Xiaoyong Pan

62 papers C 3Journal 53Unranked 6
YearRankTypeTitle / Venue / Authors
2026 C conf
High Sample Rate Audio Generation Using Neural Large Language Models for Mitigating Device Manufacturing Defects.
ICCE
Baicheng Huang, Xinyi Pan, Haiwei Chai, Feng Zhu, Dong Liu, Xiaoyong Pan
2026 C conf
High Sample Rate Evaluation of Audio Playback Quality Using Deep Learning Audition Models.
ICCE
Baicheng Huang, Xinyi Pan, Haiwei Chai, Feng Zhu, Dong Liu, Xiaoyong Pan
2026 C conf
Neural Imitation of Human Perceptual Response to High-Resolution Audio.
ICCE
Baicheng Huang, Xinyi Pan, Haiwei Chai, Dong Liu, Feng Zhu, Xiaoyong Pan
2026 J jnl
SMENET: A Multi-View Semantic Model for Multi-Level Enzyme Function Prediction.
IEEE Trans. Comput. Biol. Bioinform.
Hanwen Zhou, Wei Zhang, Zhaohong Deng, Guanjin Wang, Zhisheng Wei, Lei Wang, Xiaoyong Pan, Hong-Bin Shen, Dong-Jun Yu, Jing Wu
2025 J jnl
CATransUnetLBP: Accurate Prediction of Protein-Ligand Binding Pockets Using a Hybrid Network.
IEEE Trans. Comput. Biol. Bioinform.
Cheng Cai, Zhaohong Deng, Andong Li, Yun Zuo, Haoran Chen, Zhisheng Wei, Lei Wang, Xiaoyong Pan, Hong-Bin Shen, Dong-Jun Yu
2025 J jnl
DMMAFS: Protein Function Prediction Based on Multi-Modal Multi-Attention Fusion Features.
IEEE Trans. Comput. Biol. Bioinform.
Liangwen He, Zhaohong Deng, Fuping Hu, Zhongyu Wang, Yun Zuo, Lin Zhu, Haoran Chen, Xiaoyong Pan, Zhisheng Wei, Lei Wang, Hong-Bin Shen, Dong-Jun Yu, Jing Wu
2025 J jnl
DRAG: design RNAs as hierarchical graphs with reinforcement learning.
Briefings Bioinform.
Yichong Li, Xiaoyong Pan, Hongbin Shen, Yang Yang
2025 J jnl
Discovering the nuclear localization signal universe through a deep learning model with interpretable attention units.
Patterns
Yi-Fan Li, Xiaoyong Pan, Hong-Bin Shen
2025 J jnl
Explainable RNA-Small Molecule Binding Affinity Prediction Based on Multiview Enhancement Learning.
J. Chem. Inf. Model.
Zeyu Wu, Zhaohong Deng, Qunzhuo Wu, Yun Zuo, Xiaoyong Pan, Hongbin Shen, Xingze Fang, Yuxi Ge, Shudong Hu
2025 J jnl
FishAI 2.0: Marine Fish Image Classification with Multi-modal Few-shot Learning.
CoRR
Chenghan Yang, Peng Zhou, Dong-Sheng Zhang, Yueyun Wang, Hong-Bin Shen, Xiaoyong Pan
2025 J jnl
Integration of multi-source gene interaction networks and omics data with graph attention networks to identify novel disease genes.
Bioinform.
Kaiyuan Yang, Jiabei Cheng, Shenghao Cao, Xiaoyong Pan, Hongbin Shen, Jin Cheng, Ye Yuan
2025 J jnl
Loc4Lnc: Accurate prediction of long noncoding RNA subcellular localization via enhanced RNA sequence representation.
Quant. Biol.
Yujia Cheng, Xiaoyong Pan, Yang Yang
2025 J jnl
Modeling Enzyme Temperature Stability from Sequence Segment Perspective.
J. Chem. Inf. Model.
Ziqi Zhang, Shiheng Chen, Runze Yang, Zhisheng Wei, Wei Zhang, Lei Wang, Zhanzhi Liu, Fengshan Zhang, Jing Wu, Xiaoyong Pan, Hongbin Shen, Longbing Cao, Zhaohong Deng
2025 J jnl
Modeling enzyme temperature stability from sequence segment perspective.
CoRR
Ziqi Zhang, Shiheng Chen, Runze Yang, Zhisheng Wei, Wei Zhang, Lei Wang, Zhanzhi Liu, Fengshan Zhang, Jing Wu, Xiaoyong Pan, Hongbin Shen, Longbing Cao, Zhaohong Deng
2025 J jnl
Predicting transcriptional changes induced by molecules with MiTCP.
Briefings Bioinform.
Kaiyuan Yang, Jiabei Cheng, Shenghao Cao, Xiaoyong Pan, Hong-Bin Shen, Ye Yuan
2025 J jnl
m2ST: dual multi-scale graph clustering for spatially resolved transcriptomics.
Bioinform.
Wei Zhang, Ziqi Zhang, Hailong Yang, Te Zhang, Shu Jiang, Ning Qiao, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Dong-Jun Yu, Shitong Wang
2024 J jnl
Decoding protein binding landscape on circular RNAs with base-resolution transformer models.
Comput. Biol. Medicine
Hehe Wu, Xiaojian Liu, Yi Fang, Yang Yang, Yan Huang, Xiaoyong Pan, Hong-Bin Shen
2024 — conf
DeepSipred: A deep-learning-based approach on siRNA inhibition prediction.
BIC
Bin Liu, Huiya Huang, Weixi Liao, Xiaoyong Pan, Cheng Jin, Ye Yuan
2024 J jnl
FLIER: Few-shot Language Image Models Embedded with Latent Representations.
CoRR
Zhinuo Zhou, Peng Zhou, Xiaoyong Pan
2024 J jnl
GAN-DIRNet: A Novel Deformable Image Registration Approach for Multimodal Histological Images.
Comput. Mater. Continua
Haiyue Li, Jing Xie, Jing Ke, Ye Yuan, Xiaoyong Pan, Hongyi Xin, Hongbin Shen
2024 J jnl
GexMolGen: cross-modal generation of hit-like molecules via large language model encoding of gene expression signatures.
Briefings Bioinform.
Jiabei Cheng, Xiaoyong Pan, Yi Fang, Kaiyuan Yang, Yiming Xue, Qingran Yan, Ye Yuan
2024 J jnl
MINDG: a drug-target interaction prediction method based on an integrated learning algorithm.
Bioinform.
Hailong Yang, Yue Chen, Yun Zuo, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Dong-Jun Yu
2024 J jnl
ProtDAT: A Unified Framework for Protein Sequence Design from Any Protein Text Description.
CoRR
Xiao-Yu Guo, Yi-Fan Li, Yuan Liu, Xiaoyong Pan, Hong-Bin Shen
2024 — conf
RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs.
BIBM
Yichong Li, Xiaojian Liu, Fan Cheng, Xiaoyong Pan, Yang Yang
2023 J jnl
DG-Affinity: predicting antigen-antibody affinity with language models from sequences.
BMC Bioinform.
Ye Yuan, Qushuo Chen, Jun Mao, Guipeng Li, Xiaoyong Pan
2023 J jnl
ELMo4m6A: A Contextual Language Embedding-Based Predictor for Detecting RNA N6-Methyladenosine Sites.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yongxian Fan, Guicong Sun, Xiaoyong Pan
2023 J jnl
Leveraging scaffold information to predict protein-ligand binding affinity with an empirical graph neural network.
Briefings Bioinform.
Chun-Qiu Xia, Shi-Hao Feng, Ying Xia, Xiaoyong Pan, Hong-Bin Shen
2023 J jnl
MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering.
Bioinform.
Qunzhuo Wu, Zhaohong Deng, Wei Zhang, Xiaoyong Pan, Kup-Sze Choi, Yun Zuo, Hong-Bin Shen, Dong-Jun Yu
2022 J jnl
Cell clustering for spatial transcriptomics data with graph neural networks.
Nat. Comput. Sci.
Jiachen Li, Siheng Chen, Xiaoyong Pan, Ye Yuan, Hong-Bin Shen
2022 J jnl
Fast protein structure comparison through effective representation learning with contrastive graph neural networks.
PLoS Comput. Biol.
Chun-Qiu Xia, Shi-Hao Feng, Ying Xia, Xiaoyong Pan, Hong-Bin Shen
2022 J jnl
GCRFLDA: scoring lncRNA-disease associations using graph convolution matrix completion with conditional random field.
Briefings Bioinform.
Yongxian Fan, Meijun Chen, Xiaoyong Pan
2022 J jnl
Identifying Protein Subcellular Locations With Embeddings-Based node2loc.
IEEE ACM Trans. Comput. Biol. Bioinform.
Xiaoyong Pan, Lei Chen, Min Liu, Zhibin Niu, Tao Huang, Yu-Dong Cai
2022 J jnl
MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction.
Briefings Bioinform.
Qunzhuo Wu, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Shitong Wang, Jing Wu, Dong-Jun Yu
2022 J jnl
Molecule Generation for Drug Design: a Graph Learning Perspective.
CoRR
Nianzu Yang, Huaijin Wu, Junchi Yan, Xiaoyong Pan, Ye Yuan, Le Song
2022 J jnl
Recent Deep Learning Methodology Development for RNA-RNA Interaction Prediction.
Symmetry
Yi Fang, Xiaoyong Pan, Hong-Bin Shen
2022 J jnl
circRNA-binding protein site prediction based on multi-view deep learning, subspace learning and multi-view classifier.
Briefings Bioinform.
Hui Li, Zhaohong Deng, Haitao Yang, Xiaoyong Pan, Zhisheng Wei, Hong-Bin Shen, Kup-Sze Choi, Lei Wang, Shitong Wang, Jing Wu
2021 J jnl
RNA-binding protein recognition based on multi-view deep feature and multi-label learning.
Briefings Bioinform.
Haitao Yang, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Lei Wang, Shitong Wang, Jing Wu
2021 J jnl
Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network.
Briefings Bioinform.
Hehe Wu, Xiaoyong Pan, Yang Yang, Hong-Bin Shen
2021 J jnl
ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity.
Bioinform.
Xiaoyong Pan, Jasper Zuallaert, Xi Wang, Hong-Bin Shen, Elda Posada Campos, Denys O. Marushchak, Wesley De Neve
2021 J jnl
lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning.
Bioinform.
Yang Lin, Xiaoyong Pan, Hong-Bin Shen
2020 J jnl
IEEE Access Special Section: Sequential Data Modeling and Its Emerging Applications.
IEEE Access
Junchi Yan, Xiaoyong Pan, Liangda Li, Changsheng Li, Peng Cui, Chao Ma
2020 J jnl
Protein-ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data.
Bioinform.
Chun-Qiu Xia, Xiaoyong Pan, Hong-Bin Shen
2020 J jnl
Scoring disease-microRNA associations by integrating disease hierarchy into graph convolutional networks.
Pattern Recognit.
Xiaoyong Pan, Hong-Bin Shen
2020 J jnl
Screening Dys-Methylation Genes and Rules for Cancer Diagnosis by Using the Pan-Cancer Study.
IEEE Access
Yu-Hang Zhang, Tao Zeng, Xiaoyong Pan, Wei Guo, Zijun Gan, Yunhua Zhang, Tao Huang, Yu-Dong Cai
2020 J jnl
Signal-3L 3.0: Improving Signal Peptide Prediction through Combining Attention Deep Learning with Window-Based Scoring.
J. Chem. Inf. Model.
Wei-Xun Zhang, Xiaoyong Pan, Hong-Bin Shen
2019 — conf
CNNPSP: Pseudouridine Sites Prediction Based on Deep Learning.
IDEAL (1)
Yong-Xian Fan, Yongzhen Li, Huihua Yang, Xiaoyong Pan
2019 J jnl
Gene Expression Difference Between Primary and Metastatic Renal Cell Carcinoma Using Patient-Derived Xenografts.
IEEE Access
Yang Jiang, Xiaoyong Pan, Yu-Hang Zhang, Tao Huang, Yufei Gao
2019 J jnl
Identifying Essential Signature Genes and Expression Rules Associated With Distinctive Development Stages of Early Embryonic Cells.
IEEE Access
Lei Chen, Xiaoyong Pan, Tao Zeng, Yu-Hang Zhang, Tao Huang, Yu-Dong Cai
2019 J jnl
Identifying RNA-binding proteins using multi-label deep learning.
Sci. China Inf. Sci.
Xiaoyong Pan, Yong-Xian Fan, Jue Jia, Hong-Bin Shen
2019 J jnl
Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles.
Bioinform.
Xiaoyong Pan, Lars Juhl Jensen, Jan Gorodkin
2019 J jnl
Location, inventory and testing decisions in closed-loop supply chains: A multimedia company.
IISE Trans.
Zhi-Hai Zhang, Gemma Berenguer, Xiaoyong Pan
2018 J jnl
Learning distributed representations of RNA sequences and its application for predicting RNA-protein binding sites with a convolutional neural network.
Neurocomputing
Xiaoyong Pan, Hong-Bin Shen
2018 J jnl
Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks.
Bioinform.
Xiaoyong Pan, Hong-Bin Shen
2018 — conf
Prediction of RNA-protein interactions with distributed feature representations and a hybrid deep model.
ICIMCS
Kaiming Zhang, Yiqun Xiao, Xiaoyong Pan, Yang Yang
2018 J jnl
The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier.
Bioinform.
Zhen Cao, Xiaoyong Pan, Yang Yang, Yan Huang, Hong-Bin Shen
2017 J jnl
Attention based convolutional neural network for predicting RNA-protein binding sites.
CoRR
Xiaoyong Pan, Junchi Yan
2017 J jnl
RAIN: RNA-protein Association and Interaction Networks.
Database J. Biol. Databases Curation
Alexander Junge, Jan C. Refsgaard, Christian Garde, Xiaoyong Pan, Alberto Santos, Ferhat Alkan, Christian Anthon, Christian von Mering, Christopher T. Workman, Lars Juhl Jensen, Jan Gorodkin
2017 J jnl
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach.
BMC Bioinform.
Xiaoyong Pan, Hong-Bin Shen
2014 J jnl
Predicting protein-RNA interaction amino acids using random forest based on submodularity subset selection.
Comput. Biol. Chem.
Xiaoyong Pan, Lin Zhu, Yong-Xian Fan, Junchi Yan
2012 J jnl
A carbon emission analysis model for electronics manufacturing process based on value-stream mapping and sensitivity analysis.
Int. J. Comput. Integr. Manuf.
Hongcheng Li, Huajun Cao, Xiaoyong Pan
2012 — conf
Highly Efficient Method to Recover Silver from Discarded Plasma Display Panels.
ICDMA
Xiaoyong Pan, Jie Wang, Weihua Chen, Ling Peng, Yong Liu
2012 — conf
Particle-Stabilized High Internal Phase Emulsions as Templates for Porous Nanocomposite Materials.
ICDMA
Xiaoyong Pan, Yanyan Du, Lian Wang, Chuntang Lei, Gang Zhou, Bing Zhou