Other Members

Manabu Torii, PhD Postdoctoral Fellow

Dr. Torii received his PhD in Computer Science on January 2006, from University of Delaware. He joined the department of Biostatistics, Bioinformatics, and Biomathematics at Georgetown University on January 2006 as a Research Fellow.

Research Projects Involved:

• Study of biomedical acronyms/abbreviation/symbols [SFThesaurus]
  
• Biomedical named entity extraction [BioTagger]
  
• Information Extraction in the biomedical domain [RLIMS-P]
  
• Part-of-speech tagging in the biomedical domain
  

Publications:

1. Torii M and Liu H (2007, accepted for poster presentation) Automatic detection of acronym/abbreviation definitions in biomedical text using weakly supervised learning. ISMB/ECCB 2007

2. Miller J, Torii M, and Vijay-Shanker K (2007, accepted for publication) Building Domain-Specific Taggers without Annotated (Domain) Data. In Proc. of Conference on Empirical Methods in Natural Language Processing Conference on Computational Natural Language Learning Joint Meeting (EMNLP-CoNLL)

3. Miller J, Torii M, and Vijay-Shanker K (2007, accepted for poster presentation) Adaptation of POS Tagging for Multiple BioMedical Domains: POS Tagging in Molecular Biology and Medical Domains. ACL Workshop on BioNLP

4. Liu H, Torii M, Hu ZZ, and Wu CH (2007) Gene Mention and Gene Normalization Based on Machine Learning and Online Resources. In Proc. of BioCreAtIvE II

5. Torii M and Vijay Shanker K (2007) Sortal Anaphora Resolution in Medline Abstract. Computational Intelligence, An International Journal, Special issue: Recent PACLING Meetings. 23(1):15-27.

6. Torii M, Liu H, Hu ZZ, and Wu CH (2006) A Comparison Study of Biomedical Short Form Definition Detection Algorithms. In proc of ACM First International Workshop on Text Mining in Bioinformatics (TMBio). [pdf]

7. Liu H, Hu ZZ, Torii M, Wu CH, and Friedman C (2006) Quantitative Assessment of Dictionary-based Protein Named Entity Tagging. J Am Med Inform Assoc. Vol. 13. No. 5. pp.497-507. [pdf]

8. Yuan X, Hu ZZ, Wu HT, Torii M, Narayanaswamy M, Ravikumar KE, Vijay-Shanker K, and Wu CH (2006) An online literature mining tool for protein phosphorylation. Bioinformatics, Vol. 22. No. 13. pp.1668-1669. [pdf]

9. Miller J, Bloodgood M, Torii M, and Vijay-Shanker K (2006) Rapid adaptation of POS tagging for domain specific uses. In proc of BioNLP Workshop of HLT-NAACL. pp.118-119. [pdf]

10. Torii M and Liu H (2006) Headwords and Suffixes in Biomedical Names. In proc of Knowledge Discovery in Life Science Literature (KDLL), pp.29-41. [abstract]

11. Torii M and Vijay-Shanker K (2005) Anaphora Resolution of Demonstrative Noun Phrases in Medline Abstracts. In proc of Pacific Association for Computational Linguistics(PACLING) 2005, pp.332-339.

12. Torii M and Vijay-Shanker K (2005) An Investigation of Features for Anaphora Resolution in Medline Abstracts. Poster. The joint ISMB-ACL BioLINK SIG Workshop.

13. Torii M, Kamboj S and Vijay-Shanker K, Using name-internal and contextual features to classify biological terms. Journal of Biomedical Informatics, 37, pp.498–511. [pdf]

14. Torii M, Kamboj S and Vijay-Shanker K (2003) An Investigation of Various Information Sources for classifying Biological Names. ACL 2003 Workshop on NLP in Biomedicine, pp.113-120. [pdf]

15. Torii M and Vijay-Shanker K (2002) Using Unlabeled MEDLINE Abstracts for Biological Named Entity Classification. In Proc of Genome Informatics Workshop (GIW), pp. 567-568. [pdf]

16. Torii M and Hagan M, Stability of Steepest Descent with Momentum for Quadratic Functions. IEEE Transactions on Neural Networks, Vol. 13, No. 3, pp. 752 -756. [abstract]