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Resources

NLP

    • Specialist NLP Tools: facilitate NLP by helping developers with lexical variation and text analysis tasks in the biomedical domain. [Java]

    • LingPipe: a suite of Java libraries for the linguistic analysis of human language. [Java]

ALICE: An Algorithm to Extract Abbreviations from MEDLINE: http://3.uvdb.dbcls.jp/ALICE/ALICE_index.html

Publications

Journals

1. Larry Smith, Lorraine K. Tanabe, Rie Johnson nee Ando, Cheng-Ju Juo, I-Fang Chung, Chun-Nan Hsu, Yu-Shi Lin, Roman Klinger, Christoph M. Friedrich, Kuzman Ganchev, Manabu Torii, Hongfang Liu, Barry Haddow, Craig A. Struble, Richard J. Povinelli, Andreas Vlachos, William A. Baumgartner Jr., Lawrence Hunter, Bob Carpenter, Richard Tzong-Han Tsai, Hong-Jie Dai, Feng Liu, Yifei Chen, Chengjie Sun, Sophia Katrenko, Pieter Adriaans, Christian Blaschke, Rafel Torres Perez, Mariana Neves, Preslav Nakov, Anna Divoli, Manuel Mana, Jacinto Mata-Vazquez, and W. John Wilbur, "Overview of BioCreative II Gene Mention Recognition," To Appear in Genome Biology.

2. Richard Tzong-Han Tsai, Hsi-Chuan Hung, Hong-Jie Dai, Yi-Wen Lin, and Wen-Lian Hsu, "Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles," BMC Bioinformatics, volume 9(Suppl 1): S3, February 2008.

3. Hong-Jie Dai, Chi-Hsin Huang, Ryan T. K. Lin, Richard Tzong-Han Tsai, and Wen-Lian Hsu, "BIOSMILE web search: a web application for annotating biomedical entities and relations," Nucleic Acids Research, 2008.

4. Richard Tzong-Han Tsai, Wen-Chi Chou, Ying-Shan Su, Yu-Chun Lin, Cheng-Lung Sung, Hong-Jie Dai, Irene Tzu-Hsuan Yeh, Wei Ku, Ting-Yi Sung, and Wen-Lian Hsu, "BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features," BMC Bioinformatics, volume 8:3258:325, September 2007.

5. Richard Tzong-Han Tsai, Cheng-Lung Sung, Hong-Jie Dai, Hsieh-Chuan Hung, Ting-Yi Sung, and Wen-Lian Hsu, "NERBio: Using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition," BMC Bioinformatics, volume 7(Suppl 5) :S11, 2006.

    1. Hung C-H, Lin Y-F, Dai H-J, Chen JJ-Y: Intelligent Agent Communication By Using DAML to Build Agent Community Ontology. International Journal of Fuzzy Systems 2005, 7(2):72-75.

Conferences

1. Hong-Jie Dai, Chi-Hsin Huang, Jaimie Yi-Wen Lin, Pei-Hsuan Chou, Richard Tzong-Han Tsai, and Wen-Lian Hsu, "A Survey of State of the Art Biomedical Text Mining Techniques for Semantic Analysis," 2008 IEEE International Conference on Sensor Networks, Ubiquitous, and Trustworthy Computing (sutc 2008), pages 410-417, 2008.

2. 周佩璇, 戴鴻傑, 黃吉心, 蔡宗翰, "用於蛋白質交互作用之文件分類與基因專有名詞辨識的網際網路服務系統," Proceedings of the Cross-Strait Information Technology Conference (CSIT 2008), 2008.

3. 邱亮德, 林琮凱, 戴鴻傑, 蔡宗翰, "生物資訊問答系統處理同分狀況的準確率計算方式," Proceedings of the Cross-Strait Information Technology Conference (CSIT 2008), 2008.

4. Richard Tzong-Han Tsai, Hsieh-Chuan Hung, Hong-Jie Dai, and Yi-Wen Lin, "Protein-protein interaction abstract identification with contextual bag of words," Proceedings of the Second International Symposium on Languages in Biology and Medicine (LBM), December 2007.

5. Richard Tzong-Han Tsai, Hsi-Chuan Hung, Hong-Jie Dai, Yi-Wen Lin, and Wen-Lian Hsu, "Exploiting Likely-Positive and Unlabeled Data to Improve the Identification of Protein-Protein Interaction Articles," Proceedings of the Sixth International Conference on Bioinformatics (InCoB 2007), August 2007.

6. Richard Tzong-Han Tsai, Hong-Jei Dai, Hsi-Chuan Hung, Ryan T.K. Lin, Wen-Chi Chou, Ying-Shan Su, Min-Yuh Day, and Wen-Lian Hsu, "BESearch: A Supervised Learning Approach to Search for Molecular Event Participants," Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2007)Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2007), pages 412-417, 2007.

7. Richard Tzong-Han Tsai, Hsi-Chuan Hung, Hong-Jie Dai, and Wen-Lian Hsu, "Exploiting Unlabeled Internal Data in Conditional Random Fields to Reduce Word Segmentation Errors for Chinese Texts," Proceeding of the Interspeech-2007 Conference, 2007.

8. Hong-Jie Dai, Hsieh-Chuan Hung, Richard Tzong-Han Tsai, and Wen-Lian Hsu, "IASL Systems in the Gene Mention Tagging Task and Protein Interaction Article Sub-task," Proceedings of Second BioCreAtIvE Challenge Evaluation Workshop, pages 69-76, 2007.

9. Richard Tzong-Han Tsai, Hsieh-Chuan Hung, Cheng-Lung Sung, Hong-Jie Dai, and Wen-Lian Hsu, "On Closed Task of Chinese Word Segmentation: An Improved CRF Model Coupled with Character Clustering and Automatically Generated Template Matching," Proceedings of the Fifth SIGHAN Workshop on Chinese Language Processing, July 2006.

10. Richard Tzong-Han Tsai, Hong-Jie Dai, Hsieh-Chuan Hung, Cheng-Lung Sung, Min-Yuh Day, and Wen-Lian Hsu, "Chinese word segmentation with minimal linguistic knowledge: An improved conditional random fields coupled with character clustering and automatically discovered template matching," Proceedings of the 2006 IEEE International Conference on Information Reuse and Integration, IRI-2006Proceedings of the 2006 IEEE International Conference on Information Reuse and Integration, IRI-2006, pages 274-279, 2006.

    1. Hung C-H, Dai H-J, Chen JJ-Y: Intelligent Agent Communication by Using DAML to Build Agent Community Ontology In: Istanbul; Turkey. WEC '05: The Fourth World Enformatika Conference; 2005: 24-26.

Thesis

1. Dai H-J, Chen JJ-Y: Ontology-enhanced Multi-Agent Gateway System for Agent Interoperation. Jhongli: National Central University; 2005.