Bosheng Song

93 papers A* 3Journal 77Unranked 12
YearRankTypeTitle / Venue / Authors
2026 J jnl
A systematic review of molecular representation learning foundation models.
Briefings Bioinform.
Bosheng Song, Jiayi Zhang, Ying Liu, Yuansheng Liu, Jing Jiang, Sisi Yuan, Xia Zhen, Yiping Liu
2026 J jnl
Empowering Chemical Structures with Biological Insights for Scalable Phenotypic Virtual Screening.
CoRR
Xiaoqing Lian, Pengsen Ma, Tengfeng Ma, Zhonghao Ren, Xibao Cai, Zhixiang Cheng, Bosheng Song, He Wang, Xiang Pan, Yangyang Chen, Sisi Yuan, Chen Lin
2026 J jnl
ImageDDI: Image-enhanced molecular motif sequence representation for drug-drug interaction prediction.
Inf. Fusion
Yuqin He, Tengfei Ma, Chaoyi Li, Pengsen Ma, Hongxin Xiang, Jianmin Wang, Yiping Liu, Bosheng Song, Xiangxiang Zeng
2026 J jnl
Learnable dendrite neural P systems and applications in survival prediction of glioblastoma patients.
Neural Networks
Xiu Yin, Xiyu Liu, Shulei Chang, Bosheng Song, Guanzhong Gong, Jiaxing Yin, Dengwang Li, Jie Xue
2026 J jnl
Neuropeptide-regulated P system for semi-supervised segmentation of multiple brain metastases on MRIs.
Eng. Appl. Artif. Intell.
Jie Xue, Kexu Zhao, Xiyu Liu, Bosheng Song, Shulei Chang, Guanzhong Gong, Dengwang Li
2025 J jnl
Deep Generative Models for Therapeutic Peptide Discovery: A Comprehensive Review.
ACM Comput. Surv.
Leshan Lai, Yuansheng Liu, Bosheng Song, Keqin Li, Xiangxiang Zeng
2025 — conf
From Knowledge to Treatment: Large Language Model Assisted Biomedical Concept Representation for Drug Repurposing.
EMNLP (Findings)
Chengrui Xiang, Tengfei Ma, Xiangzheng Fu, Yiping Liu, Bosheng Song, Xiangxiang Zeng
2025 J jnl
From Knowledge to Treatment: Large Language Model Assisted Biomedical Concept Representation for Drug Repurposing.
CoRR
Chengrui Xiang, Tengfei Ma, Xiangzheng Fu, Yiping Liu, Bosheng Song, Xiangxiang Zeng
2025 J jnl
ImageDDI: Image-enhanced Molecular Motif Sequence Representation for Drug-Drug Interaction Prediction.
CoRR
Yuqin He, Tengfei Ma, Chaoyi Li, Pengsen Ma, Hongxin Xiang, Jianmin Wang, Yiping Liu, Bosheng Song, Xiangxiang Zeng
2025 A* conf
Multi-Objective Molecular Design Through Learning Latent Pareto Set.
AAAI
Yiping Liu, Jiahao Yang, Xuanbai Ren, Xinyi Zhang, Yuansheng Liu, Bosheng Song, Xiangxiang Zeng, Hisao Ishibuchi
2025 J jnl
Multilevel-evolutionary population P systems and applications in tumor segmentations.
Appl. Soft Comput.
Jie Xue, Qi Li, Bosheng Song, Xiyu Liu, Dengwang Li
2025 J jnl
Semantic substructure guided multiple objective molecular generation with discrete diffusion probabilistic model.
Neurocomputing
Shugao Chen, Bosheng Song, Ruizhe Chen, Lin Liu, Guifei Zhou, Sisi Yuan
2025 A* conf
S²DN: Learning to Denoise Unconvincing Knowledge for Inductive Knowledge Graph Completion.
AAAI
Tengfei Ma, Yujie Chen, Liang Wang, Xuan Lin, Bosheng Song, Xiangxiang Zeng
2025 J jnl
The computational properties of P systems with mutative membrane structures.
Inf. Comput.
Bosheng Song, Chuanlong Hu, David Orellana-Martín, Antonio Ramírez-de-Arellano, Mario J. Pérez-Jiménez, Xiangxiang Zeng
2025 A* conf
Towards Synergistic Path-based Explanations for Knowledge Graph Completion: Exploration and Evaluation.
ICLR
Tengfei Ma, Xiang Song, Wen Tao, Mufei Li, Jiani Zhang, Xiaoqin Pan, Yijun Wang, Bosheng Song, Xiangxiang Zeng
2024 J jnl
Attribute-guided prototype network for few-shot molecular property prediction.
Briefings Bioinform.
Linlin Hou, Hongxin Xiang, Xiangxiang Zeng, Dongsheng Cao, Li Zeng, Bosheng Song
2024 J jnl
Deep synergetic spiking neural P systems for the overall survival time prediction of glioblastoma patients.
Expert Syst. Appl.
Xiu Yin, Xiyu Liu, Jinpeng Dai, Bosheng Song, Zheng Han, Chunqiu Xia, Dengwang Li, Jie Xue
2024 J jnl
Dynamic threshold spiking neural P systems with weights and multiple channels.
Theor. Comput. Sci.
Yanyan Li, Bosheng Song, Yuansheng Liu, Xiangxiang Zeng, Shengye Huang
2024 J jnl
HANSynergy: Heterogeneous Graph Attention Network for Drug Synergy Prediction.
J. Chem. Inf. Model.
Ning Cheng, Li Wang, Yiping Liu, Bosheng Song, Changsong Ding
2024 J jnl
KGExplainer: Towards Exploring Connected Subgraph Explanations for Knowledge Graph Completion.
CoRR
Tengfei Ma, Xiang Song, Wen Tao, Mufei Li, Jiani Zhang, Xiaoqin Pan, Jianxin Lin, Bosheng Song, Xiangxiang Zeng
2024 J jnl
Learning to Denoise Biomedical Knowledge Graph for Robust Molecular Interaction Prediction.
IEEE Trans. Knowl. Data Eng.
Tengfei Ma, Yujie Chen, Wen Tao, Dashun Zheng, Xuan Lin, Patrick Cheong-Iao Pang, Yiping Liu, Yijun Wang, Longyue Wang, Bosheng Song, Xiangxiang Zeng, Philip S. Yu
2024 J jnl
MaskMol: Knowledge-guided Molecular Image Pre-Training Framework for Activity Cliffs.
CoRR
Zhixiang Cheng, Hongxin Xiang, Pengsen Ma, Li Zeng, Xin Jin, Xixi Yang, Jianxin Lin, Yang Deng, Bosheng Song, Xinxin Feng, Changhui Deng, Xiangxiang Zeng
2024 J jnl
PEB-DDI: A Task-Specific Dual-View Substructural Learning Framework for Drug-Drug Interaction Prediction.
IEEE J. Biomed. Health Informatics
Xiangzhen Shen, Zimeng Li, Yuansheng Liu, Bosheng Song, Xiangxiang Zeng
2024 J jnl
S
CoRR
Tengfei Ma, Yujie Chen, Liang Wang, Xuan Lin, Bosheng Song, Xiangxiang Zeng
2024 J jnl
SSR-DTA: Substructure-aware multi-layer graph neural networks for drug-target binding affinity prediction.
Artif. Intell. Medicine
Yuansheng Liu, Xinyan Xia, Yongshun Gong, Bosheng Song, Xiangxiang Zeng
2023 J jnl
Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction.
Briefings Bioinform.
Xuan Lin, Lichang Dai, Yafang Zhou, Zu-Guo Yu, Wen Zhang, Jian-Yu Shi, Dong-Sheng Cao, Li Zeng, Haowen Chen, Bosheng Song, Philip S. Yu, Xiangxiang Zeng
2023 J jnl
Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction.
CoRR
Xuan Lin, Lichang Dai, Yafang Zhou, Zu-Guo Yu, Wen Zhang, Jian-Yu Shi, Dong-Sheng Cao, Li Zeng, Haowen Chen, Bosheng Song, Philip S. Yu, Xiangxiang Zeng
2023 J jnl
Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoder.
Briefings Bioinform.
Jing Jiang, Junlin Xu, Yuansheng Liu, Bosheng Song, Xiulan Guo, Xiangxiang Zeng, Quan Zou
2023 J jnl
Hybrid neural-like P systems with evolutionary channels for multiple brain metastases segmentation.
Pattern Recognit.
Jie Xue, Qi Li, Xiyu Liu, Yujie Guo, Jie Lu, Bosheng Song, Pu Huang, Qiong An, Guanzhong Gong, Dengwang Li
2023 J jnl
Hypergraph-Based Numerical Neural-Like P Systems for Medical Image Segmentation.
IEEE Trans. Parallel Distributed Syst.
Jie Xue, Liwen Ren, Bosheng Song, Yujie Guo, Jie Lu, Xiyu Liu, Guanzhong Gong, Dengwang Li
2023 J jnl
KG-MTL: Knowledge Graph Enhanced Multi-Task Learning for Molecular Interaction.
IEEE Trans. Knowl. Data Eng.
Tengfei Ma, Xuan Lin, Bosheng Song, Philip S. Yu, Xiangxiang Zeng
2023 J jnl
Learning to Denoise Unreliable Interactions for Link Prediction on Biomedical Knowledge Graph.
CoRR
Tengfei Ma, Yujie Chen, Wen Tao, Dashun Zheng, Xuan Lin, Patrick Cheong-Iao Pang, Yiping Liu, Yijun Wang, Bosheng Song, Xiangxiang Zeng
2023 J jnl
Modality-DTA: Multimodality Fusion Strategy for Drug-Target Affinity Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform.
Xixi Yang, Zhangming Niu, Yuansheng Liu, Bosheng Song, Weiqiang Lu, Li Zeng, Xiangxiang Zeng
2023 J jnl
Monodirectional evolutional symport tissue P systems with channel states and cell division.
Sci. China Inf. Sci.
Bosheng Song, Kenli Li, Xiangxiang Zeng, Mario J. Pérez-Jiménez, Claudio Zandron
2023 J jnl
On the computational efficiency of tissue P systems with evolutional symport/antiport rules.
Knowl. Based Syst.
Linqiang Pan, Bosheng Song, Claudio Zandron
2023 J jnl
Prediction of multi-relational drug-gene interaction via Dynamic hyperGraph Contrastive Learning.
Briefings Bioinform.
Wen Tao, Yuansheng Liu, Xuan Lin, Bosheng Song, Xiangxiang Zeng
2023 J jnl
Sequence Alignment/Map format: a comprehensive review of approaches and applications.
Briefings Bioinform.
Yuansheng Liu, Xiangzhen Shen, Yongshun Gong, Yiping Liu, Bosheng Song, Xiangxiang Zeng
2023 J jnl
Spiking neural P system with synaptic vesicles and applications in multiple brain metastasis segmentation.
Inf. Sci.
Jie Xue, Deting Kong, Liwen Ren, Bosheng Song, Xiyu Liu, Guanzhong Gong, Dengwang Li, Hongyan Zhang
2023 J jnl
Spiking neural P systems with weights and delays on synapses.
Theor. Comput. Sci.
Yanyan Li, Bosheng Song, Xiangxiang Zeng
2023 J jnl
Tissue P Systems With States in Cells.
IEEE Trans. Computers
Bosheng Song, Kenli Li, David Orellana-Martín, Xiangxiang Zeng, Mario J. Pérez-Jiménez
2023 J jnl
Tissue P systems with evolutional communication rules with two objects in the left-hand side.
Nat. Comput.
David Orellana-Martín, Luis Valencia-Cabrera, Bosheng Song, Linqiang Pan, Mario J. Pérez-Jiménez
2022 J jnl
A Survey of Nature-Inspired Computing: Membrane Computing.
ACM Comput. Surv.
Bosheng Song, Kenli Li, David Orellana-Martín, Mario J. Pérez-Jiménez, Ignacio Pérez-Hurtado
2022 J jnl
Learning spatial structures of proteins improves protein-protein interaction prediction.
Briefings Bioinform.
Bosheng Song, Xiaoyan Luo, Xiaoli Luo, Yuansheng Liu, Zhangming Niu, Xiangxiang Zeng
2022 J jnl
Monodirectional Evolutional Symport Tissue P Systems With Promoters and Cell Division.
IEEE Trans. Parallel Distributed Syst.
Bosheng Song, Kenli Li, Xiangxiang Zeng
2022 J jnl
Predicting ncRNA-protein interactions based on dual graph convolutional network and pairwise learning.
Briefings Bioinform.
Linlin Zhuo, Bosheng Song, Yuansheng Liu, Zejun Li, Xiangzheng Fu
2022 J jnl
Rule synchronization for monodirectional tissue-like P systems with channel states.
Inf. Comput.
Yanyan Li, Bosheng Song, Xiangxiang Zeng
2021 J jnl
Deep learning methods for biomedical named entity recognition: a survey and qualitative comparison.
Briefings Bioinform.
Bosheng Song, Fen Li, Yuansheng Liu, Xiangxiang Zeng
2021 J jnl
MUFFIN: multi-scale feature fusion for drug-drug interaction prediction.
Bioinform.
Yujie Chen, Tengfei Ma, Xixi Yang, Jianmin Wang, Bosheng Song, Xiangxiang Zeng
2021 J jnl
Molecular design in drug discovery: a comprehensive review of deep generative models.
Briefings Bioinform.
Yu Cheng, Yongshun Gong, Yuansheng Liu, Bosheng Song, Quan Zou
2021 J jnl
Monodirectional Tissue P Systems With Promoters.
IEEE Trans. Cybern.
Bosheng Song, Xiangxiang Zeng, Min Jiang, Mario J. Pérez-Jiménez
2021 J jnl
Monodirectional tissue P systems with channel states.
Inf. Sci.
Bosheng Song, Xiangxiang Zeng, Alfonso Rodríguez-Patón
2021 J jnl
Rule synchronization for tissue P systems.
Inf. Comput.
Bosheng Song, Linqiang Pan
2021 J jnl
Solving a PSPACE-complete problem by symport/antiport P systems with promoters and membrane division.
J. Membr. Comput.
Bosheng Song, Xiangxiang Zeng
2021 J jnl
The computational power of monodirectional tissue P systems with symport rules.
Inf. Comput.
Bosheng Song, Shengye Huang, Xiangxiang Zeng
2021 J jnl
Time-free Solution to Independent Set Problem using P Systems with Active Membranes.
Fundam. Informaticae
Yu Jin, Bosheng Song, Yanyan Li, Ying Zhu
2021 J jnl
Time-free solution to independent set problem using P systems with active membranes.
CoRR
Yu Jin, Bosheng Song, Yanyan Li, Ying Zhu
2021 J jnl
Tuning Frontiers of Efficiency in Tissue P Systems with Evolutional Communication Rules.
Complex.
David Orellana-Martín, Luis Valencia-Cabrera, Bosheng Song, Linqiang Pan, Mario J. Pérez-Jiménez
2020 J jnl
Cell-like P systems with evolutional symport/antiport rules and membrane creation.
Inf. Comput.
Bosheng Song, Kenli Li, David Orellana-Martín, Luis Valencia-Cabrera, Mario J. Pérez-Jiménez
2020 J jnl
Cell-like P systems with polarizations and minimal rules.
Theor. Comput. Sci.
Linqiang Pan, David Orellana-Martín, Bosheng Song, Mario J. Pérez-Jiménez
2020 J jnl
P Systems with Rule Production and Removal.
Fundam. Informaticae
Linqiang Pan, Bosheng Song
2020 J jnl
P systems with symport/antiport rules: When do the surroundings matter?
Theor. Comput. Sci.
David Orellana-Martín, Miguel Ángel Martínez-del-Amor, Luis Valencia-Cabrera, Bosheng Song, Linqiang Pan, Mario J. Pérez-Jiménez
2020 J jnl
The computational power of cell-like P systems with one protein on membrane.
J. Membr. Comput.
Bosheng Song, Xiaoyan Luo, Luis Valencia-Cabrera, Xiangxiang Zeng
2020 J jnl
Time-freeness and clock-freeness and related concepts in P systems.
Theor. Comput. Sci.
Artiom Alhazov, Rudolf Freund, Sergiu Ivanov, Linqiang Pan, Bosheng Song
2020 J jnl
Tissue P systems with promoter simulation with MeCoSim and P-Lingua framework.
J. Membr. Comput.
Luis Valencia-Cabrera, Bosheng Song
2018 — ch.
An Overview of 2D Picture Array Generating Models Based on Membrane Computing.
Reversibility and Universality
K. G. Subramanian, Sastha Sriram, Bosheng Song, Linqiang Pan
2018 J jnl
Language generating alphabetic flat splicing P systems.
Theor. Comput. Sci.
Linqiang Pan, Bosheng Song, Atulya K. Nagar, K. G. Subramanian
2018 J jnl
On Distributed Solution to SAT by Membrane Computing.
Int. J. Comput. Commun. Control
Henry N. Adorna, Linqiang Pan, Bosheng Song
2018 — conf
On Languages Generated by Context-Free Matrix Insertion-Deletion Systems with Exo-Operations.
Enjoying Natural Computing
Bosheng Song, Fei Xu, Linqiang Pan
2018 J jnl
The Computational Complexity of Tissue P Systems with Evolutional Symport/Antiport Rules.
Complex.
Linqiang Pan, Bosheng Song, Luis Valencia-Cabrera, Mario J. Pérez-Jiménez
2017 J jnl
A time-free uniform solution to subset sum problem by tissue P systems with cell division.
Math. Struct. Comput. Sci.
Bosheng Song, Tao Song, Linqiang Pan
2017 J jnl
An efficient time-free solution to QSAT problem using P systems with proteins on membranes.
Inf. Comput.
Bosheng Song, Mario J. Pérez-Jiménez, Linqiang Pan
2017 — conf
Derivation Languages of Splicing P Systems.
BIC-TA
Kalpana Mahalingam, Prithwineel Paul, Bosheng Song, Linqiang Pan, K. G. Subramanian
2017 — conf
Simulating Evolutional Symport/Antiport by Evolution-Communication and vice versa in Tissue P Systems with Parallel Communication.
Int. Conf. on Membrane Computing
Henry N. Adorna, Artiom Alhazov, Linqiang Pan, Bosheng Song
2017 — conf
Tissue P Systems with Rule Production/Removal.
Int. Conf. on Membrane Computing
Linqiang Pan, Bosheng Song, Gexiang Zhang
2017 J jnl
Tissue-like P systems with evolutional symport/antiport rules.
Inf. Sci.
Bosheng Song, Cheng Zhang, Linqiang Pan
2016 — conf
A Multi-objective Optimization Algorithm Based on Tissue P System for VRPTW.
BIC-TA (2)
Wenbo Dong, Kang Zhou, Huaqing Qi, Cheng He, Jun Zhang, Bosheng Song
2016 — conf
An Improved Algorithm for Constructing Binary Trees Using the Traversal Sequences.
BIC-TA (2)
Fangxiu Wang, Kang Zhou, Huaqing Qi, Bosheng Song
2016 J jnl
An efficient time-free solution to SAT problem by P systems with proteins on membranes.
J. Comput. Syst. Sci.
Bosheng Song, Mario J. Pérez-Jiménez, Linqiang Pan
2016 J jnl
Flat maximal parallelism in P systems with promoters.
Theor. Comput. Sci.
Linqiang Pan, Gheorghe Paun, Bosheng Song
2016 — conf
Improved Multi-step Iterative Algorithms for the Fixed Points of Strongly Pseudo-Contractive Mappings.
BIC-TA (2)
Jiangrong Liu, Kang Zhou, Shan Zeng, Huaqing Qi, Bosheng Song, Tingfang Wu
2016 — conf
Matrix Flat Splicing Systems.
BIC-TA (1)
Rodica Ceterchi, Linqiang Pan, Bosheng Song, K. G. Subramanian
2016 J jnl
Membrane fission: A computational complexity perspective.
Complex.
Luis F. Macías-Ramos, Bosheng Song, Luis Valencia-Cabrera, Linqiang Pan, Mario J. Pérez-Jiménez
2016 — conf
Rewriting P Systems with Flat-Splicing Rules.
Int. Conf. on Membrane Computing
Linqiang Pan, Bosheng Song, K. G. Subramanian
2016 J jnl
The computational power of tissue-like P systems with promoters.
Theor. Comput. Sci.
Bosheng Song, Linqiang Pan
2016 J jnl
Tissue P Systems with Protein on Cells.
Fundam. Informaticae
Bosheng Song, Linqiang Pan, Mario J. Pérez-Jiménez
2015 J jnl
A P_Lingua Based Simulator for P Systems with Symport/Antiport Rules.
Fundam. Informaticae
Luis F. Macías-Ramos, Luis Valencia-Cabrera, Bosheng Song, Tao Song, Linqiang Pan, Mario J. Pérez-Jiménez
2015 J jnl
Computational efficiency and universality of timed P systems with active membranes.
Theor. Comput. Sci.
Bosheng Song, Linqiang Pan
2015 J jnl
Computational efficiency and universality of timed P systems with membrane creation.
Soft Comput.
Bosheng Song, Mario J. Pérez-Jiménez, Linqiang Pan
2015 J jnl
Efficient solutions to hard computational problems by P systems with symport/antiport rules and membrane division.
Biosyst.
Bosheng Song, Mario J. Pérez-Jiménez, Linqiang Pan
2015 J jnl
Time-free solution to SAT problem by P systems with active membranes and standard cell division rules.
Nat. Comput.
Bosheng Song, Tao Song, Linqiang Pan
2014 — conf
Computational Efficiency and Universality of Timed P Systems with Membrane Creation.
BIC-TA
Bosheng Song, Mario J. Pérez-Jiménez, Linqiang Pan
2011 J jnl
DNA Self-assembly Model for Matrix Addition Problem.
J. Comput.
Zhixiang Yin, Bosheng Song
2010 — conf
Plasmid DNA computing model of 0-1 programming problem.
BIC-TA
Zhixiang Yin, Hua Chen, Bosheng Song