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News and Events

Paper at ACL 2022 workshop: BioNLP

Health Informatics, Information Systems, Publication, Research Paper, SYSLAB

I had the pleasure of presenting a poster of a paper by Hercules Dalianis and me: Utility Preservation of Clinical Text After De-Identification. The paper investigates how automatic de-identification, a necessarily imperfect process, impacts the quality of the resulting texts. When a de-identification system incorrectly class a word as sensitive, the data will be slightly corrupted. Many researchers have been worried that this would make the data less useful, and we investigate this issue.

The impact of automatic de-identification on quality is evaluated using both qualitative and quantitative (machine learning) methods. We find no losses in utility for clinical NLP on three downstream clinical tasks. In fact, the machine learning models trained using automatic de-identification seem to work just as well as those trained using sensitive data. We also find that the experts in our study think the de-identification works well.

Participating in the 60th ACL conference was a great experience. I learned a lot from our global NLP community and met many researchers interested in our work at DSV. You can find the paper here, and the poster I presented here.

Three research application in Health Informatics are funded!

Enterprise Modelling, Health Informatics, Information Systems, New Project, SYSLAB

Three research applications from the IS unit researchers have been approved. The applications were all sent to the Stockholm County Council (SLL) – Stockholm University Call in October 2017.

KVALPA: What quality indicators in the patient journal’s free text are needed to measure the quality of care? The project aims to create an automatic method for this through machine learning. Project leader: Hercules Dalianis

IMPROVE JANUSMED WITH PROCESS MINING. The project is about developing safer drug prescription by evaluating and improving Janusmed with process mining. Janusmed is a decision support system that controls and warns whether there is a risk of serious drug interactions as well as side effects due to enhanced effects when co-administered with multiple drugs. Stockholm County Council (SLL) provides, develops and manages Janusmed. Janusmed is available today on the web via janusinfo.se and is also integrated with the SLL journal systems. To the best of our knowledge, process mining has not yet been applied in any research project in Sweden. Project leader: Paul Johannesson. Participants: Amin Jalali, Erik Perjons (and Uno Fors in a limited role).

CAPABILITY AND VALUE-BASED CHANGE ANALYSIS OF THE 1177 VÅRDGUIDEN. The aim of the project is to develop a method to support the management organization for the 1177 Vårdguiden at SLL in assessing and analyzing how change proposals of the 1177 service, including affects on the various actors involved in the network around the service – and estimates of costs and benefits for the various actors. The method is based on (1) network-based analysis of the values and abilities of the various stakeholders in the network, and (2) on existing enterprise architecture of the management organization – in form of enterprise models such as value, process and information models over the 1177 service. Project leader: Erik Perjons. Participants: Martin Henkel, Ilia Bider (and Anders Tell in a limited role).

Three accepted papers to WorldCist16′, Recife, Brazil

E-government, Information Systems, Research Paper, SYSLAB

Three accepted papers to WorldCist16′ Recife, Brazil. One Norwegian point each!

WorldCist’16 – 4th World Conference on Information Systems and Technologies, to be held at Recife, PE, Brazil, 22 – 24 March 2016.

— “A Business and IT Architecture Model Supporting Public Organizations Introducing Language Technologies”, Martin Henkel, Erik Perjons, Eriks Sneiders

— “Email Answering by Matching Question and Context-Specific Text Patterns: Performance and Error Analysis” Eriks Sneiders, Jonas Sjöbergh, Alyaa Alfalahi

— “Review of the Main Approaches to Automated Email Answering”, Eriks Sneiders

Congratulations

Text mining of cancer pathology reports at Kreftregisteret, Oslo, 8-9 april 2015

Health Informatics, Information Systems, SYSLAB

Rebecka Weegar and I had a kickoff for our Minecan project at Kreftregisteret, Oslo, 8-9 April 2015.
200 000 cancer pathology reports for cancer are sent yearly from all hospitals in Norway to Kreftregistret to be manually read and entered into a database. 25 human coders are performing this work.
Our plan is to build a prototype that automatically reads the pathology reports that are written in Norwegian and transfers some of the important information into the database. We are planning to use already coded pathology reports as training material.

Jan Nygård and Rebecka Weegar among pathology reports

Jan Nygård our host, and Rebecka Weegar among pathology reports

Hercules, Rebecka and Kjersti, coder

Hercules, Rebecka and Kjersti Østby , coder

 

Kreftregistret

Kreftregistret

Tapas

Tapas

 

 

Stockholm Natural Language Processing Meetup

Information Systems

Today I visited Stockholm Natural Language Processing Meetup. This time hosted by Gavagai at Bondegatan 21, Södermalm in Stockholm. Sahar Asadi from Meltwater, organised everything. The topic today was “Word embedding: From theory to practice. Three speakers talked: Magnus Sahgren on “Distributional semantics at Gavaga”, Hendrik Heuer on “Word2vec from theory to practice and finally Jimmy Callin on “Distributional semantic models in practice”. During two hours we obtained a nice overview of the area and different approaches to perform different forms of distributional semantics. Please try http://lexicon.gavagai.se, it is fun.

As you maybe also know Dr. Maria Skeppstedt is post doc at Gavagai and Linnaeus University under supervision of Dr. Magnus Sahlgren. Everything funded by Vetenskapsrådet.

Some photos for the meetup and a recording of the presentation 

/Hercules

Workshop: By Dan Csontos: How to publish in top ranked scientific journals

ACT, BPM and Enterprise Modeling, Consumer-oriented Mobile Services, Digital Games, Digital Systems Security, E-government, Health Informatics, ICT4D, IDEAL, Immersive Participation, Information Systems, Interaction Design, IT Management, Knowledge and Communication, Risk and Decision Analysis, SAS, Service Science, SYSLAB, TEL, TEL and Collaboration

40 participants at Dr. Dan Csontos’ Workshop, PhD-students, and PhDs, all enthusiastic. Good discussions on how to get your paper through the editor’s gate with elegantly formulated cover letters. If that does not work – appeal if necessary. Moreover we discussed how to write informative titles, smart abstracts, and well structured papers and obtain the “flow” in the paper.  As well as strategies for getting out mostly of the research and publish with high impacts and finally to get your paper understood by the reader.

The EnRiMa project successfully completed the second review

BPM and Enterprise Modeling, Information Systems, Photo, Presentation, Prototype, SYSLAB

A part of the EnRiMa system demonstrated in Brussels

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/