publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

2026

  1. AAAI
    TRACE: Transformation-Aware Graph Refinement for Reaction Condition Prediction
    Yujie Chen, Tengfei Ma, Yuansheng Liu, Leyi Wei, Shu Wu, Dongsheng Cao, Yiping Liu, and Xiangxiang Zeng
    In Proceedings of the AAAI Conference on Artificial Intelligence (Oral), 2026
  2. ACL
    CAML: A Conflict-Aware Molecular Language Model Merging Framework for Multi-Constraint Molecular Generation
    Xuanbai Ren, Luoda Tan, Pei Liu, Xiangzheng Fu, Longyue Wang, Yiping Liu, and Xiangxiang Zeng
    In Proceedings of the Annual Meeting of the Association for Computational Linguistics, 2026
  3. CVPR
    Sparse Task Vector Mixup with Hypernetworks for Efficient Knowledge Transfer in Whole-Slide Image Prognosis
    Pei Liu, Xiangxiang Zeng, Tengfei Ma, Yucheng Xing, Xuanbai Ren, and Yiping Liu
    Proceedings of the Conference on Computer Vision and Pattern Recognition, 2026
  4. JCIM
    Enhancing Retrosynthesis Prediction with Distillation Learning
    Yiping Liu, Zhou Yu, Jiayi Zhang, Yujie Chen, Shu Wu, Leyi Wei, Xiangxiang Zeng, Yuyan Han, and Yuansheng Liu
    Journal of Chemical Information and Modeling, 2026
  5. Methods
    Unravelling cell heterogeneity and gene regulation mechanisms in multiple myeloma through single-cell RNA-seq
    Jing Jiang, Junlin Xu, Peng Wang, Yuansheng Liu, and Yiping Liu
    Methods, 2026
  6. BIB
    A systematic review of molecular representation learning foundation models
    Bosheng Song, Jiayi Zhang, Ying Liu, Yuansheng Liu, Jing Jiang, Sisi Yuan, Xia Zhen, and Yiping Liu
    Briefings in Bioinformatics, 2026
  7. SWEVO
    A survey on Quality-Diversity optimization: Approaches, applications, and challenges
    Haoxiang Qin, Yi Xiang, Hainan Zhang, Yuyan Han, Yuting Wang, Xinrui Tao, and Yiping Liu
    Swarm and Evolutionary Computation, 2026

2025

  1. AAAI
    Multi-objective molecular design through learning latent Pareto set
    Yiping Liu, Jiahao Yang, Xuanbai Ren, Zhang Xinyi, Yuansheng Liu, Bosheng Song, Xiangxiang Zeng, and Hisao Ishibuchi
    In Proceedings of the AAAI Conference on Artificial Intelligence, 2025
  2. J. Med. Chem.
    HMAMP: Designing Highly Potent Antimicrobial Peptides Using a Hypervolume-Driven Multiobjective Deep Generative Model
    Li Wang, Yiping Liu, Xiangzheng Fu, Xiucai Ye, Junfeng Shi, Gary G Yen, Quan Zou, Xiangxiang Zeng, and Dongsheng Cao
    Journal of Medicinal Chemistry, 2025
  3. IEEE-JBHI
    PKAN: Leveraging Kolmogorov-Arnold Networks and Multi-modal Learning for Peptide Prediction with Advanced Language Models
    Li Wang, Xiangzheng Fu, Xiucai Ye, Tetsuya Sakurai, Xiangxiang Zeng, and Yiping Liu
    IEEE Journal of Biomedical and Health Informatics, 2025
  4. BIB
    MOFormer: navigating the antimicrobial peptide design space with Pareto-based multi-objective transformer
    Li Wang, Xiangzheng Fu, Jiahao Yang, Xinyi Zhang, Xiucai Ye, Tetsuya Sakurai, Xiangxiang Zeng, and Yiping Liu
    Briefings in Bioinformatics, 2025
  5. Inform. Fusion
    ImageDDI: Image-enhanced molecular motif sequence representation for drug-drug interaction prediction
    Yuqin He, Tengfei Ma, Chaoyi Li, Pengsen Ma, Hongxin Xiang, Jianmin Wang, Yiping Liu, Bosheng Song, and Xiangxiang Zeng
    Information Fusion, 2025
  6. JCIM
    Predicting Drug–Drug Interaction via Dual-Drug Visual Representation
    Lingxuan Xie, Tengfei Ma, Yuqin He, Yiping Liu, and Xiangxiang Zeng
    Journal of Chemical Information and Modeling, 2025
  7. EAAI
    Feature-driven double deep Q-network with iterated greedy for intelligent scheduling optimization in reentrant hybrid flow shops
    Chexiang Li, Yuyan Han, Yuting Wang, Yiping Liu, Biao Zhang, and Leilei Meng
    Engineering Applications of Artificial Intelligence, 2025
  8. IEEE-JBHI
    Enhanced Protein Network Representation with Explicit Structural Binding for Protein-Protein Interaction Prediction
    Zhuowen Zhen, Tengfei Ma, Yiping Liu, and Xiangxiang Zeng
    IEEE Journal of Biomedical and Health Informatics, 2025
  9. WIRES COMPUT MOL SCI
    Advancements in Large Language Models (LLMs): Empowering Drug Discovery
    Bosheng Song, Xiaowen Li, Xiuxiu Chao, Li Wang, Yiping Liu, Zhen Xia, Dongsheng Cao, and Xiangzheng Fu
    Wiley Interdisciplinary Reviews: Computational Molecular Science, 2025
  10. Instruction multi-constraint molecular generation using a teacher-student large language model
    Peng Zhou, Jianmin Wang, Chunyan Li, Zixu Wang, Yiping Liu, Siqi Sun, Jianxin Lin, Leyi Wei, Xibao Cai, Houtim Lai, and others
    BMC biology, 2025
  11. Energy-efficient optimization for distributed blocking hybrid flowshop scheduling: a self-regulating iterative greedy algorithm under makespan constraint
    Yong Wang, Yuyan Han, Yuting Wang, and Yiping Liu
    Optimization and Engineering, 2025
  12. IEEE-SMC-Systems
    Reinforcement learning-assisted memetic algorithm for sustainability-oriented multiobjective distributed flow shop group scheduling
    Yuhang Wang, Yuyan Han, Yuting Wang, Xianpeng Wang, Yiping Liu, and Kaizhou Gao
    IEEE Transactions on Systems, Man, and Cybernetics: Systems, 2025
  13. Methods
    Drug-target interaction prediction based on metapaths and simplified neighbor aggregation
    Di Yu, Xinyu Yang, Yifan Shang, Sisi Yuan, Yuansheng Liu, and Yiping Liu
    Methods, 2025
  14. AdaptMol: Adaptive Fusion from Sequence String to Topological Structure for Few-shot Drug Discovery
    Yifan Dai, Xuanbai Ren, Tengfei Ma, Qipeng Yan, Yiping Liu, Yuansheng Liu, and Xiangxiang Zeng
    arXiv preprint arXiv:2505.11878, 2025
  15. ASOC
    From fluid relaxations to double deep Q-network for Dynamic Multiplicity Flexible Job-Shop Scheduling
    Xiaoyu Yang, Yuyan Han, Yuting Wang, Huan Li, Kaizhou Gao, and Yiping Liu
    Applied Soft Computing, 2025
  16. IEEE-BIBM
    GSToxi: Gated Cross-Modal Modeling With Graph-Sequence Encoders for Peptide Toxicity Prediction
    Li Wang, Xiangzheng Fu, Tianyi Shi, Xiucai Ye, Tetsuya Sakurai, and Yiping Liu
    In 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2025
  17. IEEE-BIBM
    VQH-AM: Vector Quantization-Augmented Heterogeneous Graph Learning for Antibody Affinity Maturation Prediction
    Zhuowen Zhen, Tengfei Ma, Jiaxuan Li, Dashun Zheng, Patrick Cheong-Iao Pang, Yiping Liu, and Xiangxiang Zeng
    In 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2025

2024

  1. IEEE-TEVC
    Evolutionary multimodal multiobjective optimization for traveling salesman problems
    Yiping Liu, Liting Xu, Yuyan Han, Xiangxiang Zeng, Gary G Yen, and Hisao Ishibuchi
    IEEE Transactions on Evolutionary Computation, 2024
  2. SWEVO
    Evolutionary multimodal multiobjective optimization guided by growing neural gas
    Yiping Liu, Ling Zhang, Xiangxiang Zeng, and Yuyan Han
    Swarm and Evolutionary Computation, 2024
  3. IJCNN
    Multi-Objective Molecular Design in Constrained Latent Space
    Yiwei Liu, Yiping Liu, Jiahao Yang, Xinyi Zhang, Li Wang, and Xiangxiang Zeng
    In 2024 International Joint Conference on Neural Networks (IJCNN), 2024
  4. JCIM
    Evolutionary Multiobjective Molecule Optimization in an Implicit Chemical Space
    Xin Xia, Yiping Liu, Chunhou Zheng, Xingyi Zhang, Qingwen Wu, Xin Gao, Xiangxiang Zeng, and Yansen Su
    Journal of Chemical Information and Modeling, 2024
  5. Integration of hybrid and self-correction method improves the quality of long-read sequencing data
    Tao Tang, Yiping Liu, Binshuang Zheng, Rong Li, Xiaocai Zhang, and Yuansheng Liu
    Briefings in Functional Genomics, 2024
  6. JCIM
    Hansynergy: Heterogeneous graph attention network for drug synergy prediction
    Ning Cheng, Li Wang, Yiping Liu, Bosheng Song, and Changsong Ding
    Journal of Chemical Information and Modeling, 2024
  7. ESWA
    Theoretical analysis and implementation of mandatory operations-based accelerated search in graph space for hybrid flow shop scheduling
    Yuting Wang, Yuyan Han, Huan Li, Junqing Li, Kaizhou Gao, and Yiping Liu
    Expert Systems with Applications, 2024
  8. IEEE-TKDE
    Learning to denoise biomedical knowledge graph for robust molecular interaction prediction
    Tengfei Ma, Yujie Chen, Wen Tao, Dashun Zheng, Xuan Lin, Cheong-Iao Pang, Yiping Liu, Yijun Wang, Longyue Wang, Bosheng Song, and others
    IEEE Transactions on Knowledge and Data Engineering, 2024
  9. Distributed hybrid flowshop scheduling with consistent sublots under delivery time windows: A penalty lot-assisted iterated greedy algorithm
    Jinli Liu, Yuyan Han, Yuting Wang, Yiping Liu, and Biao Zhang
    Egyptian Informatics Journal, 2024
  10. SWEVO
    Multi-population coevolutionary algorithm for a green multi-objective flexible job shop scheduling problem with automated guided vehicles and variable processing speed constraints
    Chao Liu, Yuyan Han, Yuting Wang, Junqing Li, and Yiping Liu
    Swarm and Evolutionary Computation, 2024

2023

  1. IEEE-CIM
    Evolutionary multi-objective optimization in searching for various antimicrobial peptides [feature]
    Yiping Liu, Xinyi Zhang, Yuansheng Liu, Yansen Su, Xiangxiang Zeng, and Gary G Yen
    IEEE Computational Intelligence Magazine, 2023
  2. Reference vector adaptation and mating selection strategy via adaptive resonance theory-based clustering for many-objective optimization
    Takato Kinoshita, Naoki Masuyama, Yiping Liu, Yusuke Nojima, and Hisao Ishibuchi
    IEEE Access, 2023
  3. IEEE-TETIC
    Energy-efficient iterative greedy algorithm for the distributed hybrid flow shop scheduling with blocking constraints
    Haoxiang Qin, Yuyan Han, Qingda Chen, Ling Wang, Yuting Wang, Junqing Li, and Yiping Liu
    IEEE Transactions on Emerging Topics in Computational Intelligence, 2023
  4. ESWA
    An effective two-stage iterated greedy algorithm for distributed flowshop group scheduling problem with setup time
    Yuhang Wang, Yuyan Han, Yuting Wang, Junqing Li, Kaizhou Gao, and Yiping Liu
    Expert Systems with Applications, 2023
  5. BIB
    Sequence alignment/map format: a comprehensive review of approaches and applications
    Yuansheng Liu, Xiangzhen Shen, Yongshun Gong, Yiping Liu, Bosheng Song, and Xiangxiang Zeng
    Briefings in Bioinformatics, 2023
  6. GECCO
    A decomposition-based multi-modal multi-objective evolutionary algorithm with problem transformation into two-objective subproblems
    Yusuke Nojima, Yuto Fujii, Naoki Masuyama, Yiping Liu, and Hisao Ishibuchi
    In Proceedings of the Companion Conference on Genetic and Evolutionary Computation, 2023
  7. Learning to denoise unreliable interactions for link prediction on biomedical knowledge graph
    Tengfei Ma, Yujie Chen, Wen Tao, Dashun Zheng, Xuan Lin, Patrick Cheong-lao Pang, Yiping Liu, Yijun Wang, Bosheng Song, and Xiangxiang Zeng
    CoRR, 2023

2022

  1. SWEVO
    An improved iterated greedy algorithm for the energy-efficient blocking hybrid flow shop scheduling problem
    Hao-Xiang Qin, Yu-Yan Han, Biao Zhang, Lei-Lei Meng, Yi-Ping Liu, Quan-Ke Pan, and Dun-Wei Gong
    Swarm and Evolutionary Computation, 2022
  2. ASOC
    An effective iterative greedy algorithm for distributed blocking flowshop scheduling problem with balanced energy costs criterion
    Xue Han, Yuyan Han, Biao Zhang, Haoxiang Qin, Junqing Li, Yiping Liu, and Dunwei Gong
    Applied Soft Computing, 2022
  3. ESWA
    A collaborative iterative greedy algorithm for the scheduling of distributed heterogeneous hybrid flow shop with blocking constraints
    Hao-Xiang Qin, Yu-Yan Han, Yi-Ping Liu, Jun-Qing Li, Quan-Ke Pan, and others
    Expert Systems with Applications, 2022
  4. IEEE-TCYB
    A multi-population multi-objective evolutionary algorithm based on the contribution of decision variables to objectives for large-scale multi/many-objective optimization
    Ying Xu, Chong Xu, Huan Zhang, Lei Huang, Yiping Liu, Yusuke Nojima, and Xiangxiang Zeng
    IEEE Transactions on Cybernetics, 2022
  5. KBS
    Intelligent optimization under blocking constraints: A novel iterated greedy algorithm for the hybrid flow shop group scheduling problem
    Haoxiang Qin, Yuyan Han, Yuting Wang, Yiping Liu, Junqing Li, and Quanke Pan
    Knowledge-Based Systems, 2022

2021

  1. IEEE-SMC
    Multi-modal multi-objective traveling salesman problem and its evolutionary optimizer
    Yiping Liu, Liting Xu, Yuyan Han, Naoki Masuyama, Yusuke Nojima, Hisao Ishibuchi, and Gary G Yen
    In 2021 IEEE International Conference on Systems, Man, and Cybernetics (SMC), 2021
  2. Distributed flow shop scheduling with sequence-dependent setup times using an improved iterated greedy algorithm
    Xue Han, Yuyan Han, Qingda Chen, Junqing Li, Hongyan Sang, Yiping Liu, Quanke Pan, and Yusuke Nojima
    Complex system modeling and simulation, 2021
  3. An Algorithm Based on Local Search for Solving Energy-efficient Distributed Blocking Flowshop Problems with Sequence-dependent Setup Times
    Xue Han, Yuting Wang, Yuyan Han, Yi-Ping Liu, and Hongyan Sang
    In 2021 5th Asian Conference on Artificial Intelligence Technology (ACAIT), 2021
  4. An improved iterated greedy algorithm for the distributed flow shop scheduling problem with sequence-dependent setup times
    Xue Han, Yuyan Han, Yi-ping Liu, Quan-ke Pan, Hao-xiang Qin, and Junqing Li
    In 2021 11th International Conference on Information Science and Technology (ICIST), 2021

2020

  1. IEEE-TEVC
    Handling Imbalance Between Convergence and Diversity in the Decision Space in Evolutionary Multi-Modal Multi-Objective Optimization
    Yiping Liu, Hisao Ishibuchi, Gary G. Yen, Yusuke Nojima, and Naoki Masuyama
    IEEE Transactions on Evolutionary Computation, 2020
  2. IEEE-TEVC
    Adapting reference vectors and scalarizing functions by growing neural gas to handle irregular Pareto fronts
    Yiping Liu, Hisao Ishibuchi, Naoki Masuyama, and Yusuke Nojima
    IEEE Transactions on Evolutionary Computation, 2020
  3. Evol. Comput.
    A meta-objective approach for many-objective evolutionary optimization
    Dunwei Gong, Yiping Liu, and Gary G Yen
    Evolutionary computation, 2020
  4. IEEE-CEC
    On the normalization in evolutionary multi-modal multi-objective optimization
    Yiping Liu, Hisao Ishibuchi, Gary G Yen, Yusuke Nojima, Naoki Masuyama, and Yuyan Han
    In 2020 IEEE congress on evolutionary computation (CEC), 2020
  5. ASOC
    Discrete evolutionary multi-objective optimization for energy-efficient blocking flow shop scheduling with setup time
    Yuyan Han, Junqing Li, Hongyan Sang, Yiping Liu, Kaizhou Gao, and Quanke Pan
    Applied Soft Computing, 2020
  6. Meta-heuristic algorithm for solving vehicle routing problems with time windows and synchronized visit constraints in prefabricated systems
    Jun-qing Li, Yun-qi Han, Pei-yong Duan, Yu-yan Han, Ben Niu, Cheng-dong Li, Zhi-xin Zheng, and Yiping Liu
    Journal of Cleaner Production, 2020
  7. IJCNN
    Multilayer clustering based on adaptive resonance theory for noisy environments
    Narito Amako, Naoki Masuyama, Chu Kiong Loo, Yusuke Nojima, Yiping Liu, and Hisao Ishibuchi
    In 2020 International Joint Conference on Neural Networks (IJCNN), 2020

2019

  1. IEEE-CEC
    Searching for local Pareto optimal solutions: A case study on polygon-based problems
    Yiping Liu, Hisao Ishibuchi, Yusuke Nojima, Naoki Masuyama, and Yuyan Han
    In 2019 IEEE Congress on Evolutionary Computation (CEC), 2019
  2. GECCO
    Constrained multiobjective distance minimization problems
    Yusuke Nojima, Takafumi Fukase, Yiping Liu, Naoki Masuyama, and Hisao Ishibuchi
    In Proceedings of the Genetic and Evolutionary Computation Conference, 2019
  3. Topological clustering via adaptive resonance theory with information theoretic learning
    Naoki Masuyama, Chu Kiong Loo, Hisao Ishibuchi, Naoyuki Kubota, Yusuke Nojima, and Yiping Liu
    IEEE Access, 2019
  4. IEEE-CEC
    Migrating birds optimization for lot-streaming flow shop scheduling problem
    Yuyan Han, Junqing Li, Yiping Liu, Zhixin Zheng, Yuxia Pan, Hongyan Sang, and Lili Liu
    In 2019 ieee congress on evolutionary computation (cec), 2019
  5. IEEE-SSCI
    Fast topological adaptive resonance theory based on correntropy induced metric
    Naoki Masuyama, Narito Amako, Yusuke Nojima, Yiping Liu, Chu Kiong Loo, and Hisao Ishibuchi
    In 2019 IEEE Symposium Series on Computational Intelligence (SSCI), 2019

2018

  1. IEEE-TEVC
    A multimodal multiobjective evolutionary algorithm using two-archive and recombination strategies
    Yiping Liu, Gary G Yen, and Dunwei Gong
    IEEE Transactions on Evolutionary Computation, 2018
  2. PPSN
    Improving 1by1EA to handle various shapes of Pareto fronts
    Yiping Liu, Hisao Ishibuchi, Yusuke Nojima, Naoki Masuyama, and Ke Shang
    In International Conference on Parallel Problem Solving from Nature, 2018
  3. PPSN
    A double-niched evolutionary algorithm and its behavior on polygon-based problems
    Yiping Liu, Hisao Ishibuchi, Yusuke Nojima, Naoki Masuyama, and Ke Shang
    In International conference on parallel problem solving from nature, 2018
  4. GECCO
    A new R2 indicator for better hypervolume approximation
    Ke Shang, Hisao Ishibuchi, Min-Ling Zhang, and Yiping Liu
    In Proceedings of the Genetic and Evolutionary Computation Conference, 2018
  5. WAC
    Topological kernel bayesian ARTMAP
    Naoki Masuyama, Chu Kiong Loo, Hisao Ishibuchi, Yusuke Nojima, and Yiping Liu
    In 2018 world automation congress (WAC), 2018

2017

  1. IEEE-TCYB
    A many-objective evolutionary algorithm using a one-by-one selection strategy
    Yiping Liu, Dunwei Gong, Jing Sun, and Yaochu Jin
    IEEE Transactions on Cybernetics, 2017
  2. ASOC
    Many-objective evolutionary optimization based on reference points
    Yiping Liu, Dunwei Gong, Xiaoyan Sun, and Yong Zhang
    Applied Soft Computing, 2017

2016

  1. Indicator-based set evolution particle swarm optimization for many-objective problems
    Xiaoyan Sun, Yang Chen, Yiping Liu, and Dunwei Gong
    Soft Computing, 2016

2015

  1. Parallel many-objective evolutionary optimization using objectives decomposition
    DW Gong, Yiping Liu, XY Sun, and Y Han
    Acta Automatica Sinica, 2015
  2. Evolutionary algorithms with user’s preferences for solving hybrid interval multi-objective optimization problems
    Dunwei Gong, Yiping Liu, Xinfang Ji, and Jing Sun
    Applied Intelligence, 2015

2014

  1. GECCO
    A reference points-based evolutionary algorithm for many-objective optimization
    Yiping Liu, Dunwei Gong, Xiaoyan Sun, and Yong Zhang
    In Proceedings of the Companion Publication of the 2014 Annual Conference on Genetic and Evolutionary Computation, 2014