Distinguished Professor
Dept. of Computer Science and Information Engineering
National Cheng Kung University, Tainan, Taiwan
TEL: +886-6-275-7575 ext.62534
FAX: +886-6-274-7076
E-mail: jchiang@mail.ncku.edu.tw
Research Interests:


  • Biomedical Information Retrieval
  • Artificial Intelligence
  • Mobile Computing
  • Computational Intelligence
  • Cloud Healthcare
  • Cancer and Stem Cell Research
  • Big data Analysis

Dr. Jung-Hsien Chiang received his M.S. and Ph.D. degrees in computer engineering from the University of Missouri, Columbia, in 1991 and 1995, respectively. He worked as a researcher at the Computer and Communication Laboratory, Industrial Technology Research Institute, the largest information technology research institute in Taiwan. He joined the faculty of the National Cheng Kung University Computer Science and Information Engineering in February 1999 and is currently a professor of the department.

He performed his first research in computational intelligence in 1995 when he developed on algorithms for multimedia information server in cyber community. He led teams involved in the development of adaptive real-time multimedia transmission mechanism in intelligent gateway for D-Link Inc. in Taiwan. He developed and implemented fuzzy set based algorithms for user profiling and data mining. Dr. Chiang and his students created the technological foundation for the interpretations of fuzzy clustering by two novel algorithms based on support vectors, “adaptive cell growing” and “fuzzy cover”, which use competitive multisphere cells and fuzzy proximate functions for the iterative learning process respectively. The algorithms facilitate the exploration of grouping and separation uncertainty in producing meaningful interpretations of structure in the data. This research has been cited more than 400 times in Google Scholar.

In the early 2000s Chiang and his colleagues began exploring the idea of fuzzy algorithms in bioinformatics. Dr. Chiang’s prior research in bioinformatics has focused on intelligent text mining. He has contributed new techniques for developing biomedical text mining models, including data analytics, pattern extraction and literature classification. This leads to implementation of software prototypes to assist biomedical researchers in rapidly extracting useful knowledge from huge number of biomedical documents and to improve understanding of gene function annotation in the Human Genome Project. In 2003 the team was able to provide the available open source and the results have been published in Bioinformatics (Oxford University Press). This was the first study on the developing an ontology-based textmining system to efficiently extract knowledge from biomedical literature about the functions of gene products, and the web service has been utilized by more than 20 research teams and accessed more than 5,000 times since 2003.

His current research interests include fuzzy modeling in bioinformatics, text mining, pattern clustering, and modeling of systems biology problems. The research team he leads has cooperated with the Institute for Systems Biology (ISB) in Seattle, one of the top biomedical research organizations in the world. By combining its specialty in bioinformatics and computational biology, they assist the researchers in ISB to find either possible innovatively cancer related mechanisms or obtain a great quantity of experimental data for further analysis.


  1. D.A. Devyatkin1, A.I. Molodchenkov1, A.V. Lukin1, Y.S. Kim, A.A. Boyko, P.A. Karalkin, J.-H. Chiang, G.D. Volkova, A.Yu. Lupatov “Towards Automated Meta-analysis of Biomedical Texts in the Field of Cell-based Immunotherapy ” EXPERIMENTAL RESEARCH
  2. Pei-Yi Hao, Weng-Hang Cheang, Jung-Hsien Chiang “Real-time Event Embedding for POI Recommendation” Neurocomputing
  3. Kun-Hsing Yu, Tsung-Lu Michael Lee, Yu-Ju Chen, Christopher Re, Samuel C Kou, Jung-Hsien Chiang, Michael Snyder, Isaac S Kohane “A Cloud-Based Metabolite and Chemical Prioritization System for the Biology/Disease-driven Human Proteome Project” 2018, Journal of proteome research, 17(4)1383-1396 DOI: 10.1021/acs.jproteome.7b00772
  4. Jui-Hung Chang, Chen-En Tsai, Jung-Hsien Chiang “Using Heterogeneous Social Media as Auxiliary Information to Improve Hotel Recommendation Performance” 2018, IEEE Access, 6 42647-42660 DOI:10.1109/ACCESS.2018.2855690
  5. Yu Kun-Hsing, Lee Tsung-Lu Michael, Wang Chi-Shiang, Chen Yu-Ju, Re Christopher, Kou Samuel C., Chiang Jung-Hsien*, Kohane Isaac S., Snyder Michael “Systematic Protein Prioritization for Targeted Proteomics Studies through Literature Mining” 2018, Journal of proteome research, 17(4)1383-1396 DOI: 10.1021/acs.jproteome.7b00772
  6. Chia-Jung Yang, Jung-Hsien Chiang “Gene ontology concept recognition using named concept: understanding the various presentations of the gene functions in biomedical literature” Database: The Journal of Biological Databases and Curation
  7. Chi-Shiang Wang, Pei-Ju Lin, Ching-Lan Cheng, Shu-Hua Tai,Yea-Huei Kao Yang, Jung-Hsien Chiang “Detecting potential adverse drug reactions using a deep neural network model” 2018, Journal of Medical Internet Research
  8. Hsih-Te Yang, Jiun-Huang Ju, Yue-Ting Wong, Ilya Shmulevich, Jung-Hsien Chiang “Literature-based Discovery of New Candidates for Drug Repurposing” 2017, Briefings in bioinformatics, 18(3)488-497 doi: 10.1093/bib/bbw030
  9. Kim YS, Kaidina AM, Chiang JH, Yarygin KN, Lupatov AY “Cancer Stem Cell Molecular Markers Verified in vivo” 2017, BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY
  10. G.Chin-Lun Hung, MS Li, Yen-Lin Chen, JH Chiang “Capturing depression with your smartphone: Validity and utilization of iHOPE for depressed patients in Taiwan” 2016, European Psychiatry,doi:10.1016/j.eurpsy.2016.01.758
  11. Hsih-Te Yang, Jiun-Huang Ju, Yue-Ting Wong, Ilya Shmulevich, Jung-Hsien Chiang “Literature-based discovery of new candidates for drug repurposing” 2015, Briefings in bioinformatics,doi: 10.1093/bib/bbw030
  12. Chiang, Jung-Hsien, Ju, Jiun-Huang 2014 “Discovering novel protein-protein interactions by measuring the protein semantic similarity from the biomedical literature” 2014, Journal Of Bioinformatics and Computational Biology,12(6)
  13. Chiang, Jung-Hsien; Yang, Pei-Ching; Tu, Hsuan 2014 “Pattern analysis in daily physical activity data for personal health management” 2014, Pervasive and mobile computing, 13, 13-25
  14. Jung-Hsien Chiang, Wan-Shu Cheng, Leroy Hood, and Qiang Tian 2014 “An Epigenetic Biomarker Panel for Glioblastoma Multiforme Personalized Medicine through DNA Methylation Analysis of Human Embryonic Stem Cell-like Signature” 2014, OMICS: A Journal of Integrative Biology, 18(5), 310-323
  15. Jennifer M Holden, Ludek Koreny, Samson Obado, Alexander V Ratushny, Wei-Ming Chen, Jung-Hsien Chiang, Steven Kelly, Brian T Chait, John D Aitchison, Michael P Rout, Mark C Field 2014 “Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity” 2014, Molecular biology of the cell, 25(9), 1421-1436
  16. JH Chiang*, CH Lin 2014 “NCS: Incorporating positioning data to quantify nucleosome stability in yeast” 2014, Bioinformatics, 30(6), 761-767
  17. Samuel A Danziger, Alexander V Ratushny, Jennifer J Smith, Ramsey A Saleem, Yakun Wan, Christina E Arens, Abraham M Armstrong, Katherine Sitko, Wei-Ming Chen, Jung-Hsien Chiang, David J Reiss, Nitin S Baliga, John D Aitchison* 2014 “Molecular mechanisms of system responses to novel stimuli are predictable from public data” 2014, Nucleic acids research, 42(3), 1442-1460
  18. Cheng, Wan-Shu; Chiang, Jung-Hsien 2013 “CGPredictor: a systematic integrated analytic tool for mining and examining genome-scale cancer independent prognostic epigenetic marker panels” 2013, Bmc Systems biology 7(6), S10
  19. Wei-Ming Chen, Samuel A Danziger, Jung-Hsien Chiang, John D Aitchison* 2013 “PhosphoChain: A novel algorithm to predict kinase and phosphatase networks from high-throughput expression data” 2013, Bioinformatics 29(19), 2435-44
  20. Liu T, Tsai C-H, Lee W-B, Chiang J-H 2013 “Optimizing Information in Next-Generation-Sequencing (NGS) Reads for Improving De Novo Genome Assembly” 2013, PLoS ONE, 8(7), e69503
  21. Van de Vosse DW, Wan Y, Lapetina DL, Chen WM, Chiang JH, Aitchison JD, Wozniak RW 2013 “A Role for the Nucleoporin Nup170p in Chromatin Structure and Gene Silencing” 2013, CELL, 152(5), 969-983
  22. Lee TLM, Chiang JH 2012 “A Systems Biology Approach to Solving the Puzzle of Unknown Genomic Gene-Function Association Using Grid-Ready SVM Committee Machines” 2012, Computational Intelligence Magazine, IEEE, 16(2), 1087-1095
  23. Darby Tien-Hao Chang, Chao-Hsuan Ke, Jung-Hsin Lin and Chiang, J.H 2012 “AutoBind: automatic extraction of protein–ligand-binding affinity data from biological literature” 2012, Bioinformatics,28, 2162-2168
  24. Wan, YK ;Chen, WM; Xing, Jie ;Tan, JY ;Li, Bing ;Chen, HY;Lin, ZX; Chiang, JH; Saleem Ramsey 2011 “Transcriptome profiling reveals a novel role for trichostatin A in antagonizing histone chaperone Chz1 mediated telomere anti-silencing” 2011, FEBS Letters,585(15), 2519-2525
  25. Lin, JW, Chang, CH ; Lin, MW, Ebell, MH, Chiang, JH 2011 “Automating the process of critical appraisal and assessing the strength of evidence with information extraction technology” 2011, JOURNAL OF EVALUATION IN CLINICAL PRACTICE, 17(4), 832-838
  26. Chiang, JH;Liu, HH;Huang, YT 2011 “Condensing biomedical journal texts through paragraph ranking” 2011, BIOINFORMATICS,27(8), 1143-1149
  27. Yeh, CY; Shin, SM; Yeh, HH; Wu, TJ; Shin, JW; Chang, TY; Raghavaraju, G; Lee, CT; Chiang, JH; Tseng, VS; Lee, YCG; Shen, CH; Chow, NH; Liu, HS 2011 “Transcriptional activation of the Axl and PDGFR-alpha by c-Met through a ras- and Src-independent mechanism in human bladder cancer” 2011, BMC CANCER,11(139)
  28. Chao, SY; Chiang, JH; Huang, AM;Chang, WS 2011 “An integrative approach to identifying cancer chemoresistance-associated pathways” 2011, BMC MEDICAL GENOMICS,4(23)
  29. Wan, YK ;Chiang, JH ;Lin, CH; Arens, CE ; Saleem, RA ; Smith, JJ ; Aitchison, JD 2010 “Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing” 2010, Nucleic Acids Res, 38, 1431 – 1440
  30. Chiang, JH;Lin, JW;Yang, CW 2010 “Automated evaluation of electronic discharge notes to assess quality of care for cardiovascular diseases using Medical Language Extraction and Encoding System (MedLEE)” 2010, JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION,17 (3) 245-252
  31. Hao, PY;Chiang, JH;Lin, YH 2009 “A new maximal-margin spherical-structured multi-class support vector machine” 2009, APPLIED INTELLIGENCE, 30(2), 98-111
  32. Wan, YK;Saleem, RA; Ratushny, AV; Roda, O; Smith, JJ; Lin, CH; Chiang, JH and Aitchison, JD 2009 “Role of the Histone Variant H2A.Z/Htz1p in TBP Recruitment, Chromatin Dynamics, and Regulated Expression of Oleate-Responsive Genes” 2009, Molecular and Cellular Biology, 29, 2346-2358
  33. Majetl, R;Becker, MW;Tian, Q; Lee, TLM; Yan, XW; Liu, R; Chiang, JH; Hood, L;Clarke, MF and Weissman, IL 2009 “Dysregulated gene expression networks in human acute myelogenous leukemia stem cells” 2009, Proceedings of the National Academy of Sciences of the United States of America, 106, 3396-3401
  34. Yin, ZX;Chiang,JH 2008 “Novel Algorithm for Coexpression Detection in Time-Varying Microarray Data Sets” 2008, IEEE/ACM Trans on Computational Biology and Bioinformatics, 5(1), 120-135
  35. Chiang,JH ;Ho, SH 2008 “A combination of rough-based feature selection and RBF neural network for classification using gene expression data” 2008, IEEE Trans on Nanobioscience, 7(1), 91-99
  36. Hao, PY, Chiang,JH 2008 “Fuzzy regression analysis by support vector learning approach” 2008, IEEE Trans. on Fuzzy Systems, 16(2), 428-441
  37. Chiang,JH ;Ho, SH; Wang, WH 2008 “Similar genes discovery system (SGDS): Application for predicting possible pathways by using GO semantic similarity measure” 2008, Expert Systems With Applications, 35(3), 1115-1121
  38. Chiang,JH;Chao,SY 2007 “Modeling Human Cancer-Related Regulatory Modules by GA-RNN Hybrid Algorithms” 2007, BMC Bioinformatics, 8:91
  39. Chiang,JH ;Yin,ZX 2007 “Unsupervised minor prototype detection using an adaptive population partitioning algorithm” 2007, Pattern Recognition, 40, 3132-3145
  40. Chiang,JH; Liu, HS; Chao,SY; Chen,CY 2007 “Discovering Gene-Gene Relations from Sequential Sentence Patterns in Biomedical Literature” 2007, Expert Systems With Applications, 33, 1036-1041
  41. Hao,PY; Chiang,JH;Tu,YK 2007 “Hierarchically SVM Classification Based on Support Vector Clustering Method and Its Application to Document Categorization” 2007, Expert Systems With Applications, 33, 627-635
  42. Chiang,JH; Shin,JW ;Liu, HH; Chin,CL 2006 “GeneLibrarian:an effective gene-information summarization and visualization system” 2006, BMC Bioinformatics, 7:392
  43. Hao, PY;Chiang,JH 2006 “Pruning and model-selecting algorithms in the RBF frameworks constructed by support vector learning” 2006, International Journal of Neural Systems, 16(4), 283-293
  44. Chiang,JH;Yu,HC 2005 “Literature Extraction of Protein Functions Using Sentence Pattern Mining” 2005, IEEE Trans. on Knowledge and Data Engineering, 17(8), 1088-1098
  45. Chiang,JH ;Hao,PY 2004 “Support Vector Learning Mechanism for Fuzzy Rule-Based Modeling: A New Approach” 2004, IEEE Trans. on Fuzzy Systems, 12(1), 1-12
  46. Chiang,JH ;Yu,HC; Hsu,HJ 2004 “GIS: A Biomedical Text-Mining System for Gene Information Discovery” 2004, Bioinformatics, 20(1), 120-121
  47. Chiang,JH;Yin, ZX 2004 “A New Fuzzy Cover Approach to Clustering” 2004, IEEE Trans. on Fuzzy Systems, 12(2), 199-208