Curriculum Vitae

Papers

Journal Papers

• 1. Dai, H.-J.*, Wu, C.-Y., Tsai, R.T.-H., (2013) Collective Instance-level Gene Normalization on the IGN corpus, PLOS One (SCI)

  2. Chang, Y.-C., Dai, H.-J.*, Chen, J.-M., Tsai, R.T.-H, Hsu, W.-L. (2013) TEMPTing System: A Hybrid Method of Rule and Machine Learning for Temporal Relation Extraction in Patient Discharge Summaries J Biomed Inform. (SCI).

  3. Dai, H.-J., Wu, C.-Y., Tsai, R.T.-H., Pan, W.-H., Hsu, W.-L. (2013) T-HOD: A Literature-based Candidate Gene Database for Hypertension, Obesity, and Diabetes Database: The Journal of Biological Databases and Curation (SCI).

  4. Dai, H.-J., Chen, C.-Y., Wu, C.-Y., Lai, P.-T., Tsai, R.T.-H., Hsu, W.-L. (2012) Coreference resolution of medical concepts in discharge summaries by exploiting contextual information Journal of the American Medical Informatics Association : JAMIA (19):888-896 (SCI/SSCI).

  5. Fang, Y. C., Lai, P. T., Dai, H.-J., Hsu, W.-L. (2011) MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature. BMC Bioinformatics 12(1): 471. (SCI)

  6. Dai, H.-J., Chang, Y. -C., Tsai, R.T.-H., Hsu, W.-L. (2011) Integration of Gene Normalization Stages and Co-reference Resolution Using a Markov-Logic Network. Bioinformatics, 27(18):2586-2594 (SCI, IF: 4.877)

  7. Lu Z., Kao H.-Y., Wei C.-H., Huang M., Liu J., Kuo C.-J., Hsu C.-N., Tsai R.T.-H., Dai H-.J., Okazaki N. et al. (2011) The Gene Normalization Task in BioCreative III. BMC Bioinformatics, 12(Suppl 9): S2. (SCI)

  8. Dai, H.-J., Lai, P.-T. and Tsai, R.T.-H. (2010) Multi-stage gene normalization and SVM-based ranking for protein interactor extraction in full-text articles, IEEE TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, vol. 7, pp. 412-420, 2010. (SCI)

  9. Dai, H.-J., Chang, Y.-C., Tsai, R.T.-H. and Hsu, W.-L. (2010) New challenges for biological text-mining in the next decade, Journal of Computer Science and Technology, 25, 169-179. (SCI)

  10. Tsai, R.T.-H., Lai, P.-T., Dai, H.-J., Huang, C.-H., Bow, Y.-Y., Chang, Y.-C., Pan, W.-H. and Hsu, W.-L. (2009) HypertenGene: Extracting key hypertension genes from biomedical literature with position and automatically-generated template features, BMC Bioinformatics, 10, S9. (SCI)

  11. Tsai, R.T.-H., Dai, H.-J., Lai, P.-T. and Huang, C.-H. (2009) PubMed-EX: A web browser extension to enhance PubMed search with text mining features, Bioinformatics, 25, 3031-3032. (SCI)

  12. Lin, R.T.K., Dai, H.-J., Bow, Y.-Y., Chiu, J.L.-T. and Tsai, R.T.-H. (2009) Using conditional random fields for result identification in biomedical abstracts Integrated Computer-Aided Engineering, 16, 339-352. (SCI)

  13. Lin, R.T.K., Chiu, J.L.-T., Dai, H.-J., Tsai, R.T.-H., Day, M.-Y. and Hsu, W.-L. (2009) A supervised learning approach to biological question answering, Integrated Computer-Aided Engineering 16, 271-281. (SCI)

  14. Smith, L., Tanabe, L.K., Ando, R.J.n., Kuo, C.-J., Chung, I.-F., Hsu, C.-N., Lin, Y.-S., Klinger, R., Friedrich, C.M., Ganchev, K., Torii, M., Liu, H., Haddow, B., Struble, C.A., Povinelli, R.J., Vlachos, A., Jr, W.A.B., Hunter, L., Carpenter, B., Tsai, R.T.-H., Dai, H.-J., Liu, F., Chen, Y., Sun, C., Katrenko, S., Adriaans, P., Blaschke, C., Torres, R., Neves, M., Nakov, P., Divoli, A., Maña-López, M., Mata, J. and Wilbur, W.J. (2008) Overview of BioCreative II gene mention recognition, Genome Biology, 9, S2. (SCI)

  15. Tsai, R.T.-H., Dai, H.-J., Huang, C.-H. and Hsu, W.-L. (2008) Semi-automatic conversion of BioProp semantic annotation to PASBio annotation, BMC Bioinformatics, 9, S18. (SCI)

  16. Dai, H.-J., Huang, C.-H., Lin, R.T.K., Tsai, R.T.-H. and Hsu, W.-L. (2008) BIOSMILE web search: a web application for annotating biomedical entities and relations, Nucl. Acids Res., 1;36, W390-398 (SCI).

  17. Tsai, R.T.-H., Hung, H.-C., Dai, H.-J., Lin, Y.-W. and Hsu, W.-L. (2008) Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles, BMC Bioinformatics. 2008, 9, S3.

  18. Tsai, R.T.-H., Chou, W.-C., Su, Y.-S., Lin, Y.-C., Sung, C.-L., Dai, H.-J., Yeh, I.T., Ku, W., Sung, T.-Y. and Hsu, W.-L. (2007) BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features, BMC Bioinformatics, 8, 325.

  19. Tsai, R.T.-H., Sung, C.-L., Dai, H.-J., Hung, H.-C., Sung, T.-Y. and Hsu, W.-L. (2006) NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition, BMC Bioinformatics, 7, S11.

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

Conference/Workshop Papers

• 1. Dai, H.-J., R. T.-H. Tsai, et al. (2011). Entity Disambiguation Using a Markov-Logic Network. Proceedings of the 5th International Joint Conference on Natural Language Processing (IJCNLP). Chiang Mai, Thailand: 846-855.

  2. Dai, H.-J., W.-C. Tsai, R.T.-H. Tsai and W.-L. Hsu: Enhancing search results with semantic annotation using augmented browsing. In: Proceedings of the Twenty-second International Joint Conference on Artificial Intelligence (IJCAI), Barcelona, Catalonia (Spain), 2011. 2418-2423, [Demo System]

  3. Lai P-T, Dai H-J, Huang C-H, Tsai RT-H: IISR Gene Normalization System for BioCreAtIvE III. In: Proceedings of BioCreAtIvE III Challenge Evaluation Workshop: 2010; Bethesda, Maryland, USA; 2010.

  4. Dai H-J, Lai P-T, Tsai RT-H, Hsu W-L: Global Ranking via Data Fusion In: Proceedings of the 23rd International Conference on Computational Linguistics (COLING 2010). Beijing, China; 2010.

1. Dai, H.-J., Lai, P.-T., Huang, C.-H., Chang, Y.-C., Bow, Y.-Y., Wu, H.-T., Tsai, R.T.-H. and Hsu, W.-L. (2009) IASL-IISR Interactor Normalization System: Using a Multi-stage Gene Normalization Algorithm and SVM-based ranking. Proceedings of BioCreAtIvE II.5 Challenge Evaluation Workshop. Madrid, Spain.

2. Lai, P.-T., Bow, Y.-Y., Huang, C.-H., Dai, H.-J., Tsai, R.T.-H. and Hsu, W.-L. (2009) Using Contextual Information to Clarify Gene Normalization Ambiguity. The IEEE International Conference on Information Reuse and Integration (IEEE IRI 2009). Las Vegas, USA.

3. Tsai, R.T.-H., Lai, P.-T., Dai, H.-J., Huang, C.-H., Chang, Y.-C. and Hsu, W.-L. (2009) HypertenGene: Extracting key hypertension genes from biomedical literature with position and automatically-generated template features. 8th InCoB - Seventh International Conference on Bioinformatics.

4. Chiu, J.L.-T., Dai, H.-J., Tsai, R.T.-H. and Huang, C.-H. (2008) The Improvement of Biomedical Named Entity Recognition with Semi-joint labeling presentation. Proceedings of 2008 International Computer Symposium. 21-26.

5. Chou, P.-H., Dai, H.-J., Huang, C.-H., Tsai, R.T.-H. and Hsu, W.-L. (2008) A Web Application for Biomedical Entities and Relations Annotation Using the Unstructured Information Management Architecture. International Computer Symposium (ICS). Taipei, Taiwan.

6. Hung, H.-C., Wang, Y.-C., Dai, H.-J. and Tsai, R.T.-H. (2008) Chinese Grapheme‐to‐Phoneme Conversion Based on a Maximum Entropy Model. 2008 International Conference on Digital Content (ICDC).

7. Chiu, J.L.-T., Lin, R.T.K., Dai, H.-J. and Tsai, R.T.-H. (2008) Improving the Performance and Stability of Question Answering System's Accuracy with New Feature and Evaluation Measurement. 2008 International Conference on Digital Content (ICDC).

8. Lin, R.T.K., Dai, H.-J., Bow, Y.-Y., Day, M.-Y., Tsai, R.T.-H. and Hsu, W.-L. (2008) Result Identification for Biomedical Abstracts Using Conditional Random Fields. The IEEE International Conference on Information Reuse and Integration (IEEE IRI 2008). Las Vegas, Nevada, USA.

9. Lin, R.T.K., Chiu, J.L.-T., Dai, H.-J., Day, M.-Y., Tsai, R.T.-H. and Hsu, W.-L. (2008) Biological Question Answering with Syntactic and Semantic Feature Matching and an Improved Mean Reciprocal Ranking Measurement. Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2008). Las Vegas, Nevada.

10. Tsai, R.T.-H., Dai, H.-J., Huang, C.-H. and Hsu, W.-L. (2008) Semi-automatic conversion of BioProp semantic annotation to PASBio annotation Asia Pacific Bioinformatics Network (APBioNet) Seventh International Conference on Bioinformatics (InCoB2008). Taipei, Taiwan.

11. Dai, H.J., Huang, C.H., Lin, J.Y.W., Chou, P.H. and Tsai, R.T.H. (2008) 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). 410-417.

12. Tsai, R.T.-H., Hung, H.-C., Dai, H.-J. and Hsu, W.-L. (2007) Exploiting Unlabeled Internal Data in Conditional Random Fields to Reduce Word Segmentation Errors for Chinese Texts Proceeding of the Interspeech-2007 Conference.

13. Tsai, R.T.-H., Hung, H.-C., Dai, H.-J., Lin, Y.-W. and Hsu, W.-L. (2007) Exploiting Likely-Positive and Unlabeled Data to Improve the Identification of Protein-Protein Interaction Articles, 6th InCoB - Sixth International Conference on Bioinformatics.

14. Dai, H.-J., Hung, H.-C., Tsai, R.T.-H. and Hsu, W.-L. (2007) IASL Systems in the Gene Mention Tagging Task and Protein Interaction Article Sub-task. Proceedings of Second BioCreAtIvE Challenge Evaluation Workshop. Madrid, Spain, 69-76.

15. Tsai, R.T.-H., Dai, H.-J., Hung, H.-C., Sung, C.-L., Day, M.-Y. and Hsu, W.-L. (2006) Chinese Word Segmentation with Minimal Linguistic Knowledge: An Improved Conditional Random Fields Coupled with Character Clustering and Automatically Discovered Template Matching. Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2006). Waikoloa, Hawaii.

16. Tsai, R.T.-H., Hung, H.-C., Sung, C.-L., Dai, H.-J. and Hsu, W.-L. (2006) On Closed Task of Chinese Word Segmentation: An Improved CRF Model Coupled with Character Clustering and Automatically Generated Template Matching. Fifth SIGHAN Workshop on Chinese Language Processing. Sydney, Australia, 108-117.

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

    1. Dai, H.-J. and Chen, J.J.-Y. (2005) Ontology-enhanced Multi-Agent Gateway System for Agent Interoperation. The 10th Conference on Artifical Intelligence and Applications.

Thesis

1. Dai, H.-J. and Chen, J.J.-Y. (2005) Ontology-enhanced Multi-Agent Gateway System for Agent Interoperation. Department of Computer Science & Information Engineering. National Central University, Jhongli, 60.

Research Grants

Travel Grants

• • The 22th International Joint Conference on Artificial Intelligence, Barcelona, Spain, Jul. 2010. IJCAI-11 Travel Grant Award [Scanned Copy]

  • The 23th International Conference on Computational Linguistics, Beijing, China, Aug. 2010. NSC-99-2922-I-007-274

Awards, Honors, Fellowships & Activities

Program Committee Member: International Conference on Digital Content (ICDC) 2008

Memberships: Member of International Speech Communication Association (ISCA) 2007-2008

Reviewing Activities

• • Annual Meeting of the Association for Computational Linguistics: Human Language Technologies (ACL) 2011

  • IEEE International Conference on Information Reuse andIntegration (IRI) 2010

  • IEEE International Conference on Computer and Communication Technology (ICCCT) 2011

  • ISRN Artificial Intelligence 2011

Talks

• 1. 2009: BioCreAtIvE II.5 workshop recordings, [slides]

  2. 2008: InCoB 2008 Highlights & Technology I session: BIOSMILE Web Search: a Web Application for Annotating Biomedical Entities and Relations

Professional Experience