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The following publications are under the Indexing Initiative project umbrella. Where applicable, we have indicated that the Dataset Logo denoting Dataset Available - Green circle with letter 'd' or Test Collection Logo denoting Test Set Available - Blue circle with letter 't' associated with a paper is also available. In this first table, we have included our picks for the preferred first read for several of the Research Areas. Each Research Area heading itself is a link to the papers associated with it. Some papers will also appear in multiple areas - for example, an MTI Machine Learning paper will also appear in the Machine Learning area.

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Areas of Research



General Indexing Initiative
   
Mining MEDLINE for problems associated with vitamin D - PDF (201 kb) Mining MEDLINE for problems associated with vitamin D. Dina Demner-Fushman, MD, PhD, James G. Mork, MSc, Alan R. Aronson, PhD. AMIA 2013
2013 Vitamin D Dataset Available
2012 Report to the Board of Scientific Counselors - PDF (1.9 mb) 2012 Report to the Board of Scientific Counselors
2012 Presentation to the Board of Scientific Counselors - PowerPoint (7.9 mb) 2012 PowerPoint Presentation to the Board of Scientific Counselors
2012 Presentation to the Board of Scientific Counselors - PDF (12.8 mb) 2012 Powerpoint Presentation to the Board of Scientific Counselors (PDF version, no slide animations)
Presentation for NIH-sponsored Workshop on Natural Language Processing, April 2012 - PowerPoint (1 mb) Presentation for NIH-sponsored Workshop on Natural Language Processing, April 2012
Presentation for NIH-sponsored Workshop on Natural Language Processing, April 2012 - PDF (2.1 mb) Presentation for NIH-sponsored Workshop on Natural Language Processing, April 2012 (PDF version, no slide animations)
Automatic inference of indexing rules for MEDLINE, 2008 - PDF (395 kb) Automatic inference of indexing rules for MEDLINE, BMC Bioinformatics, 2008
Automatic inference of indexing rules for MEDLINE, 2008 - PDF (100 kb) Automatic inference of indexing rules for MEDLINE, BioNLP 2008
2008 Report to the Board of Scientific Counselors - PDF (1.5 mb) 2008 Report to the Board of Scientific Counselors
The NLM Indexing Initiative paper - PDF (139 kb) The NLM Indexing Initiative, 2000
1999 Report to the Board of Scientific Counselors - PDF (203 kb) 1999 Report to the Board of Scientific Counselors
 
MetaMap
   
MetaMap Fundamentals
An overview of MetaMap: historical perspective and
recent advances - PDF (201 kb) An overview of MetaMap: historical perspective and recent advances, JAMIA 2010
The Evolution of MetaMap, a Concept Search Program for Biomedical Text, AMIA 2009 - PDF (12 kb) The Evolution of MetaMap, a Concept Search Program for Biomedical Text, AMIA 2009
The Evolution of MetaMap, a Concept Search Program for Biomedical Text, Presented November 16, 2009 at AMIA 2009 - PDF (723 kb)
The Evolution of MetaMap, a Concept Search Program for Biomedical Text, Presented November 16, 2009 at AMIA 2009 - PPT (1.1 mb)
Presentation: The Evolution of MetaMap, a Concept Search Program for Biomedical Text, Presented November 16, 2009 at AMIA 2009
The Current State of MetaMap and MMTx Webcast, August 20, 2009 - PDF (716 kb)
The Current State of MetaMap and MMTx Webcast, August 20, 2009 - PPT (1.1 mb)
Presentation: The Current State of MetaMap and MMTx Webcast, August 20, 2009
MetaMap: Mapping Text to the UMLS Metathesaurus paper - PDF (280 kb) MetaMap: Mapping Text to the UMLS Metathesaurus, July 2006
MetaMap Examples & Options - PDF (50 kb) MetaMap Options and Examples, September 2006
Effective Mapping of Biomedical Text to the UMLS  Metathesaurus: The MetaMap Program, 2001 paper - PDF (58 kb) Effective Mapping of Biomedical Text to the UMLS Metathesaurus: The MetaMap Program, 2001
2014 BioNLP MetaMap Tutorial
MetaMap 2014 BioNLP Tutorial - PowerPoint (2.8 mb) MetaMap 2014 BioNLP Tutorial Slides (PowerPoint)
2010 AMIA MetaMap Tutorial
MetaMap 2010 AMIA Tutorial Description - PDF (38 kb) MetaMap 2010 AMIA Tutorial Description (PDF)
MetaMap 2010 AMIA Tutorial Description - Text (3 kb) MetaMap 2010 AMIA Tutorial Description (Text)
MetaMap 2010 AMIA Tutorial Slides - PowerPoint (3.2 mb) MetaMap 2010 AMIA Tutorial Slides (PowerPoint)
MetaMap 2010 AMIA Tutorial Slides - PDF (1.6 mb) MetaMap 2010 AMIA Tutorial Slides (PDF)
Technical Documents
Increasing UMLS Coverage and Reducing Ambiguity via Automated Creation of Synonymous Terms: First Steps toward Filling UMLS Synonymy Gaps - PDF (187 kb) Increasing UMLS Coverage and Reducing Ambiguity via Automated Creation of Synonymous Terms: First Steps toward Filling UMLS Synonymy Gaps, 2017 White Paper
Ambiguity in the UMLS Metathesaurus
  • 2013 Higher Degree Metathesaurus Ambiguity Report - Excel (17 kb) 2013 Higher Degree Metathesaurus Ambiguity Report - Excel
  • Ambiguity in the UMLS Metathesaurus 2013 - PDF (201 kb) 2013 Summary Report 
  • 2012 Higher Degree Metathesaurus Ambiguity Report - Excel (14 kb) 2012 Higher Degree Metathesaurus Ambiguity Report - Excel
  • Ambiguity in the UMLS Metathesaurus 2012 - PDF (29 kb) 2012 Summary Report
  • 2011 Higher Degree Metathesaurus Ambiguity Report - Excel (13 kb) 2011 Higher Degree Metathesaurus Ambiguity Report - Excel
  • Ambiguity in the UMLS Metathesaurus 2011 - PDF (28 kb) 2011 Summary Report
  • 2010 Higher Degree Metathesaurus Ambiguity Report - Excel (12 kb) 2010 Higher Degree Metathesaurus Ambiguity Report - Excel
  • Ambiguity in the UMLS Metathesaurus 2010 - PDF (182 kb) 2010 Summary Report
  • Ambiguity in the UMLS Metathesaurus 2009 - PDF (384 kb) 2009 Summary Report
  • Ambiguity in the UMLS Metathesaurus 2008 - PDF (144 kb) 2008 Summary Report
  • Ambiguity in the UMLS Metathesaurus 2007 - PDF (100 kb) 2007 Summary Report
  • Ambiguity in the UMLS Metathesaurus 2006 - PDF (201 kb) 2006 Summary Report
  • Ambiguity in the UMLS Metathesaurus 2005 - PDF (124 kb) 2005 Summary Report
  • Ambiguity in the UMLS Metathesaurus 2004 - PDF (72 kb) 2004 Summary Report
  • Ambiguity in the UMLS Metathesaurus 2003 - PDF (92 kb) 2003 Summary Report
  • Ambiguity in the UMLS Metathesaurus 2002 - PDF (289 kb) 2002 Summary Report
  • Ambiguity in the UMLS Metathesaurus 2001 - PDF (182 kb) 2001 Summary Report
  • Ambiguity in the UMLS Metathesaurus 2000 - PDF (112 kb) 2000 Summary Report
  • Ambiguity in the UMLS Metathesaurus 1999 - PDF (59 kb) 1999 Summary Report
Filtering the UMLS Metathesaurus for MetaMap
  • Filtering the UMLS Metathesaurus for MetaMap 2012 - PDF (22 kb) 2012 Report
  • Filtering the UMLS Metathesaurus for MetaMap 2011 - PDF (22 kb) 2011 Report
  • Filtering the UMLS Metathesaurus for MetaMap 2010 - PDF (153 kb) 2010 Report
  • Filtering the UMLS Metathesaurus for MetaMap 2009 - PDF (22 kb) 2009 Report
  • Filtering the UMLS Metathesaurus for MetaMap 2008 - PDF (210 kb) 2008 Report
  • Filtering the UMLS Metathesaurus for MetaMap 2007 - PDF (72 kb) 2007 Report
  • Filtering the UMLS Metathesaurus for MetaMap 2006 - PDF (68 kb) 2006 Report
  • Filtering the UMLS Metathesaurus for MetaMap 2005 - PDF (59 kb) 2005 Report
  • Filtering the UMLS Metathesaurus for MetaMap 2004 - PDF (145 kb) 2004 Report
  • Filtering the UMLS Metathesaurus for MetaMap 2003 - PDF (51 kb) 2003 Report
  • Filtering the UMLS Metathesaurus for MetaMap 2002 - PDF (48 kb) 2002 Report
  • Filtering the UMLS Metathesaurus for MetaMap 2001 - PDF (48 kb) 2001 Report
  • Filtering the UMLS Metathesaurus for MetaMap 2000 - PDF (48 kb) 2000 Report
  • Filtering the UMLS Metathesaurus for MetaMap 1999 - PDF (18 kb) 1999 Report
MetaMap Technical Notes paper - PDF (99 kb) MetaMap Technical Notes, 1996
MetaMap Variant Generation paper - PDF (27 kb) MetaMap Variant Generation, 2001
MetaMap Candidate Retrieval paper - PDF (25 kb) MetaMap Candidate Retrieval, 2001
MetaMap Evaluation paper - PDF (63 kb) MetaMap Evaluation, 2001
MetaMap Mapping Algorithm paper - PDF (19 kb) MetaMap Mapping Algorithm, 2001
MetaMap Update Procedures paper - PDF (36 kb) MetaMap Update Procedures, 2000
Comparison of LVG and MetaMap Functionality paper - PDF (41 kb) Comparison of LVG and MetaMap Functionality, 1994
MetaMap Indexing (MMI)
MMI project description paper - PDF (5 kb) MMI project description, 1997
MMI ranking function paper - PDF (32 kb) MMI ranking function, 1997
A MEDLINE indexing experiment paper - PDF (39 kb) A MEDLINE indexing experiment, 1997
PhraseX
Finding UMLS Metathesaurus concepts in MEDLINE - PDF (163 kb) Finding UMLS Metathesaurus concepts in MEDLINE. Srinivasan, Suresh; Thomas C. Rindflesch; William T. Hole; and Alan R. Aronson. 2002. Isaac Kohane (ed.) Proceedings of the AMIA Annual Symposium, 727-31.
General Papers
MetaMap in the CALBC Workshop II - PDF (14 kb) MetaMap in the CALBC Workshop II. J. G. Mork, L. Peters, A. Jimeno Yepes, A. R. Aronson, O. Bodenreider, CALBC Workshop II, 2011.
Semantic processing for enhanced access to biomedical knowledge - PDF (229 kb) Semantic processing for enhanced access to biomedical knowledge, Rindflesch, Thomas C., and Alan R. Aronson. 2002. Vipul Kashyap and Leon Shklar (eds.) Real World Semantic Web Applications, 157-72. IOS Press.
Analysis of biomedical text for chemical names: A comparison of three methods - PDF (50 kb) Analysis of biomedical text for chemical names: A comparison of three methods, 1999
Hierarchical concept indexing of full-text documents in the UMLS information sources map paper (1998) - PDF (92 kb) Hierarchical concept indexing of full-text documents in the UMLS information sources map. Journal of the American Society for Information Science (1998). 50(6):514-23.
Query expansion using the UMLS Metathesaurus paper - PDF (41 kb) Query expansion using the UMLS Metathesaurus. Proceedings of the 1997 AMIA Annual Fall Symposium, 485-89.
Finding the findings: Identification of findings in medical literature using restricted natural language processing paper - PDF (51 kb) Finding the findings: Identification of findings in medical literature using restricted natural language processing. Proceedings of the 1996 AMIA Annual Fall Symposium, 239-43.
The effect of textual variation on concept based information retrieval paper - PDF (46 kb) The effect of textual variation on concept based information retrieval, 1996
Exploiting a large thesaurus for information retrieval paper - PDF (70 kb) Exploiting a large thesaurus for information retrieval. (1994) Proceedings of RIAO, 197-216.
 
Medical Text Indexer (MTI)
   
General Papers
Extracting Characteristics of the Study Subjects from Full-Text Articles - PDF (73 kb) Extracting Characteristics of the Study Subjects from Full-Text Articles. Dina Demner-Fushman, James G. Mork. AMIA 2015.
2015 Subject Extraction Test Collection Available
Feature engineering for MEDLINE citation categorization with MeSH - PDF (708 kb) Feature engineering for MEDLINE citation categorization with MeSH. Antonio Jose Jimeno Yepes, Laura Plaza, Jorge Carrillo-de-Albornoz, James G Mork and Alan R Aronson. BMC Bioinformatics 2015, 16:113.
External Link to BMC Bioinformatics Paper External Link to BMC Bioinformatics 2015, 16:113.
2014 Vocabulary Density Method for Customized Indexing of MEDLINE Journals (Poster) - PDF (32 kb) Vocabulary Density Method for Customized Indexing of MEDLINE Journals (Poster). James G. Mork, Dina Demner-Fushman, Susan C. Schmidt, Alan R. Aronson. AMIA 2014.
2014 Vocabulary Density Method for Customized Indexing of MEDLINE Journals (Actual Poster) - PDF Actual Poster (111 kb)       2014 Vocabulary Density Study Datasets Available
Recent Enhancements to the NLM Medical Text Indexer - PDF (95 kb) Recent Enhancements to the NLM Medical Text Indexer. James G. Mork, Dina Demner-Fushman, Susan C. Schmidt, Alan R. Aronson. BioASQ 2014.
2014 Vocabulary Density Study Datasets Available
2014 BioASQ Poster on Recent Enhancements to the NLM Medical Text Indexer - PDF (96 kb) 2014 BioASQ Poster on Recent Enhancements to the NLM Medical Text Indexer. James G. Mork, Dina Demner-Fushman, Susan C. Schmidt, Alan R. Aronson. BioASQ 2014.
Expanded The NLM Medical Text Indexer System for Indexing Biomedical Literature - PDF (324 kb) An expanded version of our The NLM Medical Text Indexer System for Indexing Biomedical Literature paper.
This expanded version paper incorporates all of the material from our shorter 2013 BioASQ Workshop paper and also contains unpublished material providing a more comprehensive description of the MTI system.
The NLM Medical Text Indexer System for Indexing Biomedical Literature - PDF (324 kb) The NLM Medical Text Indexer System for Indexing Biomedical Literature. J.G. Mork, A. Jimeno Yepes, A.R. Aronson. BioASQ 2013.
From Indexing the Biomedical Literature to Coding Clinical Text: Experience with MTI and Machine Learning Approaches, BioNLP 2007 - PDF (158 kb) From Indexing the Biomedical Literature to Coding Clinical Text: Experience with MTI and Machine Learning Approaches, BioNLP 2007
Automatic Indexing of Specialized Documents: Using Generic vs. Domain-Specific Document Representations, BioNLP 2007 - PDF (44 kb) Automatic Indexing of Specialized Documents: Using Generic vs. Domain-Specific Document Representations, BioNLP 2007
Semi-Automatic Indexing of Full Text Biomedical Articles, AMIA 2005 - PDF (100 kb) Semi-Automatic Indexing of Full Text Biomedical Articles, AMIA 2005
Evaluation of French and English MeSH Indexing Systems ..., AMIA 2005 - PDF (50 kb) Evaluation of French and English MeSH Indexing Systems with a Parallel Corpus, AMIA 2005
The NLM Indexing Initiative's Medical Text Indexer, MedInfo 2004 - PDF (54 kb) The NLM Indexing Initiative's Medical Text Indexer, MedInfo 2004
Application of a Medical Text Indexer to an Online Dermatology Atlas, MedInfo 2004 - PDF (319 kb) Application of a Medical Text Indexer to an Online Dermatology Atlas, MedInfo 2004
Automated and Semi-automated Indexing, Report to the Board of Regents 2002 - PDF (2.1 mb) Automated and Semi-automated Indexing, Report to the Board of Regents 2002
Automatic MeSH Term Assignment and Quality Assessment, AMIA 2001 - PDF (130 kb) Automatic MeSH Term Assignment and Quality Assessment, AMIA 2001
Machine Learning
Identifying Publication Types Using Machine Learning - PDF (102 kb) Identifying Publication Types Using Machine Learning.. Antonio J. Jimeno Yepes, James G. Mork, Alan R. Aronson. BioASQ Workshop 2013.
2013 BioASQ Publication Types Dataset Available
Comparison and combination of several MeSH indexing approaches - PDF (201 kb) Comparison and combination of several MeSH indexing approaches. Jimeno-Yepes, Antonio, Mork JG, Demner-Fushman D, Aronson AR. AMIA Annual Symposium Proceedings. Vol. 2013. American Medical Informatics Association, 2013.
2013 MTI ML Dataset Available
MeSH indexing based on automatically generated summaries - PDF (1.2 mb) MeSH indexing based on automatically generated summaries Antonio J Jimeno-Yepes, Laura Plaza, James G Mork, Alan R Aronson, Alberto Diaz. BMC Bioinformatics 2013
MeSH indexing: machine learning and lessons learned - PDF (228 kb) MEDLINE MeSH Indexing: Lessons Learned from Machine Learning and Future Directions. A. Jimeno Yepes, B. Wilkowski, J.G. Mork, D. Demner Fushman, and A.R. Aronson, ACM SIGHIT International Health Informatics Symposium, Miami, FL, USA, 2012.
2012 MTI ML Dataset Available
A One-Size-Fits-All Indexing Method Does Not Exist: Automatic Selection Based on Meta-Learning - PDF (988 kb) A One-Size-Fits-All Indexing Method Does Not Exist: Automatic Selection Based on Meta-Learning. Antonio Jimeno-Yepes, James G. Mork, Dina Demner-Fushman, Alan R. Aronson, JCSE, vol. 6, no. 2, pp.151-160, 2012.
2011 MTI ML Dataset Available
Automatic algorithm selection for MeSH Heading indexing based on meta-learning - PDF (78 kb) Automatic algorithm selection for MeSH Heading indexing based on meta-learning. A. Jimeno Yepes, J.G. Mork, D. Demner Fushman, and A.R. Aronson, International Symposium on Languages in Biology and Medicine, Singapore, December, 2011.
2011 MTI ML Dataset Available
A bottom-up approach to MEDLINE indexing recommendations - PDF (262 kb) A bottom-up approach to MEDLINE indexing recommendations. A. Jimeno Yepes, B. Wilkowski, J.G. Mork, E. van Lenten, D. Demner Fushman, A. R. Aronson, AMIA, Washington DC, 2011.
Subheading Attachment
Fine-Grained Indexing of the Biomedical Literature: MeSH Subheading Attachment for a MEDLINE Indexing Tool, AMIA 2007 - PDF (39 kb) Fine-Grained Indexing of the Biomedical Literature: MeSH Subheading Attachment for a MEDLINE Indexing Tool, AMIA 2007
Multiple Approaches to Fine-Grained Indexing of the Biomedical Literature, 2007 - PDF (103 kb) Multiple Approaches to Fine-Grained Indexing of the Biomedical Literature, Proc Pacific Symposium on Biocomputing 2007
User-Centered Evaluation
User-centered Evaluation of the MTI System, 2007 - PDF (1.1 mb) User-centered Evaluation of the MTI System, 2007
A MEDLINE Indexing Experiment Using Terms Suggested by MTI, June 2002 - PDF (510 kb) A MEDLINE Indexing Experiment Using Terms Suggested by MTI, June 2002
 
Word Sense Disambiguation (WSD)
   
Knowledge-based and knowledge-lean methods combined in unsupervised word sense disambiguation - PDF (150 kb) Knowledge-based and knowledge-lean methods combined in unsupervised word sense disambiguation. A. Jimeno Yepes, A.R. Aronson, ACM SIGHIT International Health Informatics Symposium, 2012.
Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts (490 kb) Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts, Laura Plaza, Antonio J Jimeno-Yepes, Alberto Diaz, Alan R Aronson, BMC Bioinformatics, August 2011
Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation (538 kb) Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation, Antonio J Jimeno-Yepes, Bridget T McInnes, Alan R Aronson, BMC Bioinformatics, June 2011
Collocation analysis for UMLS knowledge-based word sense disambiguation (316 kb) Collocation analysis for UMLS knowledge-based word sense disambiguation, Antonio J Jimeno-Yepes, Bridget T McInnes, Alan R Aronson, BMC Bioinformatics, June 2011
Preliminary results for Biomedical Word Sense Disambiguation based on Semantic Clustering - PDF (202 kb) Preliminary results for Biomedical Word Sense Disambiguation based on Semantic Clustering. Martin-Wanton, R. Berlanga-Llavori, A. Jimeno Yepes, Proceedings of DEXA, Toulouse, France, 2011.
Self-training and co-training in biomedical word sense disambiguation - PDF (18 kb) Self-training and co-training in biomedical word sense disambiguation. A. Jimeno Yepes, A. R. Aronson, Proceedings of ACL BioNLP, Portland, USA, 2011.
Knowledge-based biomedical word sense disambiguation: comparison of approaches (18 kb) Knowledge-based biomedical word sense disambiguation: comparison of approaches, Antonio Jimeno-Yepes, Alan R. Aronson, BMC Bioinformatics, November 2010
Query expansion for UMLS Metathesaurus disambiguation based on automatic corpus extraction - PDF (51 kb) Query expansion for UMLS Metathesaurus disambiguation based on automatic corpus extraction. A. Jimeno Yepes, A. R. Aronson, Proceedings of ICMLA, Bethesda, USA, 2010.
Improving an automatically extracted corpus for UMLS Metathesaurus word sense disambiguation - PDF (87 kb) Improving an automatically extracted corpus for UMLS Metathesaurus word sense disambiguation, Antonio Jimeno-Yepes, Alan R. Aronson, BioSEPLN, 2010.
Word sense disambiguation by selecting the best semantic type based on Journal Discriptor Indexing: preliminary experiment. - PDF (386 kb) Word sense disambiguation by selecting the best semantic type based on Journal Discriptor Indexing: preliminary experiment. Humphrey, SM; Rogers, WJ; Kilicoglu H; Demner-Fushman, D; Rindflesch, TC. J Am Soc Inf Sci Technol 2006 Jan;57(1):96-113.

Erratum in: J AM Soc Inf Sci, Mar. 2006, 57(4):726.   PDF: Erratum for Word sense disambiguation by selecting ... paper  (20.6kb)
Developing a Test Collection for Biomedical Word Sense Disambiguation, AMIA 2001 - PDF (93 kb) Developing a Test Collection for Biomedical Word Sense Disambiguation, Marc Weeber, James G. Mork, Alan R. Aronson, AMIA 2001
WSD Test Collection Available
Automatic indexing by discipline and high-level categories: methodology and potential applications. - PDF (76 kb) Automatic indexing by discipline and high-level categories: methodology and potential applications. Humphrey, SM; Rindflesh, TC; Aronson, AR. In: Soergel D, Srinivasan P, Kwasnik B, editors. Proceedings of the 11th ASIST SIG/CR Classification Research Workshop; 2000 Nov 12; Chicago. Silver Spring (MD): American Society for Information Science and Technology; 2000. p. 103-16.
Automatic indexing of documents from journal descriptors: a preliminary investigation. - PDF (551 kb) Automatic indexing of documents from journal descriptors: a preliminary investigation. Humphrey, SM. J Am Soc Inf Sci. 1999 Jun;50(8):661-74.
Ambiguity resolution while mapping free text to the UMLS Metathesaurus - PDF (38 kb) Ambiguity resolution while mapping free text to the UMLS Metathesaurus. (1994) Proceedings of the 18th Annual Symposium on Computer Applications in Medical Care, 240-4.
 
Machine Learning
   
MTI ML Package
Identifying Publication Types Using Machine Learning - PDF (102 kb) Identifying Publication Types Using Machine Learning.. Antonio J. Jimeno Yepes, James G. Mork, Alan R. Aronson. BioASQ Workshop 2013.
2013 BioASQ Publication Types Dataset Available
Comparison and combination of several MeSH indexing approaches - PDF (201 kb) Comparison and combination of several MeSH indexing approaches. Jimeno-Yepes, Antonio, Mork JG, Demner-Fushman D, Aronson AR. AMIA Annual Symposium Proceedings. Vol. 2013. American Medical Informatics Association, 2013.
2013 MTI ML Dataset Available
MeSH indexing: machine learning and lessons learned - PDF (228 kb) MeSH indexing: machine learning and lessons learned. A. Jimeno Yepes, B. Wilkowski, J.G. Mork, D. Demner Fushman, and A.R. Aronson, ACM SIGHIT International Health Informatics Symposium, Miami, FL, USA, 2012.
2012 MTI ML Dataset Available
A One-Size-Fits-All Indexing Method Does Not Exist: Automatic Selection Based on Meta-Learning - PDF (988 kb) A One-Size-Fits-All Indexing Method Does Not Exist: Automatic Selection Based on Meta-Learning. Antonio Jimeno-Yepes, James G. Mork, Dina Demner-Fushman, Alan R. Aronson, JCSE, vol. 6, no. 2, pp.151-160, 2012.
2011 MTI ML Dataset Available
General Papers
MeSH indexing based on automatically generated summaries - PDF (1.2 mb) MeSH indexing based on automatically generated summaries Antonio J Jimeno-Yepes, Laura Plaza, James G Mork, Alan R Aronson, Alberto Diaz. BMC Bioinformatics 2013
GeneRIF indexing: sentence selection based on machine learning - PDF (352 kb) GeneRIF indexing: sentence selection based on machine learning. Antonio J Jimeno-Yepes, J Caitlin Sticco, James G Mork, Alan R Aronson. BMC Bioinformatics 2013
Using the argumentative structure of scientific literature to improve information access - PDF (116 kb) Using the argumentative structure of scientific literature to improve information access. Antonio Jimeno Yepes, James G Mork, Alan R Aronson. BioNLP 2013
Automatic algorithm selection for MeSH Heading indexing based on meta-learning - PDF (78 kb) Automatic algorithm selection for MeSH Heading indexing based on meta-learning. A. Jimeno Yepes, J.G. Mork, D. Demner Fushman, and A.R. Aronson, International Symposium on Languages in Biology and Medicine, Singapore, December, 2011.
2011 MTI ML Dataset Available
A bottom-up approach to MEDLINE indexing recommendations - PDF (262 kb) A bottom-up approach to MEDLINE indexing recommendations. A. Jimeno Yepes, B. Wilkowski, J.G. Mork, E. van Lenten, D. Demner Fushman, A. R. Aronson, AMIA, Washington DC, 2011.
 
Clinical Related
   
A knowledge-based approach to medical records retrieval - PDF (146 kb) A knowledge-based approach to medical records retrieval. D. Demner-Fushman, S. Abhyankar, A. Jimeno-Yepes, R. Loane, B. Rance, F. Lang, N. Ide, E. Apostolova, and A.R. Aronson, In Text Retrieval Conference (TREC 2011) Proceedings, pages 163-172.
UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text (Full Paper), JBI 2010 - PDF (148 kb) UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text (Full Paper), JBI 2010
UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text (400 Word Abstract), AMIA 2009 - PDF (25 kb) UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text (400 Word Abstract), AMIA 2009
Extracting Rx Information from Clinical Narrative (Full Paper), 2010 - PDF (508 kb) Extracting Rx Information from Clinical Narrative (Full Paper), 2010
Extracting Rx Information from Clinical Narrative (Short Paper), JAMIA 2010 - PDF (53 kb) Extracting Rx Information from Clinical Narrative (Short Paper), JAMIA 2010
Methodology for Creating UMLS Content Views Appropriate for Biomedical Natural Language Processing, AMIA 2008 - PDF (50 kb) Methodology for Creating UMLS Content Views Appropriate for Biomedical Natural Language Processing, AMIA 2008
From Indexing the Biomedical Literature to Coding Clinical Text: Experience with MTI and Machine Learning Approaches, BioNLP 2007 - PDF (158 kb) From Indexing the Biomedical Literature to Coding Clinical Text: Experience with MTI and Machine Learning Approaches, BioNLP 2007
 
Challenges Participation
   
BioASQ Challenge - 2013
Expanded The NLM Medical Text Indexer System for Indexing Biomedical Literature - PDF (324 kb) An expanded version of our The NLM Medical Text Indexer System for Indexing Biomedical Literature paper.
This expanded version paper incorporates all of the material from our shorter 2013 BioASQ Workshop paper and also contains unpublished material providing a more comprehensive description of the MTI system.
The NLM Medical Text Indexer System for Indexing Biomedical Literature - PDF (324 kb) The NLM Medical Text Indexer System for Indexing Biomedical Literature. J.G. Mork, A. Jimeno Yepes, A.R. Aronson. 2013.
TREC Medical Records Track Participation - 2011
A knowledge-based approach to medical records retrieval - PDF (146 kb) A knowledge-based approach to medical records retrieval. D. Demner-Fushman, S. Abhyankar, A. Jimeno-Yepes, R. Loane, B. Rance, F. Lang, N. Ide, E. Apostolova, and A.R. Aronson, In Text Retrieval Conference (TREC 2011) Proceedings, pages 163-172.
I2B2 - 2009
Extracting Rx Information from Clinical Narrative (Full Paper), 2010 - PDF (508 kb) Extracting Rx Information from Clinical Narrative (Full Paper), 2010
Extracting Rx Information from Clinical Narrative (Short Paper), JAMIA 2010 - PDF (53 kb) Extracting Rx Information from Clinical Narrative (Short Paper), JAMIA 2010
TREC Genomics Track - 2003, 2004, 2005, 2006, 2007
Combining Resources to Find Answers to Biomedical Questions - PDF (112 kb) Combining Resources to Find Answers to Biomedical Questions, Demner-Fushman D, Humphrey SM, Ide NC, Loane RF, et al. Proc TREC 2007, 2005-14.
Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort - PDF (156 kb) Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort, Demner-Fushman D, Humphrey SM, Ide NC, Loane RF, Ruch P, Ruiz ME, Smith LH, Tanabe LK, Wilbur WJ, Aronson AR. Proc TREC 2006, 569-76.
Fusion of knowledge-intensive and statistical approaches for retrieving and annotating textual genomics documents - PDF (296 kb) Fusion of knowledge-intensive and statistical approaches for retrieving and annotating textual genomics documents, Aronson AR, Demner-Fushman D, Humphrey SM, Lin J, Liu H, Ruch P, Ruiz ME, Smith LH, Tanabe LK, Wilbur WJ. Proc TREC 2005, 36-45.
Knowledge-intensive and statistical approaches to the retrieval and annotation of genomics MEDLINE citations - PDF (275 kb) Knowledge-intensive and statistical approaches to the retrieval and annotation of genomics MEDLINE citations, Aronson AR, Demner D, Humphrey SM, Ide NC, Kim W, Liu H, Loane RR, Mork JG, Smith LH, Tanabe LK, Wilbur WJ, Xie N. Proc TREC 2004, 503-11.
Methods for Accurate Retrieval of MEDLINE Citations in Functional Genomics - PDF (357 kb) Methods for Accurate Retrieval of MEDLINE Citations in Functional Genomics, Kayaalp, Mehmet, Aronson, Alan R, Humphrey, Susanne M, Ide, Nicholas C, Tanabe, Lorraine K. Proc TREC 2003, 175-84.
 
Lister Hill Content View (LNCV)
   
UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text (Full Paper), JBI 2010 - PDF (148 kb) UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text (Full Paper), JBI 2010
UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text (400 Word Abstract), AMIA 2009 - PDF (25 kb) UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text (400 Word Abstract), AMIA 2009
Methodology for Creating UMLS Content Views Appropriate for Biomedical Natural Language Processing, AMIA 2008 - PDF (50 kb) Methodology for Creating UMLS Content Views Appropriate for Biomedical Natural Language Processing, AMIA 2008

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