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News and Events

NoDaLiDa Conference 2013

Health Informatics, SYSLAB

Hideyuki Tanushi presented the paper “Negation Scope Delimitation in Clinical Text Using Three Approaches: NegEx, PyConTextNLP and SynNeg” at NoDaLiDa 2013, the 19th Nordic Conference on Computational Linguistics, which was held in Oslo this time. Co-authors to the paper by Hideyuki were Hercules Dalianis, Martin Duneld, Maria Kvist, Maria Skeppstedt and Sumithra Velupillai. The paper was presented as a poster and, (as it was one of the best short papers) also with an oral presentation.

Among other interesting papers can be mentioned “Normalisation of Historical Text Using Context-Sensitive Weighted Levenshtein Distance and Compound Splitting” (as these methods are now applied on our clinical texts); Two readability papers: “Statistical Machine Translation with Readability Constraints” and “Features Indicating Readability in Swedish Text”; One paper about terminology extraction “IPhraxtor: A Linguistically Informed System for Extraction of Term Candidates”; and “The Automatic Identification of Discourse Units in Dutch Text”, which presented a rule-based method for identifying discourse units.

Hideyuki at the poster

Hideyuki at the poster

View from the Opera where the conference dinner was held

View from the Opera where the conference dinner was held

Louhi 2013: The 4th International Workshop on Health Document Text Mining and Information Analysis

Health Informatics, SYSLAB

Hercules Dalianis, Sumithra Velupillai and Aron Henriksson participated in the Louhi 2013 Workshop on Health Document Text Mining and Information Analysis. This year it was hosted by NICTA in Sydney, Australia on February 11-12. Sumithra presented the paper “Porting a Rule-based Assertion Classifier for Clinical Text from English to Swedish” by Sumithra Velupillai, Maria Skeppstedt, Maria Kvist, Danielle Mowery (University of Pittsburgh), Brian Chapman (UCSD), Hercules Dalianis and Wendy Chapman (UCSD). Aron presented the paper “Optimizing the Dimensionality of Clinical Term Spaces for Improved Diagnosis Coding Support”, co-authored with Martin Hassel. Hercules was invited to give a keynote, where he talked about detecting hospital-acquired infections from patient records and the results from the Detect-HAI project. A workshop report (in Swedish) is available on request from the author.

Southern California Workshop on Medical Text Analysis and Visualization

Health Informatics, SYSLAB, Visit

Aron Henriksson and Maria Skeppstedt presented at the Southern California Workshop on Medical Text Analysis and Visualization during their visit at the Division of Biomedical Informatics, University of California, San Diego. There were many interesting presentations at the workshop, which also led to interesting discussions. The presentation topics most closely related to what is being done in our Clinical Text Mining Group at DSV were “Using Twitter to examine smoking behaviour & tobacco products” by Mike Conway (Division of Biomedical Informatics, UCSD), “Encoding Semantic and Discourse Features for Problem List Generation” by Danielle Mowery (Division of Biomedical Informatics, UCSD) and “Evidence-based Reduction of Perceived and Actual Text Difficulty Using Natural Language Processing” by Gondy Leroy (School of Information Systems & Technology Claremont Graduate University), all of them giving much useful input to our current projects.

Inspiring talks were also given by the other speakers, giving new ideas to text mining and visualisation approaches, e.g. by Andre Skupin (Department of Geography, SDSU) who talked about “Visualizing the topical structure of the medical sciences: A self-organizing
map approach” and Ricky Taira (Department of Radiological Sciences, UCLA) who talked about “Defining and organizing medical NLP tasks”.

Aron talking about automatic synonym extraction using random indexing

Aron talking about automatic synonym extraction using random indexing

Maria Talking about features for named entity recognition

Maria talking about features for named entity recognition

Research Visit at UC San Diego

Health Informatics, Photo, Presentation, SYSLAB, Visit

Maria Skeppstedt and Aron Henriksson are currently visiting the Division of Biomedical Informatics (DBMI) at the University of California, San Diego, which is located in the San Diego Supercomputer Center (SDSC). The visit will last for a month and is one of several exchanges between the Natural Language Processing (NLP) group at DBMI and the Clinical Text Mining Group at DSV that have been made possible through the Interlock project.

Last week we were invited together with Wendy Chapman to give a talk at a PACE (Predictive Analytics Center of Excellence) seminar at SDSC. Wendy first talked about NLP in general, while Maria and I talked about our respective research on NLP in the clinical domain.

Coling 2012, Bombay, India, 9-14 December

Health Informatics, Information Systems, Research Paper, SYSLAB

The 24th International Conference on Computational Linguistics, Coling 2012  took place in Bombay (Mumbai) India, December 9-14. It is the largest computational linguistics conference in the world. At the conference were 600 participants from 60 countries. 1600 papers were submitted to the conference and 400 were accepted, that gives an acceptance rate of  25 percent.

Claudia Ehrentraut my master student from Uppsala University presented our paper: Detection of Hospital Acquired Infections in sparse and noisy Swedish patient records. A machine learning approach using Naïve Bayes, Support Vector Machines and C4.5, that was written by Claudia Ehrentraut, Hideyuki Tanushi, Hercules Dalianis and Jörg Tiedemann at the workshop Sixth Workshop on Analytics for Noisy Unstructured Text Data, AND 2012 that was held in conjunction with the conference.

We have written a short report from the conference, if you would like to have it please contact me.