Health Informatics Publications

These publications describe my work in Health Informatics. These usually revolve around applying techniques we have developed for general English to the medical domain, which can include clinical notes or scholarly writing about medical topics.

2017

Improving Correlation with Human Judgments by Integrating Semantic Similarity with Second--Order Vectors (McInnes and Pedersen) Appears in the Proceeddings of the 16th Workshop on Biomedical Natural Language Processing (BioNLP 2017), August 2017, pp. 107-116, Vancouver, BC.

2016

Analysis of Anxious Word Usage on Online Health Forums (Rey-Villamizar, Shrestha, Sadeque, Bethard, Pedersen, Mukherjee, and Solorio) Appears in the Proceedings of the Seventh International Workshop on Health Text Mining and Information Analysis (Louhi 2016), November 2016, pp. 37-42, Austin, TX.
Why Do They Leave: Modeling Participation in Online Depression Forums (Sadeque, Pedersen, Solorio, Shrestha, Rey-Villamizar, and Bethard) Appears in the Proceedings of The Fourth International Workshop on Natural Language Processing for Social Media (SocialNLP-2016), November 2016, pp. 14-19, Austin, TX.
Semi-supervised CLPsych 2016 Shared Task System Submission (Rey-Villamizar, Shrestha, Solorio, Sadeque, Bethard and Pedersen) Appears in the Proceedings of the 3rd Workshop on Computational Linguistics and Clinical Psychology - From Linguistic Signal to Clinical Reality (ClPsych 2016), June 2016, pp. 171-175, San Diego, CA.
Age and Gender Prediction on Health Forum Data (Shrestha, Rey-Villamizar, Sadeque, Pedersen, Bethard, Solorio) Appears in the Proceedings of the 10th edition of the Language Resources and Evaluation Conference (LREC 2016), May 2016, pp. 3394-3401, Portoroz, Slovenia.

2015

Predicting Continued Participation in Online Health Forums (Sadeque, Solorio, Pedersen, Shrestha, Bethard) Appears in the Proceedings of the Sixth International Workshop on Health Text Mining and Information Analysis (Louhi 2015), September 2015, Lisbon, Portugal.
Screening Twitter Users for Depression and PTSD using Lexical Decision Lists (Pedersen) Appears in the Proceedings of the 2nd Computational Linguistics and Clinical Psychology Workshop - From Linguistic Signal to Clinical Reality (CLPsych 2015), June 2015, pp. 46-53, Denver, CO.
Evaluating Semantic Similarity and Relatedness over the Semantic Grouping of Clinical Term Pairs (McInnes and Pedersen) - Journal of Biomedical Informatics, 54, 329 - 336, April 2015.

2014

U-path : An undirected path-based measure of semantic similarity (McInnes, Pedersen, Liu, Melton, Pakhomov) - Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association, November 2014, Washington, DC.
Duluth: Measuring Cross-Level Semantic Similarity with First and Second Order Dictionary Overlaps (Pedersen) - Appears in the Proceedings of the 8th International Workshop on Semantic Evaluation (SemEval 2014), in conjunction with the 25th International Conference on Computational Linguistics (COLING-2014), August 23-24, 2014, pp. 247 - 251, Dublin, Ireland.

2013

Evaluating Measures of Semantic Similarity and Relatedness to Disambiguate Terms in Biomedical Text (McInnes and Pedersen) - Journal of Biomedical Informatics, 46(6), 1116 - 1124, December 2013.
UMLS::Similarity: Measuring the Relatedness and Similarity of Biomedical Concepts (McInnes, Liu, Pedersen, Melton, and Pakhomov) - Appears in the Proceedings of the 2013 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, June, 9-14, 2013, pp. 28-31, Atlanta, Georgia.(Demonstration System) [acceptance rate 53%]

2012

Using SemRep to Label Semantic Relations Extracted from Clinical Text (Liu, Bill, Fiszman, Rindflesch, Pedersen, Melton, and Pakhomov) - Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association, November 3-7, 2012, pp. 587 - 595, Chicago, IL.
Evaluating Semantic Relatedness and Similarity Measures with Standardized MedDRA Queries (Bill, Liu, McInnes, Melton, Pedersen, and Pakhomov) - Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association, November 3-7, 2012, pp. 43 - 50, Chicago, IL.
Rule-based and Lightly Supervised Methods to Predict Emotions in Suicide Notes (Pedersen) - Biomedical Informatics Insights 2012:5 (Suppl. 1) pp 185 - 193.
Semantic Relatedness Study Using Second Order Co-occurrence Vectors Computed from Biomedical Corpora, UMLS and WordNet (Liu, McInnes, Pedersen, Melton-Meaux, and Pakhomov) - Appears in the Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium, January 28-30, 2012, pp. 363-371, Miami, FL
Measuring the Similarity and Relatedness of Concepts in the Medical Domain : IHI 2012 Tutorial Overview (Pedersen, Pakhomov, McInnes, and Liu) - Appears in the Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium, January 28-30, 2012, pp. 363 - 371, Miami, FL

2011

Knowledge-based Method for Determining the Meaning of Ambiguous Biomedical Terms Using Information Content Measures of Similarity (McInnes, Pedersen, Liu, Melton, and Pakhomov) - Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association, October 22-26, 2011, pp. 895 - 904, Washington, DC.
Using Second-order Vectors in a Knowledge-based Method for Acronym Disambiguation (McInnes, Pedersen, Liu, Pakhomov, and Melton) - Appears in the Proceedings of the Fifteenth Conference on Computational Natural Language Learning (CoNLL 2011), June 23-24, 2011, pp. 145 - 153, Portland, Oregon.
Towards a Framework for Developing Semantic Relatedness Reference Standards (Pakhomov, Pedersen, McInnes, Melton, Ruggieri, and Chute) - Journal of Biomedical Informatics, 44(2), 251-265, April 2011. [Data]

2010

The Effect of Different Context Representations on Word Sense Discrimination in Biomedical Texts (Pedersen) - Appears in the Proceedings of the 1st ACM International Health Informatics Symposium, November 11 - 12, 2010, pp. 56 - 65, Arlington, VA. [acceptance rate 17%]
Semantic Similarity and Relatedness between Clinical Terms : An Experimental Study (Pakhomov, McInnes, Adam, Liu, Pedersen, and Melton) - Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association, November 13-17 2010, pp. 572 -- 576, Washington, DC. [acceptance rate 50%]

2009

UMLS-Interface and UMLS-Similarity : Open Source Software for Measuring Paths and Semantic Similarity (McInnes, Pedersen, and Pakhomov) - Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association, Nov 14-18, 2009, pp. 431-435, San Francisco, CA
Supervised and Knowledge-based Methods for Disambiguating Terms in Biomedical Text using the UMLS and MetaMap (McInnes) - PhD Dissertation, Department of Computer Science and Engineering, University of Minnesota, Twin Cities, September, 2009.

2008

Learning High Precision Rules to Make Predictions of Morbidities in Discharge Summaries (Pedersen) - Appears in the Proceedings of the Second i2b2 Workshop on Challenges in Natural Language Processing for Clinical Data, Nov 7-8, 2008, Washington, DC.

2007

Using UMLS Concept Unique Identifiers (CUIs) for Word Sense Disambiguation in the Biomedical Domain (McInnes, Pedersen, and Carlis) - Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association, Nov 10-14, 2007, pp. 533-537, Chicago, IL. [acceptance rate 45%]
Measures of Semantic Similarity and Relatedness in the Biomedical Domain (Pedersen, Pakhomov, Patwardhan, and Chute), Journal of Biomedical Informatics, 40(3), 288-299, June 2007. [Journal Citation Reports Index Factor 2006: 2.346]
Determining the Syntactic Structure of Medical Terms in Clinical Notes (McInnes, Pedersen, and Pakhomov) - Appears in the Proceedings of BioNLP 2007, June 29, 2007, pp. 9-16, Prague, Czech Republic. [acceptance rate 29%] [ppt]

2006

Determining Smoker Status using Supervised and Unsupervised Learning with Lexical Features (Pedersen) - Appears in the Working Notes of the i2b2 Workshop on Challenges in Natural Language Processing for Clinical Data, Nov 10-11, 2006, Washington, DC.
A Comparative Study of Supervised Learning as Applied to Acronym Expansion in Clinical Reports (Joshi, Pakhomov, Pedersen, and Chute) - Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association, pp. 399-403, Nov 11-16, 2006, Washington, DC. [acceptance rate 41%] [ppt]
An End-to-End Supervised Target-Word Sense Disambiguation System (Joshi, Pakhomov, Pedersen, Maclin, and Chute) - Appears in the Proceedings of the Twenty-First National Conference on Artificial Intelligence, pp. 1941-1942, July 19, 2006, Boston, MA. (Intelligent System Demonstration)

2005

A Comparative Study of Support Vector Machines Applied to the Supervised Word Sense Disambiguation Problem in the Medical Domain (Joshi, Pedersen, and Maclin) - Appears in the Proceedings of the Second Indian International Conference on Artificial Intelligence, pp. 3449-3468, December 20-22, 2005, Pune, India. [acceptance rate 35%]
Abbreviation and Acronym Disambiguation in Clinical Discourse (Pakhomov, Pedersen and Chute) - Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association, pp. 589-593, October 22-26, 2005, Washington, DC. [acceptance rate 37%]
Resolving Ambiguities in Biomedical Text with Unsupervised Clustering Approaches (Savova, Pedersen, Purandare and Kulkarni) - University of Minnesota Supercomputing Institute Research Report UMSI 2005/80 and CB Number 2005/21, May.
Measures of Semantic Similarity and Relatedness in the Medical Domain (Pedersen, Pakhomov, and Patawardhan) - University of Minnesota Digital Technology Center Research Report DTC 2005/12, May. [This is a preliminary version of the JBI 2007 article].

2004

Incorporating Ngram Statistics in the Normalization of Clinical Notes (McInnes, Pakhomov, Pedersen and Chute) - Appears in MEDINFO 2004 : Proceedings of the 11th World Congress on Medical Informatics, p. 1882, September 2004, San Francisco, CA. (Poster)

By: Ted Pedersen - tpederse AT d umn edu