Manabu Torii

Publication Activity (10 Years)

Years Active: 2002-2023
Publications (10 Years): 5

Top Topics

Natural Language

Electronic Medical Record

Information Extraction

Top Venues

Database J. Biol. Databases Curation

J. Biomed. Semant.

Publications

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 (2023)
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. (3) (2019)
Son Doan, Elly W. Yang, Sameer Tilak, Manabu Torii
Using natural language processing to extract health-related causality from Twitter messages. CoRR (2019)
Son Doan, Elly W. Yang, Sameer Tilak, Manabu Torii
Using Natural Language Processing to Extract Health-Related Causality from Twitter Messages. ICHI Workshops (2018)
Manabu Torii, Elly W. Yang, Son Doan
A Preliminary Study of Clinical Concept Detection Using Syntactic Relations. AMIA (2018)
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) (2015)
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 (2015)
Manabu Torii, Jung-Wei Fan, Daniel S. Zisook
Finding Difficult-to-Disambiguate Words: Towards an Efficient Workflow to Implement Word Sense Disambiguation. ICHI (2015)
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 (2014)
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)
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)
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 (2014)
John E. Miller, Michael Bloodgood, Manabu Torii, K. Vijay-Shanker
Rapid Adaptation of POS Tagging for Domain Specific Uses. CoRR (2014)
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)
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) (2013)
Kavishwar B. Wagholikar, Manabu Torii, Siddhartha Jonnalagadda, Hongfang Liu
Pooling annotated corpora for clinical concept extraction. J. Biomed. Semant. 4 (2013)
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)
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)
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)
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) (2012)
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)
Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker
iSimp: A sentence simplification system for biomedicail text. BIBM (2012)
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)
Jinlian Wang, Manabu Torii, Hongfang Liu, Gerald W. Hart, Zhang-Zhi Hu
dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation. BMC Bioinform. 12 (2011)
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) (2011)
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) (2011)
Kavishwar B. Wagholikar, Manabu Torii, Hongfang Liu
Human gene/protein synonym dictionary from WikiLinks. BCB (2011)
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) (2011)
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) (2010)
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)
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) (2010)
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)
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) (2009)
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)
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)
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)
Manabu Torii, K. Vijay-Shanker
Sortal Anaphora Resolution in Medline Abstracts. Comput. Intell. 23 (1) (2007)
John E. Miller, Manabu Torii, K. Vijay-Shanker
Building Domain-Specific Taggers without Annotated (Domain) Data. EMNLP-CoNLL (2007)
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)
John E. Miller, Manabu Torii, K. Vijay-Shanker
Adaptation of POS Tagging for Multiple BioMedical Domains. BioNLP@ACL (2007)
Manabu Torii, Hongfang Liu
Classifier Ensemble for Biomedical Document Retrieval. LBM (Short Papers) (2007)
Hongfang Liu, Manabu Torii, Zhang-Zhi Hu, Cathy H. Wu
Mapping Gene/Protein Names in Free Text to Biomedical Databases. ICDM Workshops (2007)
Manabu Torii, Hongfang Liu
Enhancing Acronym/Abbreviation Knowledge Bases with Semantic Information. AMIA (2007)
John E. Miller, Michael Bloodgood, Manabu Torii, K. Vijay-Shanker
Rapid Adaptation of POS Tagging for Domain Specific Uses. BioNLP@NAACL-HLT (2006)
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) (2006)
Manabu Torii, Hongfang Liu
Headwords and Suffixes in Biomedical Names. KDLL (2006)
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) (2006)
Manabu Torii, Sachin Kamboj, K. Vijay-Shanker
Using name-internal and contextual features to classify biological terms. J. Biomed. Informatics 37 (6) (2004)
Manabu Torii, Sachin Kamboj, K. Vijay-Shanker
An Investigation of Various Information Sources for Classifying Biological names. BioNLP@ACL (2003)
Manabu Torii, Martin T. Hagan
Stability of steepest descent with momentum for quadratic functions. IEEE Trans. Neural Networks 13 (3) (2002)