Azad Dehghan from University of Manchester held an IS-seminar yesterday with the title: Extracting and Modelling Clinical Pathways from Healthcare Narratives. Azad works at the HECTA – Healthcare Text Analytics @ gnTEAM group. Azad presented his work on extraction of named entities using conditional random fields with a set of features. He also showed how to use conditional random fields combined with a rule based approach to extract temporal expressions and events.
Medinfo 21-23 Aug 2013 Copenhagen
We – Mia Kvist, Sumithra Velupillai, Maria Skeppstedt, Danny Brash and I participated at SHI 2013 and Medinfo 2013 in Copenhagen. SHI 2013 is the Scandinavian Conference on Health Informatics 2013 and Medinfo 2013 is the 14th World Congress on Medical and Health Informatics and is the largest medical informatics conference.
We had three papers at SHI 2013, Nurses’ experiences with electronic medical records by Anders Jansson, Marcus Vidarsson & Danny Brash, where Anders and Marcus are bachelor students of Danny who also presented the paper. The paper with the title Professional Language in Swedish Radiology Reports – Characterization for Patient-Adapted Text Simplification by Maria Kvist and Sumithra Velupillai was presented by Mia Kvist and finally the paper with the title Functions for Personal Health Records in Sweden – Patient Perspectives by Sumithra Velupillai, Omran Ibrahim and Maria Kvist, was presented by Sumithra where Omran was Sumithras and Maria Kvists master student.
Medinfo 2013 followed directly after SHI 2013 and had 1 200 participants. We had one paper presentation, one poster presentation and organized one panel discussion. Sumithra presented the paper with the title Extending the NegEx Lexicon for Multiple Languages by Wendy Chapman, Dieter Hilert, Sumithra Velupillai, Maria Kvist , Maria Skeppstedt, Brian Chapman, Michael Conway, Melissa Tharp, Danielle Mowery and Louise Deleger, the room was packed with people so they had to stand along the walls of the room!
The poster with the title Using Text Prediction for Facilitating Input and Improving Readability of Clinical Text by Magnus Ahltorp, Maria Skeppstedt,Hercules Dalianis and Maria Kvist was presented by Maria Skeppstedt. The panel had the title Automatic Clinical Text De-Identification: Is It Worth It, and Could It Work for Me?, and was held by Stéphane M. Meystre, Hercules Dalianis and Pierre Zweigenbaum. Methods and issues of de-identification in three different countries were presented in the panel, and this also lead to intensive discussions about de-identification , ethics and how to use clinical records for research.
We have written a short project report in Swedish from the conference, if you are interested to read it, please contact me.
Here follows some photos from the conference
ACL 2013, Sofia
The clinical text mining group had three papers at workshops of this years ACL conference in Sofia. We had two papers at the BioNLP workshop (“Corpus-Driven Terminology Development: Populating Swedish SNOMED CT with Synonyms Extracted from Electronic Health Records” by Aron Henriksson, Maria Skeppstedt, Maria Kvist, Martin Duneld and Mike Conway and “Adapting a parser to clinical text by simple pre-processing rules” by Maria Skeppstedt) and a paper at the ACL student research workshop (“Annotating named entities in clinical text by combining pre-annotation and active learning” by Maria Skeppstedt).
Among the papers which I found most interesting at the conference were: “Improving Text Simplification Language Modeling Using Unsimplified Text Data” by David Kauchak, as well as the winner of the student paper competition: “A corpus-based evaluation method for Distributional Semantic Models” by Abdellah Fourtassi and Emmanuel Dupoux. Interesting workshop paper were: “Analysis of Stopping Active Learning based on Stabilizing Predictions” by Michael Bloodgood and John Grothendieck and “Towards Dynamic Word Sense Discrimination with Random Indexing” by Hans Moen, Erwin Marsi and Björn Gambäck.
Conference venue
At the conference dinner, a dance group performed traditional bulgarian folk dances and also taught us some of the dance steps.
The last day of the conference, many of the conference participants joined a walking tour, in which we were shown some of the many beautiful historic buildings of Sofia.
Paper accepted for publication in Journal of Global Information Technology Management (JGITM)
A paper written by Edephonce N. Nfuka (The Open University of Tanzania, Tanzania) and Lazar Rusu (Stockholm University, Sweden), entitled: “Critical Success Framework for Implementing Effective IT Governance in Tanzanian Public Sector Organizations “ has been accepted for publication in the Journal of Global Information Technology Management (JGITM), Vol.16, No. 3, July 2013, Ivy League Publishing. The Journal of Global Information Technology Management (JGITM) (http://jgitm.uncg.edu/) is a high quality international journal which addresses international issues of IT management. JGITM is the premier journal in Global IT and is included in Social Sciences Citation Index (SSCI).
The EnRiMa project successfully completed the second review
A part of the EnRiMa system demonstrated in Brussels
The EnRiMa project partners gathered in Brussels 29-30 May to have the projects second review meeting. During the review meeting the prototype of the EnRiMa decisions support system was demonstrated for the reviewers. It was demonstrated how the system based on information about a building, such as existing heating equipment and inner volumes, could calculate the optimal way to manage the building. Furthermore it was demonstrated how the system could collect data from external systems, such as weather forecast providers and installed building management systems. A part of the team that demonstrated the system in Brussels was SysLab members Martin Henkel and Janis Stirna. The SysLab team also includes Wayne Westmoreland that together with Martin has worked on the implementation of the system. The EnRiMa project (Energy Efficiency and Risk Management in Public Buildings) is a European Commission funded collaboration between Stockholm University, University College London, International Institute for Applied Systems Analysis, Universidad Rey Juan Carlos, Minerva Consulting and Communication, SINTEF Group, Tecnalia, and Hidrocantábrico Energía.
Project website: http://www.enrima-project.eu/
Two scholarships to Aron Henriksson
Aron Henriksson obtained two scholarships, Donationsstipendier from Stockholms universitet (John Söderberg) and Google grant to participate at two different summer schools!
Congratulation Aron!
NoDaLiDa Conference 2013
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
View from the Opera where the conference dinner was held
Ph.D. Funding from Swedish Research School of Management and Information Technology (MIT)
This year I have submitted an application to Swedish Research School of Management and Information Technology (MIT) for requesting funds for a Ph.D. student at DSV/Stockholm University that is performing research in IT Management with a focus on IT Governance. The application has been successfully, and in the next five years we will receive 1500000 SEK from MIT for financing together with our department the Ph.D. position at DSV of Parisa Aasi. For more information about Swedish Research School of Management and Information Technology (MIT) please access the following link: http://www.forskarskolan-mit.nu/