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2026

High-order correlation and consistency-aware multi-view clustering via anchor graph learningCheng Liang 0001, Wenchao Zang, Daoyuan Wang, Fei Guo 0001. NN, 200:108795, 2026. [doi]

PharmaQA: Prompt-Based Molecular Representation Learning via Pharmacophore-Oriented Question AnsweringChengwei Ai, Qiaozhen Meng, Mengwei Sun, Ruihan Dong, Hongpeng Yang, Shiqiang Ma, Xiaoyi Liu, Cheng Liang 0001, Fei Guo 0001. AAAI 2026: 19580-19588 [doi]

Piercing the Fog: Disentangling Key Features for Vision Models in Multi-Degradation ScenariosSiyu Chen, Shiqiang Ma, Fei Guo 0001. AAAI 2026: 20271-20279 [doi]

Geometry-Aware Variational Information Maximization for Deep Incomplete Multi-view ClusteringWenlan Chen, Lu Gao, Daoyuan Wang, Fei Guo 0001, Cheng Liang 0001. AAAI 2026: 20289-20297 [doi]

Closer to Biological Mechanism: Drug-Drug Interaction Prediction from the Perspective of PharmacophoreMingliang Dou, Linfeng Wen, Jinyang Xie, Jijun Tang, Shiqiang Ma, Fei Guo 0001. AAAI 2026: 20887-20895 [doi]

EdgeCLIP: Injecting Edge-Awareness Into Visual-Language Models for Zero-Shot Semantic SegmentationJiaxiang Fang, Shiqiang Ma, Guihua Duan, Fei Guo 0001, Shengfeng He. tcsv, 36(3):3070-3084, March 2026. [doi]

CCTAD: A topologically associating domains detection method integrating convolutional autoencoder and hierarchical clusteringRui-Ping Feng, Junwei Luo, Kaihua Liu, Fei Guo 0001. CANDC, 122:108913, 2026. [doi]

DualDis: A Dual Disentanglement Network for Vehicle Re-identificationWenying He, Feiyu Wang, Guangquan Xu, Yude Bai, Fei Guo 0001. WWW 2026: 5579-5587 [doi]

Refprogen: a reference-guided molecular generation model with protein-ligand joint representation for property-aware drug designXiaoyi Liu, Na Zhang, Chengwei Ai, Jijun Tang, Fei Guo 0001. eswa, 309:131230, 2026. [doi]

Make Foundation Models Trustworthy Again: Causal Fine-Adaptation for Medical Image SegmentationHongpeng Yang, Yingxin Chen, Shiqiang Ma, Fei Guo 0001. AAAI 2026: 27512-27520 [doi]

MultiPert: An adversarial alignment and dual attention framework for single-cell multi-omics perturbation predictionMengyuan Zhao, Xinyue Tang, Jiawei Li 0018, Cheng Liang 0001, Jijun Tang, Fei Guo 0001. ploscb, 22(3):1014054, 2026. [doi]

2025

RNALoc-LM: RNA subcellular localization prediction using pre-trained RNA language modelMin Zeng 0004, Xinyu Zhang, Yiming Li, Chengqian Lu, Rui Yin 0002, Fei Guo 0001, Min Li 0007. bioinformatics, 41(4), 2025. [doi]

Deep Variational Incomplete Multi-View Clustering with Information-Theoretic GuidanceWenlan Chen, Lu Gao, Cheng Liang 0001, Fei Guo 0001. mm 2025: 2457-2466 [doi]

Self-Support Prototype-Aware For Few-Shot Semantic SegmentationJiaxiang Fang, Shiqiang Ma, Shengfeng He, Fei Guo 0001. icassp 2025: 1-5 [doi]

MF-DocDDI: Drug Entity Multi-Feature Fusion for Document-Level Drug-Drug Interaction Relation ExtractionHan Han, Mingliang Dou, Jijun Tang, Fei Guo 0001. bibm 2025: 941-946 [doi]

PEFN: A Patches Enhancement and Hierarchical Fusion Network for Robust Vehicle ReidentificationWenying He, Feiyu Wang, Yude Bai, Neal N. Xiong, Guangquan Xu, Fei Guo 0001. iotj, 12(14):26898-26910, July 2025. [doi]

Catching mRNA's Hiddens Marks: A Dual-Path Network by Contrastive Learning for N4-acetylcytidine PredictionWenying He, Yu Han, Haolu Zhou, Yun Zuo 0001, Yude Bai, Fei Guo 0001. ecai 2025: 2203-2210 [doi]

LGATFormer: A Dual-Path Model Combining Line Graph Attention and Transformer for Gene Regulatory Network InferenceWenying He, Yaowei Zhu, Rentao Zhang, Haolu Zhou, Yude Bai, Fei Guo 0001. bibm 2025: 280-285 [doi]

Leveraging protein language models for cross-variant CRISPR/Cas9 sgRNA activity predictionYalin Hou, Yiming Li, Ruiqing Zheng, Fuhao Zhang, Fei Guo 0001, Min Li 0007, Min Zeng 0004. bioinformatics, 41(7), 2025. [doi]

Cancer survival prediction based on soft-label guided contrastive learning and global feature fusionHuiying Jiang, Wenlan Chen, Fei Guo 0001, Cheng Liang 0001. bioinformatics, 41(10), 2025. [doi]

RetroInText: A Multimodal Large Language Model Enhanced Framework for Retrosynthetic Planning via In-Context Representation LearningChenglong Kang, Xiaoyi Liu, Fei Guo 0001. iclr 2025: [doi]

Prediction of ncRNA-Disease Association Based on Correntropy Induced Loss Matrix Factorization ModelPing Li, Yuqing Qian, Junhai Xu, Yijie Ding, Fei Guo 0001. tcbb, 22(4):1861-1874, 2025. [doi]

2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language modelQianpei Liu, Min Zeng 0004, Yiming Li, Chengqian Lu, Shichao Kan, Fei Guo 0001, Min Li 0007. bioinformatics, 41(8), 2025. [doi]

HyperPhS: a pharmacophore-guided multimodal representation framework for metabolic stability prediction through contrastive hypergraph learningXiaoyi Liu, Na Zhang, Chenglong Kang, Chengwei Ai, Hongpeng Yang, Jijun Tang, Fei Guo 0001. bioinformatics, 41(10), 2025. [doi]

Dual-Level Distribution Alignment for Deep Incomplete Multi-View ClusteringFujian Ren, Wenlan Chen, Lu Gao, Fei Guo 0001, Cheng Liang 0001. mm 2025: 2476-2485 [doi]

MolInterAct: Multiscale Cross-Modal Interaction for Robust Molecular Representation LearningMengwei Sun, Chengwei Ai, Diya Zhang, Xiaoyi Liu, Qiaozhen Meng, Shiqiang Ma, Fei Guo 0001. bibm 2025: 1215-1220 [doi]

A novel cross-model framework for modelling urban multi-hydrological processes based on hydrogeographic elements in urban areasHaocheng Wang, Zhuo Zhang, Songshan Yue, Fei Guo 0001, Yongning Wen, Min Chen 0008, Guonian Lü. envsoft, 192:106536, 2025. [doi]

MultiPepDec: Decoupled Prompt Learning for Multi-Activity Therapeutic PeptidesXingdan Wang, Diya Zhang, Chengwei Ai, Shiqiang Ma, Qiaozhen Meng, Junwen Duan, Fei Guo 0001. bibm 2025: 721-726 [doi]

Image-Enhanced Hybrid Encoding with Reinforced Contrastive Learning for Spatial Domain Identification in Spatial TranscriptomicsDaoyuan Wang, Lu Gao, Wenlan Chen, Cheng Liang 0001, Fei Guo 0001. IJCAI 2025: 7769-7777 [doi]

Block sparse Bayes-based fuzzy system for RNA N6-methyladenosine sites predictionLeyao Wang, Mengyuan Zhao, Hao Xie, Yuqing Qian, Wenhuan Lu, Yijie Ding, Fei Guo 0001. ploscb, 21(10):1013621, 2025. [doi]

Structured Sparse Regularization-Based Deep Fuzzy Networks for RNA N6-Methyladenosine Sites PredictionLeyao Wang, Yuqing Qian, Hao Xie, Yijie Ding, Fei Guo 0001. tfs, 33(1):131-144, January 2025. [doi]

scMID: A Deep Multi-Omics Integration Framework for Comprehensive Single-Cell Data AnalysisQiu Xiao, Yan Zhang, Wanwan Shi, Li Wang, Ying Zuo, Fei Guo 0001, Jiawei Luo 0001. tcbb, 22(6):3375-3385, 2025. [doi]

Unlocking Dark Vision Potential for Medical Image SegmentationHongpeng Yang, Xiangyu Hu 0005, Yingxin Chen, Siyu Chen, Srihari Nelakuditi, Yan Tong, Shiqiang Ma, Fei Guo 0001. IJCAI 2025: 2197-2205 [doi]

Beyond Slice-by-Slice: 3D Lesion Segmentation via Cross-Frame PredictionHongpeng Yang, Yingxin Chen, Xiangyu Hu 0005, Srihari Nelakuditi, Yan Tong, Shiqiang Ma, Fei Guo 0001. ecai 2025: 715-722 [doi]

CellCircLoc: Deep Neural Network for Predicting and Explaining Cell Line-Specific CircRNA Subcellular LocalizationMin Zeng, Jingwei Lu, Yiming Li, Chengqian Lu, Shichao Kan, Fei Guo 0001, Min Li 0007. titb, 29(2):1494-1503, February 2025. [doi]

Diff-SE: A Diffusion-Augmented Contrastive Learning Framework for Super-Enhancer PredictionHaolu Zhou, Yu Han, Yude Bai, Yun Zuo 0001, Wenying He, Fei Guo 0001. jcisd, 65(14):7789-7799, 2025. [doi]

2024

MTMol-GPT: De novo multi-target molecular generation with transformer-based generative adversarial imitation learningChengwei Ai, Hongpeng Yang, Xiaoyi Liu, Ruihan Dong, Yijie Ding, Fei Guo 0001. ploscb, 20(6):1012229, 2024. [doi]

Identification of Drug-Side-Effect Association via Multiview Semisupervised Sparse ModelYijie Ding, Fei Guo 0001, Prayag Tiwari, Quan Zou 0001. tai, 5(5):2151-2162, May 2024. [doi]

Fuzzy Neural Tangent Kernel Model for Identifying DNA N4-Methylcytosine SitesYijie Ding, Prayag Tiwari, Fei Guo 0001, Quan Zou 0001, Weiping Ding 0001. tfs, 32(10):5714-5727, October 2024. [doi]

Drug-Drug Interaction Relation Extraction Based on Deep Learning: A ReviewMingliang Dou, Jijun Tang, Prayag Tiwari, Yijie Ding, Fei Guo 0001. ACM Comput. Surv., 56(6), June 2024. [doi]

Boundary-Aware Dual Biaffine Model for Sequential Sentence Classification in Biomedical DocumentsJunwen Duan, Huai Guo, Han Jiang, Fei Guo 0001, Jian-xin Wang 0001. tcbb, 21(5):1202-1210, September - October 2024. [doi]

Graph-Based Fusion of Imaging, Genetic and Clinical Data for Degenerative Disease DiagnosisRui Guo, Xu Tian, Hanhe Lin, Stephen J. McKenna, Hong-Dong Li, Fei Guo 0001, Jin Liu 0012. tcbb, 21(1):57-68, January - February 2024. [doi]

MuSE: A deep learning model based on multi-feature fusion for super-enhancer predictionWenying He, Haolu Zhou, Yun Zuo 0001, Yude Bai, Fei Guo 0001. CANDC, 113:108282, 2024. [doi]

NBCR-ac4C: A Deep Learning Framework Based on Multivariate BERT for Human mRNA N4-Acetylcytidine Sites PredictionWenying He, Yu Han, Yun Zuo 0001, Yude Bai, Fei Guo 0001. jcisd, 64(20):8074-8081, 2024. [doi]

Rapid screening of multi-point mutations for enzyme thermostability modification by utilizing computational toolsJia Jin, Qiaozhen Meng, Min Zeng, Guihua Duan, Ercheng Wang, Fei Guo 0001. fgcs, 160:724-738, 2024. [doi]

TranSiam: Aggregating multi-modal visual features with locality for medical image segmentationXuejian Li, Shiqiang Ma, Junhai Xu, Jijun Tang, Shengfeng He, Fei Guo 0001. eswa, 237(Part C):121574, March 2024. [doi]

Multi-Task Driven Multi-Level Dynamical Fusion for Single-Cell Multi-Omics Cell Type AnnotationJiawei Li, Shizhan Chen, Zongbo Han, Wei Li, Jijun Tang, Fei Guo 0001. bibm 2024: 1009-1014 [doi]

Robust Tensor Subspace Learning for Incomplete Multi-View ClusteringCheng Liang, Daoyuan Wang, Huaxiang Zhang 0001, Shichao Zhang 0001, Fei Guo 0001. tkde, 36(11):6934-6948, November 2024. [doi]

RetroCaptioner: beyond attention in end-to-end retrosynthesis transformer via contrastively captioned learnable graph representationXiaoyi Liu, Chengwei Ai, Hongpeng Yang, Ruihan Dong, Jijun Tang, Shuangjia Zheng, Fei Guo 0001. bioinformatics, 40(9), 2024. [doi]

Aggregate-aware model with bidirectional edge generation for medical image segmentationShiqiang Ma, Xuejian Li, Jijun Tang, Fei Guo 0001. asc, 163:111918, 2024. [doi]

SiamSegNet: A multimodal Segmentation Method Based on Cross-modal Generation for Medical Image SegmentationShiqiang Ma, Fei Guo 0001, Jijun Tang. dasfaa 2025: 451-466 [doi]

PPRTGI: A Personalized PageRank Graph Neural Network for TF-Target Gene Interaction DetectionKe Ma, Jiawei Li, Mengyuan Zhao, Ibrahim Zamit, Bin Lin, Fei Guo 0001, Jijun Tang. tcbb, 21(3):480-491, May - June 2024. [doi]

EPIMR: Prediction of Enhancer-Promoter Interactions by Multi-Scale ResNet on Image RepresentationQiaozhen Meng, Yinuo Lyu, Xiaoqing Peng, Junhai Xu, Jijun Tang, Fei Guo 0001. bigdatama, 7(3):668-681, 2024. [doi]

DMAMP: A Deep-Learning Model for Detecting Antimicrobial Peptides and Their Multi-ActivitiesQiaozhen Meng, Genlang Chen, Bin Lin, Shixin Zheng, Yulai Lin, Jijun Tang, Fei Guo 0001. tcbb, 21(6):2025-2034, November - December 2024. [doi]

scRNMF: An imputation method for single-cell RNA-seq data by robust and non-negative matrix factorizationYuqing Qian, Quan Zou 0001, Mengyuan Zhao, Yi Liu, Fei Guo 0001, Yijie Ding. ploscb, 20(8):1012339, 2024. [doi]

Weighted Fuzzy System for Identifying DNA N4-Methylcytosine Sites With Kernel Entropy Component AnalysisLeyao Wang, Prayag Tiwari, Yijie Ding, Fei Guo 0001. tai, 5(2):895-903, February 2024. [doi]

Structured Sparse Regularization based Random Vector Functional Link Networks for DNA N4-methylcytosine sites predictionHao Xie, Yijie Ding, Yuqing Qian, Prayag Tiwari, Fei Guo 0001. eswa, 235:121157, January 2024. [doi]

RGCNPPIS: A Residual Graph Convolutional Network for Protein-Protein Interaction Site PredictionJian Zhong, Haochen Zhao, Qichang Zhao, Ruikang Zhou, Lishen Zhang, Fei Guo 0001, Jianxin Wang 0001. tcbb, 21(6):1676-1684, November - December 2024. [doi]

2023

MixUNet: Mix the 2D and 3D Models for Robust Medical Image SegmentationJiawei Li 0018, Shizhan Chen, Shiqiang Ma, Fei Guo 0001, Jijun Tang. bibm 2023: 1242-1247 [doi]

Identification of DNA N4-methylcytosine Sites via Multiview Kernel Sparse Representation ModelChengwei Ai, Prayag Tiwari, Hongpeng Yang, Yijie Ding, Jijun Tang, Fei Guo 0001. tai, 4(5):1236-1245, October 2023. [doi]

Low Rank Matrix Factorization Algorithm Based on Multi-Graph Regularization for Detecting Drug-Disease AssociationChengwei Ai, Hongpeng Yang, Yijie Ding, Jijun Tang, Fei Guo 0001. tcbb, 20(5):3033-3043, September - October 2023. [doi]

A multi-scale multi-model deep neural network via ensemble strategy on high-throughput microscopy image for protein subcellular localizationJiaqi Ding, Junhai Xu, Jianguo Wei, Jijun Tang, Fei Guo 0001. eswa, 212:118744, 2023. [doi]

Multi-correntropy fusion based fuzzy system for predicting DNA N4-methylcytosine sitesYijie Ding, Prayag Tiwari, Fei Guo 0001, Quan Zou 0001. inffus, 100:101911, December 2023. [doi]

Laplacian Regularized Sparse Representation Based Classifier for Identifying DNA N4-Methylcytosine Sites via $L_{2,1/2}$L2,1/2-Matrix NormYijie Ding, Wenying He, Jijun Tang, Quan Zou 0001, Fei Guo 0001. tcbb, 20(1):500-511, January - February 2023. [doi]

IK-DDI: a novel framework based on instance position embedding and key external text for DDI extractionMingliang Dou, Jiaqi Ding, Genlang Chen, Junwen Duan, Fei Guo 0001, Jijun Tang. bib, 24(3), May 2023. [doi]

MVML-MPI: Multi-View Multi-Label Learning for Metabolic Pathway InferenceXiaoyi Liu, Hongpeng Yang, Chengwei Ai, Yijie Ding, Fei Guo 0001, Jijun Tang. bib, 24(6), September 2023. [doi]

Improved structure-related prediction for insufficient homologous proteins using MSA enhancement and pre-trained language modelQiaozhen Meng, Fei Guo 0001, Jijun Tang. bib, 24(4), July 2023. [doi]

ComDock: A novel approach for protein-protein docking with an efficient fusing strategyQiaozhen Meng, Fei Guo 0001, Ercheng Wang, Jijun Tang. cbm, 167:107660, December 2023. [doi]

Multi-View Kernel Sparse Representation for Identification of Membrane Protein TypesYuqing Qian, Yijie Ding, Quan Zou 0001, Fei Guo 0001. tcbb, 20(2):1234-1245, March - April 2023. [doi]

Pmf-cpi: assessing drug selectivity with a pretrained multi-functional model for compound-protein interactionsNan Song, Ruihan Dong, Yuqian Pu, Ercheng Wang, Junhai Xu, Fei Guo 0001. jcheminf, 15(1):97, December 2023. [doi]

Development of a component-based integrated modeling framework for urban flood simulationHaocheng Wang, Songshan Yue, Zhuo Zhang, Fei Guo 0001, Yongning Wen, Min Chen 0008, Guonian Lü. envsoft, 169:105839, November 2023. [doi]

A deep multiple kernel learning-based higher-order fuzzy inference system for identifying DNA N4-methylcytosine sitesLeyao Wang, Yijie Ding, Prayag Tiwari, Junhai Xu, Wenhuan Lu, Khan Muhammad, Victor Hugo C. de Albuquerque, Fei Guo 0001. isci, 630:40-52, June 2023. [doi]

2022

A multi-layer multi-kernel neural network for determining associations between non-coding RNAs and diseasesChengwei Ai, Hongpeng Yang, Yijie Ding, Jijun Tang, Fei Guo 0001. ijon, 493:91-105, 2022. [doi]

C-Loss Based Higher Order Fuzzy Inference Systems for Identifying DNA N4-Methylcytosine SitesYijie Ding, Prayag Tiwari, Quan Zou 0001, Fei Guo 0001, Hari Mohan Pandey. tfs, 30(11):4754-4765, 2022. [doi]

Identification of protein-nucleotide binding residues via graph regularized k-local hyperplane distance nearest neighbor modelYijie Ding, Chao Yang, Jijun Tang, Fei Guo 0001. apin, 52(6):6598-6612, 2022. [doi]

Shared subspace-based radial basis function neural network for identifying ncRNAs subcellular localizationYijie Ding, Prayag Tiwari, Fei Guo 0001, Quan Zou 0001. NN, 156:170-178, 2022. [doi]

DeepBLI: A Transferable Multichannel Model for Detecting β-Lactamase-Inhibitor InteractionRuihan Dong, Hongpeng Yang, Chengwei Ai, Guihua Duan, Jianxin Wang, Fei Guo 0001. jcisd, 62(22):5830-5840, 2022. [doi]

BP-DDI: Drug-drug interaction prediction based on biological information and pharmacological textMingliang Dou, Han Han, Genlang Chen, Fei Guo 0001, Jijun Tang. bibm 2022: 410-415 [doi]

Microbe-bridged disease-metabolite associations identification by heterogeneous graph fusionJitong Feng, Shengbo Wu, Hongpeng Yang, Chengwei Ai, Jianjun Qiao, Junhai Xu, Fei Guo 0001. bib, 23(6), 2022. [doi]

Res2Unet: A multi-scale channel attention network for retinal vessel segmentationXuejian Li, Jiaqi Ding, Jijun Tang, Fei Guo 0001. nca, 34(14):12001-12015, 2022. [doi]

Sparse regularized joint projection model for identifying associations of non-coding RNAs and human diseasesPing Li, Prayag Tiwari, Junhai Xu, Yuqing Qian, Chengwei Ai, Yijie Ding, Fei Guo 0001. kbs, 258:110044, 2022. [doi]

Integrating Prior Knowledge with Graph Encoder for Gene Regulatory Inference from Single-cell RNA-Seq DataJiawei Li, Fan Yang, Fang Wang, Yu Rong, Peilin Zhao, Shizhan Chen, Jianhua Yao 0001, Jijun Tang, Fei Guo 0001. bibm 2022: 102-107 [doi]

DeepFusionDTA: Drug-Target Binding Affinity Prediction With Information Fusion and Hybrid Deep-Learning Ensemble ModelYuqian Pu, Jiawei Li, Jijun Tang, Fei Guo 0001. tcbb, 19(5):2760-2769, 2022. [doi]

Identification of drug-side effect association via restricted Boltzmann machines with penalized termYuqing Qian, Yijie Ding, Quan Zou 0001, Fei Guo 0001. bib, 23(6), 2022. [doi]

Identification of DNA N4-methylcytosine sites via fuzzy model on self representationLeyao Wang, Yijie Ding, Junhai Xu, Wenhuan Lu, Jijun Tang, Fei Guo 0001. asc, 122:108840, 2022. [doi]

HDIContact: a novel predictor of residue-residue contacts on hetero-dimer interfaces via sequential information and transfer learning strategyWei Zhang, Qiaozhen Meng, Jianxin Wang, Fei Guo 0001. bib, 23(4), 2022. [doi]

Multi-scale Neighborhood Attention Transformer on U-Net for Medical Image SegmentationNanxing Zhang, Shiqiang Ma, Xuejian Li, Jiahui Zhang, Jijun Tang, Fei Guo 0001. bibm 2022: 1381-1386 [doi]

Identify ncRNA Subcellular Localization via Graph Regularized $k$k-Local Hyperplane Distance Nearest Neighbor Model on Multi-Kernel LearningHaohao Zhou, Hao Wang, Jijun Tang, Yijie Ding, Fei Guo 0001. tcbb, 19(6):3517-3529, 2022. [doi]

2017

Identification of Protein-Ligand Binding Sites by Sequence Information and Ensemble ClassifierYijie Ding, Jijun Tang, Fei Guo 0001. jcisd, 57(12):3149-3161, December 2017. [doi]

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