Jiajie Peng

Publication Activity (10 Years)

Years Active: 2013-2024
Publications (10 Years): 70

Top Topics

Semantic Similarity

Reinforcement Learning

Small Sample Size

Top Venues

Briefings Bioinform.

Publications

Shujian Jiao, Bingxuan Li, Lei Wang, Xiaojin Zhang, Wei Chen, Jiajie Peng, Zhongyu Wei
Beyond ESM2: Graph-Enhanced Protein Sequence Modeling with Efficient Clustering. CoRR (2024)
Tao Wang, Han Shu, Jialu Hu, Yongtian Wang, Jin Chen, Jiajie Peng, Xuequn Shang
Accurately deciphering spatial domains for spatially resolved transcriptomics with stCluster. Briefings Bioinform. 25 (4) (2024)
Jingcong Liang, Junlong Wang, Xinyu Zhai, Yungui Zhuang, Yiyang Zheng, Xin Xu, Xiandong Ran, Xiaozheng Dong, Honghui Rong, Yanlun Liu, Hao Chen, Yuhan Wei, Donghai Li, Jiajie Peng, Xuanjing Huang, Chongde Shi, Yansong Feng, Yun Song, Zhongyu Wei
Overview of the CAIL 2023 Argument Mining Track. CoRR (2024)
Tao Wang, Zhihao Yan, Yiming Zhang, Zhuofei Lou, Xiaozhu Zheng, Duoduo Mai, Yongtian Wang, Xuequn Shang, Bing Xiao, Jiajie Peng, Jin Chen
postGWAS: A web server for deciphering the causality post the genome-wide association studies. Comput. Biol. Medicine 171 (2024)
Menghan Zhang, Jingru Wang, Wei Wang, Guang Yang, Jiajie Peng
Predicting cell-type specific disease genes of diabetes with the biological network. Comput. Biol. Medicine 169 (2024)
Yihang Xiao, Jinyi Liu, Yan Zheng, Xiaohan Xie, Jianye Hao, Mingzhi Li, Ruitao Wang, Fei Ni, Yuxiao Li, Jintian Luo, Shaoqing Jiao, Jiajie Peng
CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis. CoRR (2024)
Xi Zeng, Xiaotian Hao, Hongyao Tang, Zhentao Tang, Shaoqing Jiao, Dazhi Lu, Jiajie Peng
Designing Biological Sequences without Prior Knowledge Using Evolutionary Reinforcement Learning. AAAI (2024)
Wei Chen, Zhiwei Li, Hongyi Fang, Qianyuan Yao, Cheng Zhong, Jianye Hao, Qi Zhang, Xuanjing Huang, Jiajie Peng, Zhongyu Wei
A benchmark for automatic medical consultation system: frameworks, tasks and datasets. Bioinform. 39 (1) (2023)
Jingqi Wang, Jiajie Peng, Zhiming Liu, Hengjun Zhao
HQProtoPNet: An Evidence-Based Model for Interpretable Image Recognition. IJCNN (2023)
Tao Wang, Jinjin Yang, Yifu Xiao, Jingru Wang, Yuxian Wang, Xi Zeng, Yongtian Wang, Jiajie Peng
DFinder: a novel end-to-end graph embedding-based method to identify drug-food interactions. Bioinform. 39 (1) (2023)
Wei Chen, Cheng Zhong, Jiajie Peng, Zhongyu Wei
DxFormer: a decoupled automatic diagnostic system based on decoder-encoder transformer with dense symptom representations. Bioinform. 39 (1) (2023)
Yongtian Wang, Xinmeng Liu, Yewei Shen, Xuerui Song, Tao Wang, Xuequn Shang, Jiajie Peng
Collaborative deep learning improves disease-related circRNA prediction based on multi-source functional information. Briefings Bioinform. 24 (2) (2023)
Zhijie Bao, Wei Chen, Shengze Xiao, Kuang Ren, Jiaao Wu, Cheng Zhong, Jiajie Peng, Xuanjing Huang, Zhongyu Wei
DISC-MedLLM: Bridging General Large Language Models and Real-World Medical Consultation. CoRR (2023)
Tao Wang, Hengbo Xu, Ranye Zhang, Yifu Xiao, Jiajie Peng, Xuequn Shang
Hypergraph-based Gene Ontology Embedding for Disease Gene Prediction. BIBM (2022)
Wei Wang, Ruijiang Han, Menghan Zhang, Yuxian Wang, Tao Wang, Yongtian Wang, Xuequn Shang, Jiajie Peng
A network-based method for brain disease gene prediction by integrating brain connectome and molecular network. Briefings Bioinform. 23 (1) (2022)
Cheng Zhong, Kangenbei Liao, Wei Chen, Qianlong Liu, Baolin Peng, Xuanjing Huang, Jiajie Peng, Zhongyu Wei
Hierarchical reinforcement learning for automatic disease diagnosis. Bioinform. 38 (16) (2022)
Wei Chen, Cheng Zhong, Jiajie Peng, Zhongyu Wei
DxFormer: A Decoupled Automatic Diagnostic System Based on Decoder-Encoder Transformer with Dense Symptom Representations. CoRR (2022)
Tao Wang, Yongzhuang Liu, Quanwei Yin, Jiaquan Geng, Jin Chen, Xipeng Yin, Yongtian Wang, Xuequn Shang, Chunwei Tian, Yadong Wang, Jiajie Peng
Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation. Briefings Bioinform. 23 (1) (2022)
Caiwei Zhen, Yuxian Wang, Jiaquan Geng, Lu Han, Jingyi Li, Jinghao Peng, Tao Wang, Jianye Hao, Xuequn Shang, Zhongyu Wei, Peican Zhu, Jiajie Peng
A review and performance evaluation of clustering frameworks for single-cell Hi-C data. Briefings Bioinform. 23 (6) (2022)
Ruijiang Han, Wei Wang, Yuxi Long, Jiajie Peng
Deep Representation Debiasing via Mutual Information Minimization and Maximization (Student Abstract). AAAI (2022)
Tao Wang, Yongzhuang Liu, Quanwei Yin, Jiaquan Geng, Jin Chen, Xipeng Yin, Yongtian Wang, Xuequn Shang, Chunwei Tian, Yadong Wang, Jiajie Peng
Correction to: Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation. Briefings Bioinform. 23 (3) (2022)
Jiajie Peng, Jinjin Yang, D. Vijay Anand, Xuequn Shang, Kelin Xia
Flexibility and rigidity index for chromosome packing, flexibility and dynamics analysis. Frontiers Comput. Sci. 16 (4) (2022)
Xinyi Mou, Zhongyu Wei, Changjian Jiang, Jiajie Peng
A Two Stage Adaptation Framework for Frame Detection via Prompt Learning. COLING (2022)
Tao Wang, Hui Zhao, Yifu Xiao, Hanzi Yang, Xipeng Yin, Yongtian Wang, Bing Xiao, Xuequn Shang, Jiajie Peng
Discovering eQTL Regulatory Patterns Through eQTLMotif. BIBM (2022)
Wei Chen, Zhiwei Li, Hongyi Fang, Qianyuan Yao, Cheng Zhong, Jianye Hao, Qi Zhang, Xuanjing Huang, Jiajie Peng, Zhongyu Wei
A Benchmark for Automatic Medical Consultation System: Frameworks, Tasks and Datasets. CoRR (2022)
Jiajie Peng, Yuxian Wang, Jiaojiao Guan, Jingyi Li, Ruijiang Han, Jianye Hao, Zhongyu Wei, Xuequn Shang
An end-to-end heterogeneous graph representation learning-based framework for drug-target interaction prediction. Briefings Bioinform. 22 (5) (2021)
Tao Wang, Zhiyuan Shao, Yifu Xiao, Xuchao Zhang, Yitian Chen, Binze Shi, Siyu Chen, Yuxian Wang, Jiajie Peng, Xuequn Shang
Predicting Hepatoma-Related Genes Based on Representation Learning of PPI network and Gene Ontology Annotations. BIBM (2021)
Tianyi Zhao, Shuxuan Lyu, Guilin Lu, Liran Juan, Xi Zeng, Zhongyu Wei, Jianye Hao, Jiajie Peng
SC2disease: a manually curated database of single-cell transcriptome for human diseases. Nucleic Acids Res. 49 (Database-Issue) (2021)
Jiajie Peng, Hansheng Xue, Zhongyu Wei, Idil Tuncali, Jianye Hao, Xuequn Shang
Integrating multi-network topology for gene function prediction using deep neural networks. Briefings Bioinform. 22 (2) (2021)
Tianyi Zhao, Yang Hu, Linda R. Valsdottir, Tianyi Zang, Jiajie Peng
Identifying drug-target interactions based on graph convolutional network and deep neural network. Briefings Bioinform. 22 (2) (2021)
Tianyi Zhao, Jinxin Liu, Xi Zeng, Wei Wang, Sheng Li, Tianyi Zang, Jiajie Peng, Yang Yang
Prediction and collection of protein-metabolite interactions. Briefings Bioinform. 22 (5) (2021)
Jiwen Zhang, Zhongyu Wei, Jianqing Fan, Jiajie Peng
Curriculum Learning for Vision-and-Language Navigation. NeurIPS (2021)
Jiajie Peng, Lu Han, Xuequn Shang
A novel method for predicting cell abundance based on single-cell RNA-seq data. BMC Bioinform. (9) (2021)
Jiwen Zhang, Zhongyu Wei, Jianqing Fan, Jiajie Peng
Curriculum Learning for Vision-and-Language Navigation. CoRR (2021)
Cong Wang, Tianpei Yang, Jianye Hao, Yan Zheng, Hongyao Tang, Fazl Barez, Jinyi Liu, Jiajie Peng, Haiyin Piao, Zhixiao Sun
ED2: An Environment Dynamics Decomposition Framework for World Model Construction. CoRR (2021)
Shuhui Liu, Yupei Zhang, Jiajie Peng, Xuequn Shang
DCAE: Selecting Discriminative Genes on Single-cell RNA-seq Data for Cell-type Quantification. BIBM (2021)
Tao Wang, Yongzhuang Liu, Junpeng Ruan, Xianjun Dong, Yadong Wang, Jiajie Peng
A pipeline for RNA-seq based eQTL analysis with automated quality control procedures. BMC Bioinform. (9) (2021)
Yanjian Zhang, Qin Chen, Yiteng Zhang, Zhongyu Wei, Yixu Gao, Jiajie Peng, Zengfeng Huang, Weijian Sun, Xuanjing Huang
Automatic Term Name Generation for Gene Ontology: Task and Dataset. EMNLP (Findings) (2020)
Jiajie Peng, Linjiao Zhu, Yadong Wang, Jin Chen
Mining Relationships among Multiple Entities in Biological Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (3) (2020)
Leilei Liu, Xianglei Zhu, Yi Ma, Haiyin Piao, Yaodong Yang, Xiaotian Hao, Yue Fu, Li Wang, Jiajie Peng
Combining sequence and network information to enhance protein-protein interaction prediction. BMC Bioinform. (16) (2020)
Tianpei Yang, Jianye Hao, Zhaopeng Meng, Zongzhang Zhang, Weixun Wang, Yujing Hu, Yingfeng Chen, Changjie Fan, Zhaodong Wang, Jiajie Peng
Efficient Deep Reinforcement Learning through Policy Transfer. CoRR (2020)
Tianpei Yang, Jianye Hao, Zhaopeng Meng, Zongzhang Zhang, Yujing Hu, Yingfeng Chen, Changjie Fan, Weixun Wang, Wulong Liu, Zhaodong Wang, Jiajie Peng
Efficient Deep Reinforcement Learning via Adaptive Policy Transfer. IJCAI (2020)
Jiajie Peng, Jingyi Li, Xuequn Shang
A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network. BMC Bioinform. (13) (2020)
Tianpei Yang, Jianye Hao, Zhaopeng Meng, Zongzhang Zhang, Yujing Hu, Yingfeng Chen, Changjie Fan, Weixun Wang, Zhaodong Wang, Jiajie Peng
Efficient Deep Reinforcement Learning through Policy Transfer. AAMAS (2020)
Tianyi Zhao, Yang Hu, Jiajie Peng, Liang Cheng, Pier Luigi Martelli
DeepLGP: a novel deep learning method for prioritizing lncRNA target genes. Bioinform. 36 (16) (2020)
Jiajie Peng, Junya Lu, Donghee Hoh, Ayesha S. Dina, Xuequn Shang, David M. Kramer, Jin Chen
Identifying emerging phenomenon in long temporal phenotyping experiments. Bioinform. 36 (2) (2020)
Jiajie Peng, Guilin Lu, Hansheng Xue, Tao Wang, Xuequn Shang
TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology. BMC Bioinform. (18) (2019)
Hansheng Xue, Jiajie Peng, Jiying Li, Xuequn Shang
Integrating Multi-Network Topology via Deep Semi-supervised Node Embedding. CIKM (2019)
Jiajie Peng, Xiaoyu Wang, Xuequn Shang
Combining gene ontology with deep neural networks to enhance the clustering of single cell RNA-Seq data. BMC Bioinform. (8) (2019)
Hansheng Xue, Jiajie Peng, Xuequn Shang
Towards Gene Function Prediction via Multi-Networks Representation Learning. AAAI (2019)
Yongtian Wang, Liran Juan, Jiajie Peng, Tianyi Zang, Yadong Wang
LncDisAP: a computation model for LncRNA-disease association prediction based on multiple biological datasets. BMC Bioinform. (16) (2019)
Jiajie Peng, Lu Han, Xuequn Shang
A deconvolution method for predicting cell abundance based on single cell RNA-seq data. BIBM (2019)
Leilei Liu, Yi Ma, Xianglei Zhu, Yaodong Yang, Xiaotian Hao, Li Wang, Jiajie Peng
Integrating Sequence and Network Information to Enhance Protein-Protein Interaction Prediction Using Graph Convolutional Networks. BIBM (2019)
Hansheng Xue, Jiajie Peng, Xuequn Shang
Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO. BMC Syst. Biol. (2) (2019)
Jiajie Peng, Weiwei Hui, Qianqian Li, Bolin Chen, Jianye Hao, Qinghua Jiang, Xuequn Shang, Zhongyu Wei
A learning-based framework for miRNA-disease association identification using neural networks. Bioinform. 35 (21) (2019)
Yongtian Wang, Liran Juan, Jiajie Peng, Tianyi Zang, Yadong Wang
Prioritizing candidate diseases-related metabolites based on literature and functional similarity. BMC Bioinform. (18) (2019)
Jiajie Peng, Xuanshuo Zhang, Weiwei Hui, Junya Lu, Qianqian Li, Shuhui Liu, Xuequn Shang
Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach. BMC Syst. Biol. 12 (S-2) (2018)
Jiajie Peng, Guilin Lu, Hansheng Xue, Tao Wang, Xuequn Shang
TSGOE: A web tool for tissue-specific gene ontology enrichment. BIBM (2018)
Jiajie Peng, Weiwei Hui, Xuequn Shang
Measuring phenotype-phenotype similarity through the interactome. BMC Bioinform. (5) (2018)
Hansheng Xue, Jiajie Peng, Xuequn Shang
Deep Feature Learning of Multi-Network Topology for Node Classification. CoRR (2018)
Yongtian Wang, Liran Juan, Jiajie Peng, Tianyi Zang, Yadong Wang
Predicting candidate disease-related lncRNAs based on network random walk. BIBM (2018)
Tao Wang, Jiajie Peng, Yadong Wang, Jin Chen
Identifying Representative Network Motifs for Inferring Higher-order Structure of Biological Networks. BIBM (2018)
Jiajie Peng, Qianqian Li, Xuequn Shang
Investigations on factors influencing HPO-based semantic similarity calculation. J. Biomed. Semant. (1) (2017)
Jiajie Peng, Honggang Wang, Junya Lu, Weiwei Hui, Yadong Wang, Xuequn Shang
Identifying term relations cross different gene ontology categories. BMC Bioinform. 18 (16) (2017)
Jiajie Peng, Weiwei Hui, Xuequn Shang
Measuring phenotype-phenotype similarity through the interactome. BIBM (2017)
Jiajie Peng, Hansheng Xue, Yukai Shao, Xuequn Shang, Yadong Wang, Jin Chen
A novel method to measure the semantic similarity of HPO terms. Int. J. Data Min. Bioinform. 17 (2) (2017)
Jiajie Peng, Hansheng Xue, Yukai Shao, Xuequn Shang, Yadong Wang, Jin Chen
Measuring phenotype semantic similarity using Human Phenotype Ontology. BIBM (2016)
Jiajie Peng, Tao Wang, Jixuan Wang, Yadong Wang, Jin Chen
Extending gene ontology with gene association networks. Bioinform. 32 (8) (2016)
Yongzhuang Liu, Jian Liu, Jianguo Lu, Jiajie Peng, Liran Juan, Xiaolin Zhu, Bingshan Li, Yadong Wang
Joint detection of copy number variations in parent-offspring trios. Bioinform. 32 (8) (2016)
Jiajie Peng, Qianqian Li, Bolin Chen, Jialu Hu, Xuequn Shang
Analyzing factors involved in the HPO-based semantic similarity calculation. BIBM (2016)
Jiajie Peng, Hongxiang Li, Yadong Wang, Jin Chen
A web tool for measuring gene semantic similarities by combining gene ontology and gene co-function networks. BCB (2015)
Qinghua Jiang, Jixuan Wang, Xiaoliang Wu, Rui Ma, Tianjiao Zhang, Shuilin Jin, Zhijie Han, Renjie Tan, Jiajie Peng, Guiyou Liu, Yu Li, Yadong Wang
LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression. Nucleic Acids Res. 43 (Database-Issue) (2015)
Jiajie Peng, Sahra Uygun, Taehyong Kim, Yadong Wang, Seung Y. Rhee, Jin Chen
Measuring semantic similarities by combining gene ontology annotations and gene co-function networks. BMC Bioinform. 16 (2015)
Jiajie Peng, Hongxiang Li, Qinghua Jiang, Yadong Wang, Jin Chen
An integrative approach for measuring semantic similarities using gene ontology. BMC Syst. Biol. 8 (S-5) (2014)
Jiajie Peng, Yadong Wang, Jin Chen
Towards integrative gene functional similarity measurement. BMC Bioinform. 15 (S-2) (2014)
Jiajie Peng, Jin Chen, Yadong Wang
Identifying cross-category relations in gene ontology and constructing genome-specific term association networks. BMC Bioinform. 14 (S-2) (2013)