基本信息
蔡云鹏  男  博导  中国科学院深圳先进技术研究院
电子邮件: yp.cai@siat.ac.cn
通信地址: 深圳市南山区大学城学苑大道1068号B-316
邮政编码: 518055

招生信息

   
招生专业
081203-计算机应用技术
083100-生物医学工程
招生方向
生物信息学,模式识别与机器学习
健康信息学
生物医学大数据

教育背景

2001-09--2007-01   清华大学   博士学位
1997-09--2001-07   清华大学   工学学士学位

工作经历

   
工作简历
2011-06~现在, 中国科学院深圳先进技术研究院, 副研究员,研究员
2007-10~2011-04,美国佛罗里达大学, 博士后

专利与奖励

   
奖励信息
(1) 深圳市“孔雀人才”B类, , 市地级, 2013

出版信息

   
发表论文
[1] Ji, Chaojie, Zheng, Yijia, Wang, Ruxin, Cai, Yunpeng, Wu, Hongyan. Graph Polish: A Novel Graph Generation Paradigm for Molecular Optimization. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS[J]. 2023, 第 4 作者  通讯作者  34(5): 2323-2337, http://dx.doi.org/10.1109/TNNLS.2021.3106392.
[2] Yang, Bokai, Yang, Yujie, Li, Qi, Lin, Denan, Li, Ye, Zheng, Jing, Cai, Yunpeng. Classification of Medical Image Notes for Image Labeling by Using MinBERT. TSINGHUA SCIENCE AND TECHNOLOGY[J]. 2023, 第 7 作者  通讯作者  28(4): 613-627, http://dx.doi.org/10.26599/TST.2022.9010012.
[3] Ji, Chaojie, Chen, Hongwei, Wang, Ruxin, Cai, Yunpeng, Wu, Hongyan. Smoothness Sensor: Adaptive Smoothness-Transition Graph Convolutions for Attributed Graph Clustering. IEEE TRANSACTIONS ON CYBERNETICS[J]. 2022, 第 4 作者  通讯作者  52(12): 12771-12784, http://dx.doi.org/10.1109/TCYB.2021.3088880.
[4] Zhu, Rongxiang, Ji, Chaojie, Wang, Yingying, Cai, Yunpeng, Wu, Hongyan. Heterogeneous Graph Convolutional Networks and Matrix Completion for miRNA-Disease Association Prediction. FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY[J]. 2020, 第 4 作者  通讯作者  8: https://doaj.org/article/219da45e07d0401ea1b75a2e005e7fd7.
[5] Fan, Xiaomao, Hu, Zhejing, Wang, Ruxin, Yin, Liyan, Li, Ye, Cai, Yunpeng. A novel hybrid network of fusing rhythmic and morphological features for atrial fibrillation detection on mobile ECG signals. NEURAL COMPUTING & APPLICATIONS[J]. 2020, 第 6 作者  通讯作者  32(12): 8101-8113, http://dx.doi.org/10.1007/s00521-019-04318-2.
[6] Li, Xia, Cai, Yunpeng. Risk stratification of cutaneous melanoma reveals carcinogen metabolism enrichment and immune inhibition in high-risk patients. AGING-US[J]. 2020, 第 2 作者  通讯作者  12(16): 16457-16475, http://dx.doi.org/10.18632/aging.103734.
[7] Du, Zhenzhen, Yang, Yujie, Zheng, Jing, Li, Qi, Lin, Denan, Li, Ye, Fan, Jianping, Cheng, Wen, Chen, XieHui, Cai, Yunpeng. Accurate Prediction of Coronary Heart Disease for Patients With Hypertension From Electronic Health Records With Big Data and Machine-Learning Methods: Model Development and Performance Evaluation. JMIR MEDICAL INFORMATICS[J]. 2020, 第 10 作者  通讯作者  8(7): https://doaj.org/article/e66f0240f1a4495ab31e31cbd8f96a6b.
[8] 蔡云鹏. A System Analysis of the Relationships between Anemia and Ischemic Stroke Rehabilitation based on RNA-Seq data. Frontiers in Genetics. 2019, 第 1 作者  通讯作者  
[9] Xia Li, Yunpeng Cai. Better prognostic determination and feature characterization of cutaneous melanoma through integrative genomic analysis. AGING (ALBANY NY). 2019, 第 2 作者11(14): 5081-5107, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6746212/.
[10] Wang, Yingying, Wu, Hongyan, Cai, Yunpeng. A benchmark study of sequence alignment methods for protein clustering. BMC BIOINFORMATICS[J]. 2018, 第 3 作者  通讯作者  19(S19): http://ir.siat.ac.cn:8080/handle/172644/14049.
[11] Fan, Xiaomao, Yao, Qihang, Li, Ye, Chen, Runge, Cai, Yunpeng. Mobile GPU-based implementation of automatic analysis method for long-term ECG. BIOMEDICAL ENGINEERING ONLINE[J]. 2018, 第 5 作者  通讯作者  17(1): https://doaj.org/article/ec7486f5020d4ca0b55b6320314d3a5e.
[12] Cai, Yunpeng, Zheng, Wei, Yao, Jin, Yang, Yujie, Mai, Volker, Mao, Qi, Sun, Yijun. ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time. PLOS COMPUTATIONAL BIOLOGY[J]. 2017, 第 1 作者  通讯作者  13(4): http://www.chinair.org.cn/handle/1471x/1747931.
[13] Pu Wang, Ruiquan Ge, Liming Liu, Xuan Xiao, Ye Li, Yunpeng Cai. Multi-label Learning for Predicting the Activities of Antimicrobial Peptides. SCIENTIFIC REPORTS[J]. 2017, 第 6 作者  通讯作者  7(1): http://www.chinair.org.cn/handle/1471x/1747930.
[14] Wang, Yingying, Cai, Yunpeng. A survey on database resources for microRNA-disease relationships. BRIEFINGS IN FUNCTIONAL GENOMICS[J]. 2017, 第 2 作者  通讯作者  16(3): 146-151, https://www.webofscience.com/wos/woscc/full-record/WOS:000405940000003.
[15] Wang, Yingying, Cai, Yunpeng. Obtaining Human Ischemic Stroke Gene Expression Biomarkers from Animal Models: A Cross-species Validation Study. SCIENTIFIC REPORTS[J]. 2016, 第 2 作者  通讯作者  6: http://dx.doi.org/10.1038/srep29693.
[16] Wang, Yingying, Cai, Yunpeng, Miao, Yingbo. Evolving-Pattern Analysis of Transient and Long-Term Biomarkers for Cancers: Hepatocellular Carcinoma as a Case. INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES[J]. 2015, 第 2 作者  通讯作者  7(4): 414-422, https://www.webofscience.com/wos/woscc/full-record/WOS:000362293500010.
[17] Miao, Fen, Cai, YunPeng, Zhang, YuXiao, Li, Ye, Zhang, YuanTing. Risk Prediction of One-Year Mortality in Patients with Cardiac Arrhythmias Using Random Survival Forest. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE[J]. 2015, 第 2 作者2015: https://doaj.org/article/36068317cc604caf9d03868eee084a0d.
[18] Zheng, Zhuoyuan, Cai, Yunpeng, Li, Ye. OVERSAMPLING METHOD FOR IMBALANCED CLASSIFICATION. COMPUTING AND INFORMATICS[J]. 2015, 第 2 作者34(5): 1017-1037, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000368864300003.
[19] Sen, Ruchira, Raychoudhury, Rhitoban, Cai, Yunpeng, Sun, Yijun, Lietze, VerenaUlrike, Boucias, Drion G, Scharf, Michael E. Differential impacts of juvenile hormone, soldier head extract and alternate caste phenotypes on host and symbiont transcriptome composition in the gut of the termite Reticulitermes flavipes. BMCGENOMICS[J]. 2013, 第 3 作者14(1): 491-491, http://dx.doi.org/10.1186/1471-2164-14-491.
[20] Boucias, Drion G, Cai, Yunpeng, Sun, Yijun, Lietze, VerenaUlrike, Sen, Ruchira, Raychoudhury, Rhitoban, Scharf, Michael E. The hindgut lumen prokaryotic microbiota of the termite Reticulitermes flavipes and its responses to dietary lignocellulose composition. MOLECULAR ECOLOGY[J]. 2013, 第 2 作者22(7): 1836-1853, https://www.webofscience.com/wos/woscc/full-record/WOS:000316575800007.
[21] Raychoudhury, R, Sen, R, Cai, Y, Sun, Y, Lietze, V U, Boucias, D G, Scharf, M E. Comparative metatranscriptomic signatures of wood and paper feeding in the gut of the termite Reticulitermes flavipes (Isoptera: Rhinotermitidae). INSECT MOLECULAR BIOLOGY[J]. 2013, 22(2): 155-171, https://www.webofscience.com/wos/woscc/full-record/WOS:000315854100003.
[22] Urquidi, Virginia, Goodison, Steve, Cai, Yunpeng, Sun, Yijun, Rosser, Charles J. A Candidate Molecular Biomarker Panel for the Detection of Bladder Cancer. CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION[J]. 2012, 第 3 作者21(12): 2149-2158, http://dx.doi.org/10.1158/1055-9965.EPI-12-0428.
[23] Wang, Xiaoyu, Cai, Yunpeng, Sun, Yijun, Knight, Rob, Mai, Volker. Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences. ISME JOURNAL. 2012, 第 2 作者6(7): 1277-1280, https://www.webofscience.com/wos/woscc/full-record/WOS:000305631100002.
[24] Sun, Yijun, Cai, Yunpeng, Huse, Susan M, Knight, Rob, Farmerie, William G, Wang, Xiaoyu, Mai, Volker. A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. BRIEFINGS IN BIOINFORMATICS[J]. 2012, 第 2 作者13(1): 107-121, https://www.webofscience.com/wos/woscc/full-record/WOS:000298888200008.
[25] Cai, Yunpeng, Sun, Yijun. ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time. NUCLEIC ACIDS RESEARCH[J]. 2011, 第 1 作者39(14): e95-e95, http://dx.doi.org/10.1093/nar/gkr349.
[26] 蔡云鹏. Fast Implementation of l1 Regularized Learning Algorithms Using Gradient Descent Methods. 10th SIAM International Conference on Data Mining. 2010, 第 1 作者
[27] Sun, Yijun, Cai, Yunpeng, Mai, Volker, Farmerie, William, Yu, Fahong, Li, Jian, Goodison, Steve. Advanced computational algorithms for microbial community analysis using massive 16S rRNA sequence data. NUCLEIC ACIDS RESEARCH[J]. 2010, 第 2 作者38(22): e205-e205, https://www.webofscience.com/wos/woscc/full-record/WOS:000285420300009.
[28] 蔡云鹏. Effective structure learning for EDA via L1-regularizedbayesian networks. Proceedings of the 12th annual conference on Genetic and evolutionary computation conference. 2010, 第 1 作者
[29] Sun, Yijun, Cai, Yunpeng, Liu, Li, Yu, Fahong, Farrell, Michael L, McKendree, William, Farmerie, William. ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. NUCLEIC ACIDS RESEARCH[J]. 2009, 第 2 作者37(10): e76-e76, https://www.webofscience.com/wos/woscc/full-record/WOS:000266966700036.
[30] Cai Yunpeng, Sun Yijun, Li Jian, Goodison Steve, Theeramunkong T, Kijsirikul B, Cercone N, Ho TB. Online Feature Selection Algorithm with Bayesian l(1) Regularization. ADVANCESINKNOWLEDGEDISCOVERYANDDATAMININGPROCEEDINGS. 2009, 第 11 作者5476: 401-+, 
[31] CAI YunPeng, XU Hua, SUN XiaoMin, JIA PeiFa, LIU ZeHua. Duple-EDA and sample density balancing. 中国科学F辑英文版[J]. 2009, 第 1 作者1640-1650, http://lib.cqvip.com/Qikan/Article/Detail?id=31573712.
[32] Cheng Yubo, Cai Yunpeng, Sun Yijun, Li Jian, IEEE. Semi-Supervised Feature Selection Under Logistic I-RELIEF Framework. 19TH INTERNATIONAL CONFERENCE ON PATTERN RECOGNITION, VOLS 1-6. 2008, 第 2 作者1397-+, 
[33] Sun Yijun, Cai Yunpeng, Goodison Steve, IEEE. Combining Nomogram and Microarray Data for Predicting Prostate Cancer Recurrence. 8TH IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOENGINEERING, VOLS 1 AND 2. 2008, 第 2 作者260-+, 
[34] Cai Yunpeng, Sun Xiaomin, Xu Hua, Jia Peifa, ACM. Cross Entropy and Adaptive Variance Scaling in Continuous EDA. GECCO 2007: GENETIC AND EVOLUTIONARY COMPUTATION CONFERENCE, VOL 1 AND 2. 2007, 第 11 作者609-616, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000268226900114.
[35] Cai Yunpeng, Sun Xiaomin, Jia Peifa, Keijzer M. Probabilistic Modeling for continuous EDA with Boltzmann selection and Kullback-Leibeler divergence. GECCO 2006: GENETIC AND EVOLUTIONARY COMPUTATION CONFERENCE, VOL 1 AND 2. 2006, 第 11 作者389-+, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000249917300062.
[36] 蔡云鹏. Global planning from local eyeshot: An implementation of observation-based plan coordination in robocup simulation games. Lecture Notes in Computer Science 2377. 2002, 第 1 作者

科研活动

   
科研项目
( 1 ) 先进院择优中心资助, 参与, 市地级, 2012-01--2012-12
( 2 ) 先进院低成本健康2012年重点突破经费/子课题, 主持, 市地级, 2012-01--2013-12
( 3 ) 基于伪度量空间分割树的超高深度测序比对处理与定量基因组学分析, 主持, 国家级, 2013-01--2015-12
( 4 ) 心脑血管疾病的异构数据整合性预警建模技术, 参与, 省级, 2013-01--2015-12
( 5 ) 面向进化基因组学的高通量测序数据流形建模, 主持, 国家级, 2015-01--2018-12
( 6 ) 穿戴式睡眠监测与夜间心脑血管事件预 警系统, 主持, 省级, 2016-01--2018-12
( 7 ) 健康大数据分析技术工程实验室, 主持, 省级, 2016-01--2018-12
( 8 ) 脑肿瘤网络登记平台的建立和维护, 主持, 国家级, 2015-01--2017-12
( 9 ) 慢病运动康复服务系统在社区的示范应用, 主持, 部委级, 2016-01--2017-12
( 10 ) 面向代谢疾病的肠道菌群分析关键技术研发, 主持, 省级, 2017-07--2019-06
( 11 ) 新型生物医学研究支撑系统的知识整合研究服务体系, 主持, 部委级, 2020-01--2024-12