; Minchao Zhao; Zhili Chang; Yang Shao; Haitao Zhang; Shuanying Yang; Jiayin Wang 002 (Briefings Bioinform., 2025)

BioWorkflow: Retrieving comprehensive bioinformatics workflows from publications. - Yidan Wang; Jiayin Wang 002 (Briefings Bioinform., 2025)

TMBclaw: tumor clone-aware graph learning improves immunotherapy response prediction across heterogeneous cohorts. - Yixuan Wang; Tianyi Zhu; Xiaofeng Song; Peng Chen; Xiaoyan Zhu 003; Zhili Chang; Xiaonan Wang; Xin Lai 003; Jiayin Wang 002 (Briefings Bioinform., 2025)

Mosaic Pruning: A Hierarchical Framework for Generalizable Pruning of Mixture-of-Experts Models. - Wentao Hu; Mingkuan Zhao; Shuangyong Song; Xiaoyan Zhu 003; Xin Lai 003; Jiayin Wang 002 (AAAI, 2026)

Making Every Head Count: Sparse Attention Without the Speed-Performance Trade-off. - Mingkuan Zhao; Wentao Hu; Jiayin Wang 002; Xin Lai 003; Tianchen Huang; Yuheng Min; Rui Yan; Xiaoyan Zhu 003 (AAAI, 2026)

PScnv: personalized self-normalizing CNV detection with a hierarchical multi-phase framework. - Xuwen Wang; Zhili Chang; Wansheng Lv; Akhatov Akmal; Xamidov Munis; Xunbiao Liu; Shenjie Wang; Xiaoyan Zhu 003; Chong Du; Shuqun Zhang; Jiayin Wang 002 (Bioinform., 2026)

UF-CDDFM: A unified framework for code defect detection using multi-modal inputs and few-shot learning. - Xianglu Zhou; Tianxiang Cui; Xiaoyan Zhu 003; Jiayin Wang 002; Xin Lai 003 (Inf. Softw. Technol., 2026)

Reaching Software Quality for Bioinformatics Applications: How Far Are We? - Xiaoyan Zhu 003; Tianxiang Xu; Xin Lai 003; Xin Lian; Hangyu Cheng; Jiayin Wang 002 (IEEE Trans. Software Eng., 2026)

Do Papers Match Code? A Benchmark and Framework for Paper-Code Consistency Detection in Bioinformatics Software. - Tianxiang Xu; Xiaoyan Zhu 003; Xin Lai 003; Sizhe Dang; Xin Lian; Hangyu Cheng; Jiayin Wang 002 (CoRR, 2026)