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2020 – today
- 2023
[i3]Manabu Torii, Ian M. Finn, Son Doan, Paul Wang, Elly W. Yang, Daniel S. Zisook:
Task formulation for Extracting Social Determinants of Health from Clinical Narratives. CoRR abs/2301.11386 (2023)
2010 – 2019
- 2019
- [j24]Son Doan, Elly W. Yang, Sameer S. Tilak, Peter W. Li, Daniel S. Zisook, Manabu Torii:
Extracting health-related causality from twitter messages using natural language processing. BMC Medical Informatics Decis. Mak. 19-S(3): 71-77 (2019) - [i2]Son Doan, Elly W. Yang, Sameer Tilak, Manabu Torii:
Using natural language processing to extract health-related causality from Twitter messages. CoRR abs/1911.06488 (2019) - 2018
- [c23]Manabu Torii, Elly W. Yang, Son Doan:
A Preliminary Study of Clinical Concept Detection Using Syntactic Relations. AMIA 2018 - [c22]Son Doan, Elly W. Yang, Sameer Tilak, Manabu Torii:
Using Natural Language Processing to Extract Health-Related Causality from Twitter Messages. ICHI Workshops 2018: 84-85 - 2015
- [j23]Manabu Torii
, Jung-Wei Fan, Weili Yang, Theodore Lee, Matthew T. Wiley, Daniel S. Zisook, Yang Huang:
Risk factor detection for heart disease by applying text analytics in electronic medical records. J. Biomed. Informatics 58: S164-S170 (2015) - [j22]Manabu Torii, Cecilia N. Arighi, Gang Li, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker:
RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information. IEEE ACM Trans. Comput. Biol. Bioinform. 12(1): 17-29 (2015) - [c21]Manabu Torii, Jung-Wei Fan, Daniel S. Zisook:
Finding Difficult-to-Disambiguate Words: Towards an Efficient Workflow to Implement Word Sense Disambiguation. ICHI 2015: 448 - 2014
- [j21]Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker:
iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system. Database J. Biol. Databases Curation 2014 (2014) - [j20]Manabu Torii, Gang Li, Zhiwen Li, Rose Oughtred, Francesca Diella, Irem Çelen, Cecilia N. Arighi, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu:
RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information. Database J. Biol. Databases Curation 2014 (2014) - [j19]Manabu Torii, Kavishwar B. Wagholikar, Hongfang Liu:
Detecting concept mentions in biomedical text using hidden Markov model: multiple concept types at once or one at a time? J. Biomed. Semant. 5: 3 (2014) - [j18]Yifan Peng, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker:
A Generalizable NLP Framework for Fast Development of Pattern-based Biomedical Relation Extraction Systems. BMC Bioinform. 15: 285 (2014) - [i1]John E. Miller, Michael Bloodgood, Manabu Torii, K. Vijay-Shanker:
Rapid Adaptation of POS Tagging for Domain Specific Uses. CoRR abs/1411.0007 (2014) - 2013
- [j17]Donald C. Comeau, Rezarta Islamaj Dogan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur:
BioC: a minimalist approach to interoperability for biomedical text processing. Database J. Biol. Databases Curation 2013 (2013) - [j16]Kavishwar B. Wagholikar, Manabu Torii, Siddhartha Jonnalagadda, Hongfang Liu:
Pooling annotated corpora for clinical concept extraction. J. Biomed. Semant. 4: 3 (2013) - [j15]Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Catalina O. Tudor, Manabu Torii, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu:
A framework for biomedical figure segmentation towards image-based document retrieval. BMC Syst. Biol. 7(S-4): S8 (2013) - [c20]Manabu Torii, Cecilia N. Arighi, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker:
Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach. BCB 2013: 201 - [c19]Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Manabu Torii, K. Vijay-Shanker, Hongzhan Huang, Cathy H. Wu:
An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature. BCB 2013: 412 - 2012
- [j14]Siddhartha Jonnalagadda, Dingcheng Li, Sunghwan Sohn, Stephen Tze-Inn Wu, Kavishwar B. Wagholikar, Manabu Torii, Hongfang Liu:
Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules. J. Am. Medical Informatics Assoc. 19(5): 867-874 (2012) - [c18]Xia Bi, Hongzhan Huang, Sherri Matis-Mitchell, Peter B. McGarvey, Manabu Torii, Hagit Shatkay, Cathy H. Wu:
Building a classifier for identifying sentences pertaining to disease-drug relationships in tardive dyskinesia. BIBM 2012: 1-4 - [c17]Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker:
iSimp: A sentence simplification system for biomedicail text. BIBM 2012: 1-6 - [c16]Carl J. Schmidt, Liang Sun, Cecilia N. Arighi, Keith Decker, K. Vijay-Shanker, Manabu Torii, Catalina O. Tudor, Cathy H. Wu, Peter D'Eustachio:
Pathway curation: Application of text-mining tools eGIFT and RLIMS-P. BIBM Workshops 2012: 523-528 - 2011
- [j13]Jinlian Wang, Manabu Torii, Hongfang Liu, Gerald W. Hart, Zhang-Zhi Hu:
dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation. BMC Bioinform. 12: 91 (2011) - [j12]Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illés Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, Padmini Srinivasan, Hongfang Liu, Manabu Torii, Sérgio Matos, David Campos, Karin Verspoor, Kevin M. Livingston, W. John Wilbur:
The gene normalization task in BioCreative III. BMC Bioinform. 12(S-8): S2 (2011) - [j11]Manabu Torii, Lanlan Yin, Thang Nguyen, Chand T. Mazumdar, Hongfang Liu, David M. Hartley, Noele P. Nelson:
An exploratory study of a text classification framework for Internet-based surveillance of emerging epidemics. Int. J. Medical Informatics 80(1): 56-66 (2011) - [j10]Manabu Torii, Kavishwar B. Wagholikar, Hongfang Liu:
Using machine learning for concept extraction on clinical documents from multiple data sources. J. Am. Medical Informatics Assoc. 18(5): 580-587 (2011) - [c15]Kavishwar B. Wagholikar, Manabu Torii, Hongfang Liu:
Human gene/protein synonym dictionary from WikiLinks. BCB 2011: 462-464 - [c14]Yang Chen, Manabu Torii, Chang-Tien Lu, Hongfang Liu:
Learning from positive and unlabeled documents for automated detection of alternative splicing sentences in medline abstracts. BIBM Workshops 2011: 530-537 - 2010
- [j9]Lanlan Yin, Guixian Xu, Manabu Torii, Zhendong Niu, José M. Maisog, Cathy H. Wu, Zhang-Zhi Hu, Hongfang Liu:
Document classification for mining host pathogen protein-protein interactions. Artif. Intell. Medicine 49(3): 155-160 (2010) - [j8]Hongfang Liu, Manabu Torii, Guixian Xu, Johannes Goll:
Classification Systems for Bacterial Protein-Protein Interaction Document Retrieval. Int. J. Comput. Model. Algorithms Medicine 1(1): 34-44 (2010) - [c13]Manabu Torii, Burt-Ujin Bayarsaikhan, Hongfang Liu, Thang Nguyen, Kevin Jones, Noele P. Nelson, David M. Hartley:
An exploratory study of news article clustering for web-based bio-surveillance. IHI 2010: 435-439 - [c12]Chong Min Lee, Manabu Torii, Zhang-Zhi Hu, Yi-Ting Tsai, Jinesh Shah, Hongfang Liu:
Evaluating gene/protein name tagging and mapping for article retrieval. Semantic Mining in Biomedicine 2010
2000 – 2009
- 2009
- [j7]Manabu Torii, Zhang-Zhi Hu, Cathy H. Wu, Hongfang Liu:
Research Paper: BioTagger-GM: A Gene/Protein Name Recognition System. J. Am. Medical Informatics Assoc. 16(2): 247-255 (2009) - [c11]Manabu Torii, Hongfang Liu, Zhang-Zhi Hu:
Support Vector Machine-Based Mucin-Type O-linked Glycosylation Site Prediction Using Enhanced Sequence Feature Encoding. AMIA 2009 - 2008
- [c10]Guixian Xu, Lanlan Yin, Manabu Torii, Zhendong Niu, Cathy H. Wu, Zhang-Zhi Hu, Hongfang Liu:
Document Classification for Mining Host Pathogen Protein-Protein Interactions. BIBM 2008: 461-466 - [c9]Hongfang Liu, Manabu Torii, Guixian Xu, Zhang-Zhi Hu, Johannes Goll:
Learning from Positive and Unlabeled Documents for Retrieval of Bacterial Protein-Protein Interaction Literature. BioLINK@ISMB/ECCB 2008: 62-70 - 2007
- [j6]Manabu Torii, Zhang-Zhi Hu, Min Song, Cathy H. Wu, Hongfang Liu:
A comparison study on algorithms of detecting long forms for short forms in biomedical text. BMC Bioinform. 8(S-9) (2007) - [j5]Manabu Torii, K. Vijay-Shanker:
Sortal Anaphora Resolution in Medline Abstracts. Comput. Intell. 23(1): 15-27 (2007) - [c8]Manabu Torii, Hongfang Liu:
Enhancing Acronym/Abbreviation Knowledge Bases with Semantic Information. AMIA 2007 - [c7]John E. Miller, Manabu Torii, K. Vijay-Shanker:
Adaptation of POS Tagging for Multiple BioMedical Domains. BioNLP@ACL 2007: 179-180 - [c6]John E. Miller, Manabu Torii, K. Vijay-Shanker:
Building Domain-Specific Taggers without Annotated (Domain) Data. EMNLP-CoNLL 2007: 1103-1111 - [c5]Hongfang Liu, Manabu Torii, Zhang-Zhi Hu, Cathy H. Wu:
Mapping Gene/Protein Names in Free Text to Biomedical Databases. ICDM Workshops 2007: 101-106 - [c4]Manabu Torii, Hongfang Liu:
Classifier Ensemble for Biomedical Document Retrieval. LBM (Short Papers) 2007 - 2006
- [j4]X. Yuan, Zhang-Zhi Hu, H. T. Wu, Manabu Torii, Meenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, Cathy H. Wu:
An online literature mining tool for protein phosphorylation. Bioinform. 22(13): 1668-1669 (2006) - [j3]Hongfang Liu, Zhang-Zhi Hu, Manabu Torii, Cathy H. Wu, Carol Friedman:
Research Paper: Quantitative Assessment of Dictionary-based Protein Named Entity Tagging. J. Am. Medical Informatics Assoc. 13(5): 497-507 (2006) - [c3]John E. Miller, Michael Bloodgood, Manabu Torii, K. Vijay-Shanker:
Rapid Adaptation of POS Tagging for Domain Specific Uses. BioNLP@NAACL-HLT 2006: 118-119 - [c2]Manabu Torii, Hongfang Liu:
Headwords and Suffixes in Biomedical Names. KDLL 2006: 29-41 - 2004
- [j2]Manabu Torii, Sachin Kamboj, K. Vijay-Shanker:
Using name-internal and contextual features to classify biological terms. J. Biomed. Informatics 37(6): 498-511 (2004) - 2003
- [c1]Manabu Torii, Sachin Kamboj, K. Vijay-Shanker:
An Investigation of Various Information Sources for Classifying Biological names. BioNLP@ACL 2003: 113-120 - 2002
- [j1]Manabu Torii, Martin T. Hagan:
Stability of steepest descent with momentum for quadratic functions. IEEE Trans. Neural Networks 13(3): 752-756 (2002)
Coauthor Index
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