Plasmid DNA computing model of 0-1 programming problem. - Zhixiang Yin; Hua Chen; Bosheng Song (BIC-TA, 2010)

DNA Self-assembly Model for Matrix Addition Problem. - Zhixiang Yin; Bosheng Song (J. Comput., 2011)

Computational Efficiency and Universality of Timed P Systems with Membrane Creation. - Bosheng Song; Mario J. Pérez-Jiménez; Linqiang Pan (BIC-TA, 2014)

Efficient solutions to hard computational problems by P systems with symport/antiport rules and membrane division. - Bosheng Song; Mario J. Pérez-Jiménez; Linqiang Pan (Biosyst., 2015)

A P_Lingua Based Simulator for P Systems with Symport/Antiport Rules. - Luis F. Macías-Ramos; Luis Valencia-Cabrera; Bosheng Song; Tao Song 001; Linqiang Pan; Mario J. Pérez-Jiménez (Fundam. Informaticae, 2015)

Time-free solution to SAT problem by P systems with active membranes and standard cell division rules. - Bosheng Song; Tao Song 001; Linqiang Pan (Nat. Comput., 2015)

Computational efficiency and universality of timed P systems with active membranes. - Bosheng Song; Linqiang Pan (Theor. Comput. Sci., 2015)

Matrix Flat Splicing Systems. - Rodica Ceterchi; Linqiang Pan; Bosheng Song; K. G. Subramanian 001 (BIC-TA (1), 2016)

A Multi-objective Optimization Algorithm Based on Tissue P System for VRPTW. - Wenbo Dong; Kang Zhou 005; Huaqing Qi; Cheng He 001; Jun Zhang; Bosheng Song (BIC-TA (2), 2016)

Improved Multi-step Iterative Algorithms for the Fixed Points of Strongly Pseudo-Contractive Mappings. - Jiangrong Liu; Kang Zhou 005; Shan Zeng; Huaqing Qi; Bosheng Song; Tingfang Wu (BIC-TA (2), 2016)

An Improved Algorithm for Constructing Binary Trees Using the Traversal Sequences. - Fangxiu Wang; Kang Zhou 005; Huaqing Qi; Bosheng Song (BIC-TA (2), 2016)

Rewriting P Systems with Flat-Splicing Rules. - Linqiang Pan; Bosheng Song; K. G. Subramanian 001 (Int. Conf. on Membrane Computing, 2016)

Membrane fission: A computational complexity perspective. - Luis F. Macías-Ramos; Bosheng Song; Luis Valencia-Cabrera; Linqiang Pan; Mario J. Pérez-Jiménez (Complex., 2016)

Tissue P Systems with Protein on Cells. - Bosheng Song; Linqiang Pan; Mario J. Pérez-Jiménez (Fundam. Informaticae, 2016)

An efficient time-free solution to SAT problem by P systems with proteins on membranes. - Bosheng Song; Mario J. Pérez-Jiménez; Linqiang Pan (J. Comput. Syst. Sci., 2016)

Flat maximal parallelism in P systems with promoters. - Linqiang Pan; Gheorghe Paun; Bosheng Song (Theor. Comput. Sci., 2016)

The computational power of tissue-like P systems with promoters. - Bosheng Song; Linqiang Pan (Theor. Comput. Sci., 2016)

Derivation Languages of Splicing P Systems. - Kalpana Mahalingam; Prithwineel Paul; Bosheng Song; Linqiang Pan; K. G. Subramanian 001 (BIC-TA, 2017)

Simulating Evolutional Symport/Antiport by Evolution-Communication and vice versa in Tissue P Systems with Parallel Communication. - Henry N. Adorna; Artiom Alhazov; Linqiang Pan; Bosheng Song (Int. Conf. on Membrane Computing, 2017)

Tissue P Systems with Rule Production/Removal. - Linqiang Pan; Bosheng Song; Gexiang Zhang (Int. Conf. on Membrane Computing, 2017)

An efficient time-free solution to QSAT problem using P systems with proteins on membranes. - Bosheng Song; Mario J. Pérez-Jiménez; Linqiang Pan (Inf. Comput., 2017)

Tissue-like P systems with evolutional symport/antiport rules. - Bosheng Song; Cheng Zhang 017; Linqiang Pan (Inf. Sci., 2017)

A time-free uniform solution to subset sum problem by tissue P systems with cell division. - Bosheng Song; Tao Song 001; Linqiang Pan (Math. Struct. Comput. Sci., 2017)

An Overview of 2D Picture Array Generating Models Based on Membrane Computing. - K. G. Subramanian 001; Sastha Sriram; Bosheng Song; Linqiang Pan (Reversibility and Universality, 2018)

On Languages Generated by Context-Free Matrix Insertion-Deletion Systems with Exo-Operations. - Bosheng Song; Fei Xu; Linqiang Pan (Enjoying Natural Computing, 2018)

The Computational Complexity of Tissue P Systems with Evolutional Symport/Antiport Rules. - Linqiang Pan; Bosheng Song; Luis Valencia-Cabrera; Mario J. Pérez-Jiménez (Complex., 2018)

On Distributed Solution to SAT by Membrane Computing. - Henry N. Adorna; Linqiang Pan; Bosheng Song (Int. J. Comput. Commun. Control, 2018)

Language generating alphabetic flat splicing P systems. - Linqiang Pan; Bosheng Song; Atulya K. Nagar; K. G. Subramanian 001 (Theor. Comput. Sci., 2018)

P Systems with Rule Production and Removal. - Linqiang Pan; Bosheng Song (Fundam. Informaticae, 2020)

Cell-like P systems with evolutional symport/antiport rules and membrane creation. - Bosheng Song; Kenli Li 001; David Orellana-Martín; Luis Valencia-Cabrera; Mario J. Pérez-Jiménez (Inf. Comput., 2020)

The computational power of cell-like P systems with one protein on membrane. - Bosheng Song; Xiaoyan Luo; Luis Valencia-Cabrera; Xiangxiang Zeng (J. Membr. Comput., 2020)

Tissue P systems with promoter simulation with MeCoSim and P-Lingua framework. - Luis Valencia-Cabrera; Bosheng Song (J. Membr. Comput., 2020)

Time-freeness and clock-freeness and related concepts in P systems. - Artiom Alhazov; Rudolf Freund; Sergiu Ivanov 001; Linqiang Pan; Bosheng Song (Theor. Comput. Sci., 2020)

P systems with symport/antiport rules: When do the surroundings matter? - David Orellana-Martín; Miguel Ángel Martínez-del-Amor; Luis Valencia-Cabrera; Bosheng Song; Linqiang Pan; Mario J. Pérez-Jiménez (Theor. Comput. Sci., 2020)

Cell-like P systems with polarizations and minimal rules. - Linqiang Pan; David Orellana-Martín; Bosheng Song; Mario J. Pérez-Jiménez (Theor. Comput. Sci., 2020)

Molecular design in drug discovery: a comprehensive review of deep generative models. - Yu Cheng; Yongshun Gong; Yuansheng Liu; Bosheng Song; Quan Zou 001 (Briefings Bioinform., 2021)

Deep learning methods for biomedical named entity recognition: a survey and qualitative comparison. - Bosheng Song; Fen Li; Yuansheng Liu; Xiangxiang Zeng (Briefings Bioinform., 2021)

MUFFIN: multi-scale feature fusion for drug-drug interaction prediction. - Yujie Chen; Tengfei Ma 002; Xixi Yang; Jianmin Wang 016; Bosheng Song; Xiangxiang Zeng (Bioinform., 2021)

Tuning Frontiers of Efficiency in Tissue P Systems with Evolutional Communication Rules. - David Orellana-Martín; Luis Valencia-Cabrera; Bosheng Song; Linqiang Pan; Mario J. Pérez-Jiménez (Complex., 2021)

Time-free Solution to Independent Set Problem using P Systems with Active Membranes. - Yu Jin; Bosheng Song; Yanyan Li; Ying Zhu (Fundam. Informaticae, 2021)

The computational power of monodirectional tissue P systems with symport rules. - Bosheng Song; Shengye Huang; Xiangxiang Zeng (Inf. Comput., 2021)

Rule synchronization for tissue P systems. - Bosheng Song; Linqiang Pan (Inf. Comput., 2021)

Monodirectional tissue P systems with channel states. - Bosheng Song; Xiangxiang Zeng; Alfonso Rodríguez-Patón (Inf. Sci., 2021)

Solving a PSPACE-complete problem by symport/antiport P systems with promoters and membrane division. - Bosheng Song; Xiangxiang Zeng (J. Membr. Comput., 2021)

Monodirectional Tissue P Systems With Promoters. - Bosheng Song; Xiangxiang Zeng; Min Jiang 005; Mario J. Pérez-Jiménez (IEEE Trans. Cybern., 2021)

Learning spatial structures of proteins improves protein-protein interaction prediction. - Bosheng Song; Xiaoyan Luo; Xiaoli Luo; Yuansheng Liu; Zhangming Niu; Xiangxiang Zeng (Briefings Bioinform., 2022)

Predicting ncRNA-protein interactions based on dual graph convolutional network and pairwise learning. - Linlin Zhuo; Bosheng Song; Yuansheng Liu; Zejun Li; Xiangzheng Fu (Briefings Bioinform., 2022)

A Survey of Nature-Inspired Computing: Membrane Computing. - Bosheng Song; Kenli Li 001; David Orellana-Martín; Mario J. Pérez-Jiménez; Ignacio Pérez-Hurtado (ACM Comput. Surv., 2022)

Rule synchronization for monodirectional tissue-like P systems with channel states. - Yanyan Li; Bosheng Song; Xiangxiang Zeng (Inf. Comput., 2022)

Monodirectional Evolutional Symport Tissue P Systems With Promoters and Cell Division. - Bosheng Song; Kenli Li 001; Xiangxiang Zeng (IEEE Trans. Parallel Distributed Syst., 2022)

Learning to Denoise Unreliable Interactions for Link Prediction on Biomedical Knowledge Graph. - Tengfei Ma 002; Yujie Chen; Wen Tao; Dashun Zheng; Xuan Lin; Patrick Cheong-lao Pang; Yiping Liu; Yijun Wang 002; Bosheng Song; Xiangxiang Zeng (CoRR, 2023)

Modality-DTA: Multimodality Fusion Strategy for Drug-Target Affinity Prediction. - Xixi Yang; Zhangming Niu; Yuansheng Liu; Bosheng Song; Weiqiang Lu; Li Zeng; Xiangxiang Zeng (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

On the computational efficiency of tissue P systems with evolutional symport/antiport rules. - Linqiang Pan; Bosheng Song; Claudio Zandron (Knowl. Based Syst., 2023)

Monodirectional evolutional symport tissue P systems with channel states and cell division. - Bosheng Song; Kenli Li 001; Xiangxiang Zeng; Mario J. Pérez-Jiménez; Claudio Zandron (Sci. China Inf. Sci., 2023)

Tissue P systems with evolutional communication rules with two objects in the left-hand side. - David Orellana-Martín; Luis Valencia-Cabrera; Bosheng Song; Linqiang Pan; Mario J. Pérez-Jiménez (Nat. Comput., 2023)

Hypergraph-Based Numerical Neural-Like P Systems for Medical Image Segmentation. - Jie Xue 001; Liwen Ren; Bosheng Song; Yujie Guo; Jie Lu; Xiyu Liu 001; Guanzhong Gong; Dengwang Li (IEEE Trans. Parallel Distributed Syst., 2023)

Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoder. - Jing Jiang; Junlin Xu; Yuansheng Liu; Bosheng Song; Xiulan Guo; Xiangxiang Zeng; Quan Zou 001 (Briefings Bioinform., 2023)

Spiking neural P system with synaptic vesicles and applications in multiple brain metastasis segmentation. - Jie Xue 001; Deting Kong; Liwen Ren; Bosheng Song; Xiyu Liu 001; Guanzhong Gong; Dengwang Li; Hongyan Zhang (Inf. Sci., 2023)

Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction. - Xuan Lin; Lichang Dai; Yafang Zhou; Zu-Guo Yu; Wen Zhang; Jian-Yu Shi; Dong-Sheng Cao 001; Li Zeng; Haowen Chen; Bosheng Song; Philip S. Yu; Xiangxiang Zeng (Briefings Bioinform., 2023)

KG-MTL: Knowledge Graph Enhanced Multi-Task Learning for Molecular Interaction. - Tengfei Ma 002; Xuan Lin; Bosheng Song; Philip S. Yu; Xiangxiang Zeng (IEEE Trans. Knowl. Data Eng., 2023)

Spiking neural P systems with weights and delays on synapses. - Yanyan Li; Bosheng Song; Xiangxiang Zeng (Theor. Comput. Sci., 2023)

Sequence Alignment/Map format: a comprehensive review of approaches and applications. - Yuansheng Liu; Xiangzhen Shen; Yongshun Gong; Yiping Liu; Bosheng Song; Xiangxiang Zeng (Briefings Bioinform., 2023)

Prediction of multi-relational drug-gene interaction via Dynamic hyperGraph Contrastive Learning. - Wen Tao; Yuansheng Liu; Xuan Lin; Bosheng Song; Xiangxiang Zeng (Briefings Bioinform., 2023)

Tissue P Systems With States in Cells. - Bosheng Song; Kenli Li 001; David Orellana-Martín; Xiangxiang Zeng; Mario J. Pérez-Jiménez (IEEE Trans. Computers, 2023)

Hybrid neural-like P systems with evolutionary channels for multiple brain metastases segmentation. - Jie Xue 001; Qi Li; Xiyu Liu 001; Yujie Guo; Jie Lu; Bosheng Song; Pu Huang; Qiong An; Guanzhong Gong; Dengwang Li (Pattern Recognit., 2023)

SSR-DTA: Substructure-aware multi-layer graph neural networks for drug-target binding affinity prediction. - Yuansheng Liu; Xinyan Xia; Yongshun Gong; Bosheng Song; Xiangxiang Zeng (Artif. Intell. Medicine, 2024)

Attribute-guided prototype network for few-shot molecular property prediction. - Linlin Hou; Hongxin Xiang; Xiangxiang Zeng; Dongsheng Cao 001; Li Zeng; Bosheng Song (Briefings Bioinform., 2024)

KGExplainer: Towards Exploring Connected Subgraph Explanations for Knowledge Graph Completion. - Tengfei Ma 002; Xiang Song 003; Wen Tao; Mufei Li; Jiani Zhang 003; Xiaoqin Pan; Jianxin Lin; Bosheng Song; Xiangxiang Zeng (CoRR, 2024)

MaskMol: Knowledge-guided Molecular Image Pre-Training Framework for Activity Cliffs. - Zhixiang Cheng; Hongxin Xiang; Pengsen Ma; Li Zeng; Xin Jin; Xixi Yang; Jianxin Lin; Yang Deng; Bosheng Song; Xinxin Feng; Changhui Deng; Xiangxiang Zeng (CoRR, 2024)

S2DN: Learning to Denoise Unconvincing Knowledge for Inductive Knowledge Graph Completion. - Tengfei Ma 002; Yujie Chen; Liang Wang; Xuan Lin; Bosheng Song; Xiangxiang Zeng (CoRR, 2024)

Deep synergetic spiking neural P systems for the overall survival time prediction of glioblastoma patients. - Xiu Yin; Xiyu Liu 001; Jinpeng Dai; Bosheng Song; Zheng Han; Chunqiu Xia; Dengwang Li; Jie Xue 001 (Expert Syst. Appl., 2024)

HANSynergy: Heterogeneous Graph Attention Network for Drug Synergy Prediction. - Ning Cheng; Li Wang; Yiping Liu; Bosheng Song; Changsong Ding (J. Chem. Inf. Model., 2024)

Dynamic threshold spiking neural P systems with weights and multiple channels. - Yanyan Li; Bosheng Song; Yuansheng Liu; Xiangxiang Zeng; Shengye Huang (Theor. Comput. Sci., 2024)

PEB-DDI: A Task-Specific Dual-View Substructural Learning Framework for Drug-Drug Interaction Prediction. - Xiangzhen Shen; Zimeng Li; Yuansheng Liu; Bosheng Song; Xiangxiang Zeng (IEEE J. Biomed. Health Informatics, 2024)

Learning to Denoise Biomedical Knowledge Graph for Robust Molecular Interaction Prediction. - Tengfei Ma 002; Yujie Chen; Wen Tao; Dashun Zheng; Xuan Lin; Patrick Cheong-Iao Pang; Yiping Liu; Yijun Wang 002; Longyue Wang; Bosheng Song; Xiangxiang Zeng; Philip S. Yu (IEEE Trans. Knowl. Data Eng., 2024)

S²DN: Learning to Denoise Unconvincing Knowledge for Inductive Knowledge Graph Completion. - Tengfei Ma 002; Yujie Chen; Liang Wang; Xuan Lin; Bosheng Song; Xiangxiang Zeng (AAAI, 2025)

Multi-Objective Molecular Design Through Learning Latent Pareto Set. - Yiping Liu; Jiahao Yang; Xuanbai Ren; Xinyi Zhang; Yuansheng Liu; Bosheng Song; Xiangxiang Zeng; Hisao Ishibuchi (AAAI, 2025)

Towards Synergistic Path-based Explanations for Knowledge Graph Completion: Exploration and Evaluation. - Tengfei Ma 002; Xiang Song 003; Wen Tao; Mufei Li; Jiani Zhang 003; Xiaoqin Pan; Yijun Wang 002; Bosheng Song; Xiangxiang Zeng (ICLR, 2025)

Multilevel-evolutionary population P systems and applications in tumor segmentations. - Jie Xue 001; Qi Li; Bosheng Song; Xiyu Liu 001; Dengwang Li (Appl. Soft Comput., 2025)

The computational properties of P systems with mutative membrane structures. - Bosheng Song; Chuanlong Hu; David Orellana-Martín; Antonio Ramírez-de-Arellano; Mario J. Pérez-Jiménez; Xiangxiang Zeng (Inf. Comput., 2025)

Semantic substructure guided multiple objective molecular generation with discrete diffusion probabilistic model. - Shugao Chen; Bosheng Song; Ruizhe Chen; Lin Liu; Guifei Zhou; Sisi Yuan (Neurocomputing, 2025)

Deep Generative Models for Therapeutic Peptide Discovery: A Comprehensive Review. - Leshan Lai; Yuansheng Liu; Bosheng Song; Keqin Li 001; Xiangxiang Zeng (ACM Comput. Surv., 2025)

ImageDDI: Image-enhanced molecular motif sequence representation for drug-drug interaction prediction. - Yuqin He; Tengfei Ma 002; Chaoyi Li; Pengsen Ma; Hongxin Xiang; Jianmin Wang 016; Yiping Liu; Bosheng Song; Xiangxiang Zeng (Inf. Fusion, 2026)