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Journal papers:

  1. G.-B. Chen and H.-Y. Kao, "Re-organized Topic Modeling for Micro-blogging Data, ˇ§ accepted by Intelligent Data Analysis, 2017.
  2. S.-L. Wang, Y.-C. Tsai, T.-P. Hong, H.-Y. Kao, "k^{-}-anonymization of multiple shortest paths, " Soft Computing, 1-12, doi:10.1007/s00500-016-2032-2, 2016.
  3. H.-C. Lee, Y.-Y. Hsu, and H.-Y. Kao, "AuDis: an automatic CRF-enhanced disease normalization in biomedical text, " Database Vol. 2016: article ID baw091; doi:10.1093/database/baw091, 2016.
  4. H.-J. Dai, C.-H. Wei, H.-Y. Kao, R.-L. Liu, R. T.-H. Tsai, Z. Lu, "Text Mining for Translational Bioinformatics, "BioMed Research International, 2015.
  5. G.-B. Chen and H.-Y. Kao, "Word Co-occurrence Augmented Topic Model in Short Text, " International Journal of Computational Linguistics & Chinese Language Processing, Vol. 20, No. 2, December 2015.
  6. C.-H. Wei, H.-Y. Kao, and Zhiyong Lu, ˇ§GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains,ˇ¨ BioMed Research International, vol. 2015, Article ID 918710, 7 pages, 2015. doi:10.1155/2015/918710
  7. Y.-Y. Hsu and H.-Y. Kao, "Curatable Named-entity Recognition using Semantic Relations, " IEEE/ACM Transactions on Computational Biology and Bioinformatics (IEEE TCBB), Vol. 12, Issue 4, July-Aug. 2015.
  8. S.-L. Wang, Y.-C. Tsai, H.-Y. Kao, T.-P. Hong, "On anonymizing transactions with sensitive items, " Applied Intelligence, Vol. 4, No.41, pp. 1043-1-58, 2014.
  9. Y.-W. Guo, Y.-T. Tang and H.-Y. Kao, "Genealogical-based Method for Multiple Ontology Self-extension in MeSH, "IEEE Transactions on NanoBioscience (IEEE TNB), Vol. 13, No. 2, PP 785-792, June 2014.
  10. Y.-J. Chang, Y.-C. Tsai, and H.-Y. Kao, "Bipartite Editing Prediction in Wikipedia, "Journal of Information Science and Engineering Vol. 30, No. 3, 587-603, May 2014.
  11. H.-D. Huang, C.-S. Lee, M.-H. Wang, H.-Y. Kao, "IT2FS-based ontology with soft-computing mechanism for malware behavior analysis, "Soft Computing 18(2): 267-284, 2014.
  12. Y.-T. Tang, H.-Y. Kao, S.-J. Tsai, H.-C. Wang, "A semi-supervised, weighted pattern-learning approach for extraction of gene regulation relationships from scientific literature, " International Journal of Data Mining and Bioinformatics Vol. 9, No. 4, pp.401 - 416, 2014.
  13. J.-C. Hsiao, C.-H. Wei and H.-Y. Kao, "Gene Name Disambiguation using Multi-Scope Species Detection, " IEEE/ACM Transactions on Computational Biology and Bioinformatics (IEEE TCBB), doi: 10.1109/TCBB.2013.139, Vol. 11, NO. 1, Jan/Feb, 2014.
  14. Y.-Y. Hsu, W.-J. Chen, S.-H. Chen and H.-Y. Kao, "Using Hidden Markov Models to Predict DNA-binding Proteins with Sequence and Structure Information, "Soft Computing DOI 10.1007/s00500-013-1210-8, Dec 2013.
  15. Y.-Y. Hsu, H.-Y. Chen, H.-Y. Kao,"Using a Search Engine-based Mutually Reinforcing Approach to Assess the Semantic Relatedness of Biomedical Terms, " PLoS ONE 8(11): e77868. doi:10.1371/journal.pone.0077868, Nov 2013.
  16. H.-C. Wang, T.-K. Kooi, H.-Y. Kao, S.-C. Lin, S.-J. Tsai, "Using positive and negative patterns to extract information from journal articles regarding the regulation of a target gene by a transcription factor, " Computers in Biology and Medicine, DOI: 10.1016/j.compbiomed.2013.10.011, 2013.
  17. Y.-Y. Hsu, H.-Y. Kao, "CoIN: a network analysis for document triage," Database-The Journal of Biological Databases and Curation, Vol. 2013: bat076 doi:10.1093/database/bat076, November 11, 2013.
  18. S.-L. Wang, Y.-C. Tsai, H.-Y. Kao, I-H. Ting, T.-P. Hong, "Shortest Paths Anonymization on Weighted Graphs, " International Journal of Software Engineering and Knowledge Engineering 23(1): 65-80, 2013.
  19. C.-H. Wei and H.-Y. Kao,"Unsupervised Corpus Distillation for Represented Indicator Measurement on Focus Species Detection," International Journal of Data Mining and Bioinformatics, 8(4): 413-426, 2013.
  20. W.-T. Yang, and H.-Y. Kao, "Measuring Semantic Relatedness using Wikipedia Signed Network," Journal of Information Science and Engineering Vol. 29, No. 4, 615-630, July 2013.
  21. C.-H. Wei, H.-Y. Kao, Z. Lu, "PubTator: a Web-based text mining tool for assisting Biocuration," Nucleic Acids Research 2013 Jul;41(Web Server issue):W518-22, doi: 10.1093/nar/gkt441 (SCI IF: 8.026, Rank=26/290)
  22. S. V. Landeghem, J. Bjorne, C.-H. Wei, K. Hakala, S. Pyysalo, S. Ananiadou, H.-Y. Kao, Z. Lu, T. Salakoski, Y. V. de Peer, F. Ginter, "Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization," PLoS ONE, April 2013. doi/10.1371/journal.pone.0055814.
  23. C.-H. Wei, B. R. Harris, H.-Y. Kao, Z. Lu, ˇ§tmVar: A text mining approach for extracting sequence variants in biomedical literatureˇ¨ Bioinformatics, 29(11):1433-9, 2013, doi:10.1093/bioinformatics/btt156.
  24. Z.-H. Yang and H.-Y. Kao, "Location-Aware Time-Series Clustering on Optimal Sensor Arrangement, " International Journal of Electrical Engineering, Vol.20, No.2, PP.65-71, April 2013.
  25. C.-H. Wei, B. R. Harris, D. Li, T. Z. Berardini, E. H., H.-Y. Kao, and Z. Lu, ˇ§Accelerating literature curation with text mining tools: A case study of using PubTator to curate genes in PubMed abstracts,ˇ¨ Database-The Journal of Biological Databases and Curation, 2012 Nov 17;2012:bas041. doi: 10.1093/database/bas041, 2012 (SCI IF: 3.179, Rank=4/47).
  26. Y.-T. Tang and H.-Y. Kao, " Augmented Transitive Relationships with High Impact Protein Distillation in Protein Interaction Prediction," BBA - Proteins and Proteomics, Volume 1824, Issue 12, December 2012, Pages 1468ˇV1475, DOI:10.1016/j.bbapap.2012.05.013. (SCI IF=2.773 Rank=36/73)
  27. C.-H. Wei, H.-Y. Kao, Z. Lu, "SR4GN: A Species Recognition Software Tool for Gene Normalization, " PLoS ONE 7(6): e38460. doi:10.1371/journal.pone.0038460, 2012.(SCI IF=4.351 Rank=12/86)
  28. Z. Lu, H.-Y. Kao, C.-H. Wei, et. al., "The Gene Normalization Task in BioCreative III, "BMC Bioinformatics 12(Suppl 8):S2, 2011. (SCI IF= 4.029 Rank=4/37)
  29. C.-H. Wei and H.-Y. Kao, "Cross-species gene normalization by species inference," BMC Bioinformatics 12(Suppl 8):S5, 2011. (SCI IF= 4.029 Rank=4/37)
  30. Y.-T. Tang, S.-J. Li, H.-Y. Kao, S.-J. Tsai and H.-C. Wang, ˇ§Using Unsupervised Patterns to Extract Gene Regulation Relationships for Network Construction," PLoS ONE 6(5): e19633. doi:10.1371/journal.pone.0019633, May 2011.(SCI IF=4.351 Rank=12/86)
  31. H.-C. Wang, Y.-S. Chen, H.-Y. Kao and S.-J. Tsai, ˇ§Inference of transcriptional regulatory network by bootstrapping patterns," Bioinformatics, 27(10), 1422-1428, 2011. (SCI IF= 4.926 Rank=2/37)
  32. C.-L. Lin, H.-Y. Kao, "Blog Popularity Mining Using Social Interconnection Analysis," IEEE Internet Computing, vol. 14, no. 4, pp. 41-49, July/August, 2010. (SCI IF= 2.514 Rank=7/99)
  33. H.-Y. Kao, J.-M. Ho and M.-S. Chen, "WISDOM: Web Intra-page Informative Structure Mining based on Document Object Model," IEEE Trans. on Knowledge and Data Engineering, Vol. 17, No. 5, May 2005.
  34. H.-Y. Kao, S.-H. Lin, J.-M. Ho and M.-S. Chen, "Mining Web Information Structures and Contents based on Entropy Analysis," IEEE Trans. on Knowledge and Data Engineering, Vol. 16, No. 1, January 2004.

Conference papers:

  1. G. Tumenbayar and H.-Y. Kao, "Topic Suggestion by Bayesian Network Enhanced Tag Inference in Community Question Answering, " Proc. of the 2016 Conference on Technologies and Applications of Artificial Intelligence (TAAI-2016), November 25-27, 2016.
  2. H.-C. Lee, Y.-Y. Hsu, H.-Y. Kao, "An enhanced CRF-based system for disease name entity recognition and normalization on BioCreative V DNER Task, " Proc. of the Fifth BioCreative Challenge Evaluation Workshop, 2015.
  3. S.-T. Huang, P.-S. Li, H.-Y. Kao, "Identification of item features in microblogging data, "Proc. of the 2015 Conference on Technologies and Applications of Artificial Intelligence (TAAI-2015), November 20-22, 2015.
  4. J.-D. Chen and H.-Y. Kao, "LDA Based Semi-supervised Learning from Streaming Short Text, " Proc. of the 2nd IEEE International Conference on Data Science and Advanced Analytics (DSAA-2015), Oct. 19-21, 2015.
  5. G.-B. Chen and H.-Y. Kao, "Re-organized Topic Modeling for Micro-blogging Data, " Proc. of the 5th ASE International Conference on Big Data (BigData 2015), Oct 7-9, 2015.
  6. Y.-C. Tsai, S.-L. Wang, T.-P. Hong, H.-Y. Kao, "Extending [K 1, K 2] Anonymization of Shortest Paths for Social Networks, " Proc. of the 2015 International Conference on Multidisciplinary Social Networks Research, 2015.
  7. Y.-C. Chen and H.-Y. Kao, "One-Class Recommendation System with PU learning, " Proc. of 6th International Workshop on Social Recommender Systems (SRS 2015), in conjunction with 21st ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD 2015), Aug. 10, 2015.
  8. Y.-Y. Hsu and H.-Y. Kao, "Curatable Named-entity Recognition using Semantic Relations, " Proc. of the 25th International Conference on Genome Informatics (GIW-2014), Dec. 15-17, 2014.
  9. Z.-H. Yang and H.-Y. Kao, User preference space partition and product filters for reverse top-k queries, " Prof. of the 1st IEEE International Conference on Data Science and Advanced Analytics (DSAA-2014), Oct. 30 - Nov. 1, 2014.
  10. M.-C. Chen, H.-Y. Kao, "Latent Features Based Prediction on New Usersˇ¦ Tastes, " Proc. of the 18th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD-2014), May 13-16, 2014.
  11. Y.-W. Guo and H.-Y. Kao, "Genealogical-based Method for Ontology Self-extension in MeSH, " Proc. of 2013 IEEE International Conference on Bioinformatics & Biomedicine (BIBM-2013), December 18-21, 2013.
  12. Y.-X. Lin and H.-Y. Kao, "An Adaptive Page Clustering Based weighting Method for Information Retrieval, " Proc. of the 2013 Conference on Technologies and Applications of Artificial Intelligence (TAAI 2013), December 6-8, 2013.
  13. J.-C. Hsiao, C.-H. Wei and H.-Y. Kao, "Gene Name Disambiguation using Multi-Scope Species Detection, " Proc. of the 24th International Conference on Genome Informatics (GIW-2013), 2013.
  14. J.-Y. Wang, and H.-Y. Kao, "RSOL: A Trust-based Recommender System with an Opinion Leadership Measurement for Cold Start Users, " Proc. of the Ninth Asia Information Retrieval Symposium (AIRS-2013), December 9-11, 2013.
  15. Y.-T. Chen and H.-Y. Kao, "Up or Down? Click-Through Rate Prediction from Social Intention for Search Advertising, "Proc. of the 15th International Conference on Information Integration and Web-based Applications & Services (iiWAS-2013), pp. 102-106, December 2-4, 2013.
  16. Y.-J. Tai and H.-Y. Kao, "Automatic Domain-Specific Sentiment Lexicon Generation with Label Propagation, "Proc. of the 15th International Conference on Information Integration and Web-based Applications & Services (iiWAS-2013), pp. 53-62, December 2-4, 2013.
  17. Y.-J. Chang and H.-Y. Kao. ˇ§Link Prediction in a Bipartite Network using Wikipedia Revision Information, ˇ§ Proc. of the 2012 Conference on Technologies and Applications of Artificial Intelligence (TAAI 2012), Nov. 16-18, 2012.
  18. Z.-H. Yang and H.-Y. Kao. "Location Time-series Clustering on Optimal Sensor Arrangement, ˇ§ Proc. of the 2012 Conference on Technologies and Applications of Artificial Intelligence (TAAI 2012), Nov. 16-18, 2012.
  19. Y.-F. Lin and H.-Y. Kao, "The Retrieval of Important News Stories by Influence Propagation among Communities and Categories,ˇ¨ Proc. of IEEE/WIC/ACM International Conference on Web Intelligence (WI-2012), Dec. 4 - Dec. 6, 2012.
  20. H.-D. Huang, C.-S. Lee, H. Hagras, H.-Y. Kao, "TWMAN+: A Type-2 fuzzy ontology model for malware behavior analysis, " IEEE International Conference on Systems, Man, and Cybernetics (SMC-2012), 2821-2826, Korea, 2012.
  21. L.-C. Lai and H.-Y. Kao, "Question Routing by Modeling User Expertise and Activity in cQA services," Proc. of the 26th Annual Conference of JSAI, Yamaguchi, Japan, 2012.
  22. C.-H. Wei, H.-Y. Kao and Z. Lu, "PubTator: A PubMed-like interactive curation system for document triage and literature curation", BioCreative 2012 workshop, Washington DC, USA, 145-150, 2012.
  23. Y.-Y. Hsu and H.-Y. Kao, "CoIN: a network exploration for document triage", BioCreative 2012 workshop, Washington DC, USA, 39-44, 2012.
  24. Y.-T. Tang and H.-Y. Kao, " Augmented Transitive Relationships with High Impact Protein Distillation in Protein Interaction Prediction," Proc. of the 10th Asia Pacific Bioinformatics Conference (APBC-2012), Jan. 17-19, 2012.
  25. H.-D. Huang, G. Acampora, V. Loia, C.-S. Lee, H.-Y. Kao, "Applying FML and Fuzzy Ontologies to malware behavioural analysis," IEEE International Conference on Fuzzy Systems (FUZZ-IEEE-2011), 2018-2025, Taiwan, 2011.
  26. S.-L. Wang, Y.-C. Tsai, H.-Y. Kao, Tzung-Pei Hong, "K-anonymity on sensitive transaction items," IEEE International Conference on Granular Computing, GrC-2011 (GrC-2011), 723-727, 2011.
  27. Wen-Teng Yang and H.-Y. Kao, "Measuring Semantic Relatedness using Wikipedia Revision Information in a Signed Network," Proc. of the 2011 Conference on Technologies and Applications of Artificial Intelligence (TAAI 2011), Nov. 11-13.
  28. H.-Y. Kao, Y.-T. Tang and J.-F. Wang, ˇ§Evolutional dependency parse trees for biological relation extraction," Proc. of 2011 IEEE International Conference on Bioinformatics and Bioengineering (BIBE-2011), Oct. 24-26, 2011.
  29. H.-C. Huang and H.-Y. Kao , "CAIS: Community based Annotation Insight Search in a Folksonomy Network," Proc. of 2011 International Conference on Social Networks Analysis and Mining (ASONAM-2011), July 25-July 27, 2011. (acceptance rate 25%)
  30. Y.-T. Tang and H.-Y. Kao, "Augmented Transitive Relationships in Direct ProteinˇVProtein Interaction Prediction, " Proc. of 4th International Workshop on Intelligent Informatics in Biology and Medicine (IIBM-2011), June 30- July 2, 2011.
  31. Y.-T. Tang and H.-Y. Kao, "TransDomain: A Transitive Domain-Based Method in ProteinˇVProtein Interaction Prediction, " Proc. of 7th International Symposium on Bioinformatics Research and Applications (ISBRA-2011), May 27-29, 2011.
  32. Y.-F. Lin, J.-H. Wang, L.-C. Lai, H.-Y. Kao, "Top Stories Identification From Blog to News In TREC 2010 Blog Track," Proc. of TREC-2010, 2010.
  33. H.-Y. Kao and C.-H. Wei, "Inference network method on cross species gene normalization in full-text articles," Proc. of 2010 BioCreative III workshop, Bethesda, Maryland, 73-81, 2010.
  34. C.-H. Wei and H.-Y. Kao, "Represented Indicator Measurement and Corpus Distillation on Focus Species Detection,ˇ¨ Proc. of 2010 IEEE International Conference on Bioinformatics & Biomedicine (BIBM-2010), Dec. 18-21, 2010. (acceptance rate 18.8%)
  35. Y.-L. Chen and H.-Y. Kao, ˇ§Finding Hard Questions by Knowledge Gap Analysis in Question Answer Communities,ˇ¨ Proc. of the Sixth Asia Information Retrieval Symposium (AIRS-2010), December 1-3, 2010.
  36. H.-Y. Kao and Z.-Y. Lin, "A Categorized Sentiment Analysis of Chinese Reviews by Mining Dependency in Product Features and Opinions from Blogs, " Proc. of IEEE/WIC/ACM International Conference on Web Intelligence (WI-2010), Sept 1-3, 2010.
  37. C.-L. Lin, H.-L. Tang and H.-Y. Kao, "Utilizing Social Relationships for Blog Popularity Mining," Proc. of the The Fifth Asia Information Retrieval Symposium (AIRS-2009), October 21-23, 2009.
  38. H.-Y. Kao and W.-T. Cho, "Entropy-based Visual Tree Evaluation on Block Extraction," Proc. of IEEE/WIC/ACM International Conference on Web Intelligence (WI-2009), Sept 15-18, 2009.
  39. W.-J. Chen, P.-C. Chuang and H.-Y. Kao, "Hidden Markov Model Based DNA-binding Proteins Prediction by Mining on Sequence and Structure Information," Proc. of 2008 International Computer Symposium (ICS-2008), Nov13-15. 2008.
  40. H.-Y. Kao, C.-S. Liu, C.-C. Shih and T.-M. Tsai, "DRANK+: a directory based pagerank prediction method for fast pagerank convergence,"Proc. of 4th International Conference on Web Information Systems and Technologies (WEBIST-08), May 4-7, 2008.
  41. H.-Y. Kao, H.-W. Hsiao, C.-L. Lin, C.-C. Shih and T.-M. Tsai, "An Entropy-Based Hierarchical Search Result Clustering Method by Utilizing Augmented Information," Proc. of the Asia Information Retrieval Symposium (AIRS-08), January 16-18, 2008.
  42. H.-Y. Kao and S.-F. Lin, "A Fast PageRank Convergence Method based on the Cluster Prediction," Proc. of IEEE/WIC/ACM International Conference on Web Intelligence (WI-2007), Nov. 2-5, 2007.
  43. Y.-F. Tseng and H.-Y. Kao, "The Mining and Extraction of Primary Informative Blocks and Data Objects from Systematic Web Pages," Proc. of IEEE/WIC/ACM International Conference on Web Intelligence (WI-2006), 2006.
  44. C.-L. Lin and H.-Y. Kao, "Query Result Aggregation on Multiple Search Engines," Proc. of International Workshop on Software Engineering, Databases, and Knowledge Discovery, 2006.
  45. Y.-F. Tseng and H.-Y. Kao, "Web Information Hierarchy and Importance Mining Based on DOM Information Distillation," Proceedings of the 5th Emerging Information Technology Conference (EITC-05), August 15-16, 2005.
  46. H.-Y. Kao, J.-M. Ho and M.-S. Chen, "DOMISA: DOM-based Information Space Adsorption for Web Information Hierarchy Mining," Proc. of the 4th SIAM Intern'l Conference on Data Mining (SDM-04), April 22-24, 2004.
  47. I-A. Huang, J.-M. Ho, H.-Y. Kao and W.-C. Lin, "Extracting Citation Metadata from Online Publication Lists Using BLAST," Proc. of the Eighth Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD-04), May 26-28, 2004.
  48. H.-Y. Kao, J.-M. Ho and M.-S. Chen, "Clustering for Web Information Hierarchy Mining," Proc. of the IEEE 2003 Intern'l Conf. on Web Intelligence (WI-2003), October 13-17, 2003.
  49. H.-Y. Kao, S.-H. Lin, J.-M. Ho and M.-S. Chen, "Entropy-Based Link Analysis for Mining Web Informative Structures," Proc. of the ACM 11th International Conf. on Information and Knowledge Management (CIKM-02), November 4-9, 2002.
  50. Chia-Hui Wang, H.-Y. Kao, Shin-Hung Chang, Ray-I Chang, Shun-Chin Hsu and Jan-Ming Ho, "Design and Implementation of an Interactive True VOD System on ADSL with Scarce Resources at the Set-top Box," The International Computer Symposium on Workshop on Computer Networks, Internet, and Multimedia, Taiwan, Aug., 2000.
  51. H.-Y. Kao, S.-Y. Iap, Y.-T. Lee, S.-H. Lin, et. al. "Design and Implementation of ASIS Multimedia Digital Library," Proc. of SPIE on Multimedia Systems and Applications, 1999.
  52. H.-Y. Kao, S.-Y. Iap, C.-F. Ku, Y.-T. Lee, S.-H. Lin, Y.-C. Pan, C.-S. Shih, C.-H. Wang, Y.-C. Wang, M.-C. Chen, J.-M. Ho and M.-T. Kao, "ASIS MDL: a prototype electronic content service," IEEE workshop on Dependable and Real-time E-Commerce Systems, Denver, U.S.A , 1998.
  53. H.-Y. Kao, Y.-C. Kuo, S.-T. Huang and B.-F. Wang, "Design and Implementation of a PC-based Video-On-Demand System," The 12th International Conference on information Networking (ICOIN-12), Jan. 1998.

Thesis:

  1. H.-Y. Kao, "Informative Structure and Information Hierarchy Mining in a Systematic Web Site," Ph.D Thesis, Department of Electrical Engineering at National Taiwan University, R.O.C.
  2. H.-Y. Kao, "Design and Implementation of a PC-based Video-On-Demand System" Master Thesis, Department of Computer Science at National Tsing Hua University, R.O.C.