Manabu Torii

50 papers Misc 3Journal 27Unranked 20
YearRankTypeTitle / Venue / Authors
2023 J jnl
Task formulation for Extracting Social Determinants of Health from Clinical Narratives.
CoRR
Manabu Torii, Ian M. Finn, Son Doan, Paul Wang, Elly W. Yang, Daniel S. Zisook
2019 J jnl
Extracting health-related causality from twitter messages using natural language processing.
BMC Medical Informatics Decis. Mak.
Son Doan, Elly W. Yang, Sameer S. Tilak, Peter W. Li, Daniel S. Zisook, Manabu Torii
2019 J jnl
Using natural language processing to extract health-related causality from Twitter messages.
CoRR
Son Doan, Elly W. Yang, Sameer Tilak, Manabu Torii
2018 Misc conf
A Preliminary Study of Clinical Concept Detection Using Syntactic Relations.
AMIA
Manabu Torii, Elly W. Yang, Son Doan
2018 — conf
Using Natural Language Processing to Extract Health-Related Causality from Twitter Messages.
ICHI Workshops
Son Doan, Elly W. Yang, Sameer Tilak, Manabu Torii
2015 — conf
Finding Difficult-to-Disambiguate Words: Towards an Efficient Workflow to Implement Word Sense Disambiguation.
ICHI
Manabu Torii, Jungwei Fan, Daniel S. Zisook
2015 J jnl
RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information.
IEEE ACM Trans. Comput. Biol. Bioinform.
Manabu Torii, Cecilia N. Arighi, Gang Li, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker
2015 J jnl
Risk factor detection for heart disease by applying text analytics in electronic medical records.
J. Biomed. Informatics
Manabu Torii, Jungwei Fan, Weili Yang, Theodore Lee, Matthew T. Wiley, Daniel S. Zisook, Yang Huang
2014 J jnl
A Generalizable NLP Framework for Fast Development of Pattern-based Biomedical Relation Extraction Systems.
BMC Bioinform.
Yifan Peng, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker
2014 J jnl
Detecting concept mentions in biomedical text using hidden Markov model: multiple concept types at once or one at a time?
J. Biomed. Semant.
Manabu Torii, Kavishwar B. Wagholikar, Hongfang Liu
2014 J jnl
RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information.
Database J. Biol. Databases Curation
Manabu Torii, Gang Li, Zhiwen Li, Rose Oughtred, Francesca Diella, Irem Çelen, Cecilia N. Arighi, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu
2014 J jnl
Rapid Adaptation of POS Tagging for Domain Specific Uses.
CoRR
John E. Miller, Michael Bloodgood, Manabu Torii, K. Vijay-Shanker
2014 J jnl
iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system.
Database J. Biol. Databases Curation
Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker
2013 J jnl
A framework for biomedical figure segmentation towards image-based document retrieval.
BMC Syst. Biol.
Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Catalina O. Tudor, Manabu Torii, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu
2013 — conf
An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature.
BCB
Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Manabu Torii, K. Vijay-Shanker, Hongzhan Huang, Cathy H. Wu
2013 J jnl
BioC: a minimalist approach to interoperability for biomedical text processing.
Database J. Biol. Databases Curation
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
2013 J jnl
Pooling annotated corpora for clinical concept extraction.
J. Biomed. Semant.
Kavishwar B. Wagholikar, Manabu Torii, Siddhartha Jonnalagadda, Hongfang Liu
2013 — conf
Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach.
BCB
Manabu Torii, Cecilia N. Arighi, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker
2012 — conf
Building a classifier for identifying sentences pertaining to disease-drug relationships in tardive dyskinesia.
BIBM
Xia Bi, Hongzhan Huang, Sherri Matis-Mitchell, Peter B. McGarvey, Manabu Torii, Hagit Shatkay, Cathy H. Wu
2012 J jnl
Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules.
J. Am. Medical Informatics Assoc.
Siddhartha Jonnalagadda, Dingcheng Li, Sunghwan Sohn, Stephen Tze-Inn Wu, Kavishwar B. Wagholikar, Manabu Torii, Hongfang Liu
2012 — conf
Pathway curation: Application of text-mining tools eGIFT and RLIMS-P.
BIBM Workshops
Carl J. Schmidt, Liang Sun, Cecilia N. Arighi, Keith Decker, K. Vijay-Shanker, Manabu Torii, Catalina O. Tudor, Cathy H. Wu, Peter D'Eustachio
2012 — conf
iSimp: A sentence simplification system for biomedicail text.
BIBM
Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker
2011 J jnl
An exploratory study of a text classification framework for Internet-based surveillance of emerging epidemics.
Int. J. Medical Informatics
Manabu Torii, Lanlan Yin, Thang Nguyen, Chand T. Mazumdar, Hongfang Liu, David M. Hartley, Noele P. Nelson
2011 — conf
Human gene/protein synonym dictionary from WikiLinks.
BCB
Kavishwar B. Wagholikar, Manabu Torii, Hongfang Liu
2011 — conf
Learning from positive and unlabeled documents for automated detection of alternative splicing sentences in medline abstracts.
BIBM Workshops
Yang Chen, Manabu Torii, Chang-Tien Lu, Hongfang Liu
2011 J jnl
The gene normalization task in BioCreative III.
BMC Bioinform.
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
2011 J jnl
Using machine learning for concept extraction on clinical documents from multiple data sources.
J. Am. Medical Informatics Assoc.
Manabu Torii, Kavishwar B. Wagholikar, Hongfang Liu
2011 J jnl
dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation.
BMC Bioinform.
Jinlian Wang, Manabu Torii, Hongfang Liu, Gerald W. Hart, Zhang-Zhi Hu
2010 — conf
An exploratory study of news article clustering for web-based bio-surveillance.
IHI
Manabu Torii, Burt-Ujin Bayarsaikhan, Hongfang Liu, Thang Nguyen, Kevin Jones, Noele P. Nelson, David M. Hartley
2010 J jnl
Classification Systems for Bacterial Protein-Protein Interaction Document Retrieval.
Int. J. Comput. Model. Algorithms Medicine
Hongfang Liu, Manabu Torii, Guixian Xu, Johannes Goll
2010 J jnl
Document classification for mining host pathogen protein-protein interactions.
Artif. Intell. Medicine
Lanlan Yin, Guixian Xu, Manabu Torii, Zhendong Niu, José M. Maisog, Cathy H. Wu, Zhang-Zhi Hu, Hongfang Liu
2010 — conf
Evaluating gene/protein name tagging and mapping for article retrieval.
Semantic Mining in Biomedicine
Chong Min Lee, Manabu Torii, Zhang-Zhi Hu, Yi-Ting Tsai, Jinesh Shah, Hongfang Liu
2009 J jnl
Research Paper: BioTagger-GM: A Gene/Protein Name Recognition System.
J. Am. Medical Informatics Assoc.
Manabu Torii, Zhang-Zhi Hu, Cathy H. Wu, Hongfang Liu
2009 Misc conf
Support Vector Machine-Based Mucin-Type O-linked Glycosylation Site Prediction Using Enhanced Sequence Feature Encoding.
AMIA
Manabu Torii, Hongfang Liu, Zhang-Zhi Hu
2008 — conf
Document Classification for Mining Host Pathogen Protein-Protein Interactions.
BIBM
Guixian Xu, Lanlan Yin, Manabu Torii, Zhendong Niu, Cathy H. Wu, Zhang-Zhi Hu, Hongfang Liu
2008 — conf
Learning from Positive and Unlabeled Documents for Retrieval of Bacterial Protein-Protein Interaction Literature.
BioLINK@ISMB/ECCB
Hongfang Liu, Manabu Torii, Guixian Xu, Zhang-Zhi Hu, Johannes Goll
2007 J jnl
A comparison study on algorithms of detecting long forms for short forms in biomedical text.
BMC Bioinform.
Manabu Torii, Zhang-Zhi Hu, Min Song, Cathy H. Wu, Hongfang Liu
2007 — conf
Adaptation of POS Tagging for Multiple BioMedical Domains.
BioNLP@ACL
John E. Miller, Manabu Torii, K. Vijay-Shanker
2007 — conf
Building Domain-Specific Taggers without Annotated (Domain) Data.
EMNLP-CoNLL
John E. Miller, Manabu Torii, K. Vijay-Shanker
2007 — conf
Classifier Ensemble for Biomedical Document Retrieval.
LBM (Short Papers)
Manabu Torii, Hongfang Liu
2007 Misc conf
Enhancing Acronym/Abbreviation Knowledge Bases with Semantic Information.
AMIA
Manabu Torii, Hongfang Liu
2007 — conf
Mapping Gene/Protein Names in Free Text to Biomedical Databases.
ICDM Workshops
Hongfang Liu, Manabu Torii, Zhang-Zhi Hu, Cathy H. Wu
2007 J jnl
Sortal Anaphora Resolution in Medline Abstracts.
Comput. Intell.
Manabu Torii, K. Vijay-Shanker
2006 J jnl
An online literature mining tool for protein phosphorylation.
Bioinform.
X. Yuan, Zhang-Zhi Hu, H. T. Wu, Manabu Torii, Meenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, Cathy H. Wu
2006 — conf
Headwords and Suffixes in Biomedical Names.
KDLL
Manabu Torii, Hongfang Liu
2006 — conf
Rapid Adaptation of POS Tagging for Domain Specific Uses.
BioNLP@NAACL-HLT
John E. Miller, Michael Bloodgood, Manabu Torii, K. Vijay-Shanker
2006 J jnl
Research Paper: Quantitative Assessment of Dictionary-based Protein Named Entity Tagging.
J. Am. Medical Informatics Assoc.
Hongfang Liu, Zhang-Zhi Hu, Manabu Torii, Cathy H. Wu, Carol Friedman
2004 J jnl
Using name-internal and contextual features to classify biological terms.
J. Biomed. Informatics
Manabu Torii, Sachin Kamboj, K. Vijay-Shanker
2003 — conf
An Investigation of Various Information Sources for Classifying Biological names.
BioNLP@ACL
Manabu Torii, Sachin Kamboj, K. Vijay-Shanker
2002 J jnl
Stability of steepest descent with momentum for quadratic functions.
IEEE Trans. Neural Networks
Manabu Torii, Martin T. Hagan