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IEEE Conference on Bioinformatics and Biomedicine (BIBM) in Belfast

Health Informatics, Photo, Presentation, SYSLAB

Jing Zhao and Aron Henriksson attended the IEEE International Conference on Bioinformatics and Biomedicine (BIBM) in Belfast, UK on November 2-5, 2014. The scientific program this year consisted of 111 papers, including two regular papers from DSV. Jing presented the paper “Detecting Adverse Drug Events with Multiple Representations of Clinical Measurements”, co-authored with Aron Henriksson, Lars Asker and Henrik Boström. Aron presented the paper “Generating Features for Named Entity Recognition by Learning Prototypes in Semantic Space: The Case of De-Identifying Health Records”, co-authored with Hercules Dalianis and Stewart Kowalski.

Open Seminar with Dr. Dragos Vieru

IT Management, Photo, Presentation, Slides, SYSLAB

On October 24, 2014 at DSV, Dr. Dragos Vieru from Distance Learning University of Quebec (Télé-Université du Québec), Canada has given an open seminar regarding “Working Under Grey Skies: Information Systems Development and Social Mechanisms in a Post-merger Context”. The seminar was organized by the IT Management group within IS unit at DSV.  The slides of the presentation are available here Presentation-Dragos Vieru
A short description about our guest speaker and a picture from the seminar you could find below.

Speaker:
Dragos Vieru is an Assistant Professor at Distance Learning University of Quebec. He received his Ph.D. in Information Technology at HEC Montréal and a MSc in MIS from John Molson School of Business (Concordia University) in Montreal. His research interests are in the areas of IT-enabled organizational change, knowledge sharing, and IT governance. Dragos Vieru has published papers in International Journal of Information Management (journal ranked ‘A’ in Information and Library Sciences category), the International Journal of Social & Organizational Dynamics in Information Technology and in the Lecture Notes in Business Information Processing. He is chair of the minitrack (Organizational and Social Dynamics in Information Technology mini-track) at the AMCIS and co-chair of the same minitrack at the Hawaii International Conference on System Sciences (HICSS). He has over 15 years of professional experience in IT project management in the health care industry.

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EnRiMa Final Review held in Brussels

BPM and Enterprise Modeling, Networking, Photo, Presentation, Prototype, SYSLAB

The 28 May, Janis and I went to the final review meeting of the FP7 EU project EnRiMa. The purpose of the EnRiMa project has been to reduce the energy consumption in public buildings by providing an innovative decision support system. During the review meeting the consortium demonstrated how the final system worked. Particular emphasis was put the systems integration with building management systems, making is possible for the system to control equipment installed in the building based on preferred indoor temperatures, weather forecasts and minimized energy consumption. Stockholm University has been the coordinator of the project, and has worked with the systems software and information architecture, graphical user interface and the evaluation of the system.
For further information on the project visit http://enrima-project.eu

The EnRiMa review

Visiting UCSD and University of Utah

Health Informatics, Photo, Presentation, SYSLAB, Visit

Aron Henriksson spent two weeks in April at the University of California, San Diego (UCSD), continuing his ongoing collaboration with Dr. Mike Conway, who is currently at the Department of Family and Preventive Medicine. A small project was initiated that aims to develop techniques for detecting signals of adverse drug events (ADEs) in Twitter streams, in particular ADEs that are perceived to have been caused by tobacco cessation products. This project will continue over the coming months.

Sumithra Velupillai, who is currently doing a postdoc in San Diego, and Aron also visited Salt Lake City, where they gave a joint talk at the Department of Biomedical Informatics at the University of Utah, headed by Professor Wendy Chapman. The talk described their respective research efforts and that of the Clinical Text Mining group as a whole.

Both visits were very inspiring, and on our way from San Diego to Salt Lake City, we took the opportunity to take in the spectacular Grand Canyon!

Prof Sophia Ananiadou: Integrating and ranking the evidence from pathways to text

Health Informatics, Presentation, SYSLAB

Invited speaker professor Sophia Ananiadou hold a talk with the title Integrating and ranking the evidence from pathways to text, on Friday 25. She described her system, for mapping events, genes, interactions described in natural language in biomedical literature into a formal structure that can be used for faceted information retrieval.

Professor Sophia Ananiadou is director of the National Centre for Text Mining (NaCTeM) at University of Manchester, U.K.  The talk was funded by Wenner-Gren stiftelsens Gästföreläsaranslag. The audience consisted of the Clinical text mining group and several students from the master course in Health Informatics.

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Two research visits – New York and Boston

Health Informatics, Presentation, Visit

Sumithra Velupillai traveled to the northeastern US coast on February 18-21 for two research visits. In New York, she visited Noemie Elhadad and her group at the Department of Biomedical Informatics, Columbia University, and in Boston, she visited Guergana Savova and her group at the Natural Language Processing Lab, Childrens Hospital Boston and Harvard Medical School. Sumithra gave a talk on both occasions describing her past and ongoing research, as well as current research projects in the Clinical Text Mining group at DSV.

Noemie and Guergana are both part of the ongoing ShARe (Sharing Annotated Resources) project. Data from the ShARe project is used in this year’s ShARe/CLEFeHealth Evaluation Lab 2014’s Task 2 on information extraction (disease/disorder template filling), which Sumithra is co-leading together with Danielle Mowery. Guergana is also one of the main researchers in the Temporal Histories of Your Medical Event (THYME) project, a project very relevant to Sumithra’s current postdoctoral research. During these visits, Sumithra learned a lot from the extensive experience in the area of applying natural language processing technologies to clinical documentation that these two groups have, which hopefully will lead to further future collaborations.

These visits were part of Sumithra’s international postdoctoral fellowship funded by the Swedish Research Council and in part by the Swedish Fulbright Commission.

Symposium on Languages in Biology and Medicine (LBM 2013)

Health Informatics, Presentation, SYSLAB

I attended the 5th international symposium on Languages in Biology and Medicine (LBM 2013), held at Tokyo University. There, I presented the paper “Vocabulary Expansion by Semantic Extraction of Medical Terms” by Maria Skeppstedt, Magnus Ahltorp and Aron Henriksson. The paper was a result of the work conducted during my internship at the Language Media Lab at Hokkaido University, but with important additional contributions from Magnus and Aron. The paper was about automatic extraction of terms for expressing Medical Findings and Pharmaceutical Drugs from the Swedish journal Läkartidningen. The slides for the presentation can be found here.

There were many presentations related to the research conducted by our Clinical Text Mining Group at DSV. Sampo Pyysalo presented a paper (“Distributional Semantics Resources for Biomedical Text Processing”) in which the performance of a named entity recogniser was enhanced using features in form of clustered vectors from a word space constructed by the neural networks-based word2vec package. The study also made use of a word space constructed with Martin Duneld’s random indexing package. Sampo  also gave a high-light talk of another study (which later will be published in BMC Bioinformatics) in which named entity recognition of mentions of anatomical structures was enhanced by features based on cluster membership in clusters constructed through Brown’s clustering. Mizuki Morita presented a comparison between influenza monitoring through Google search terms and through an SVM classifier of Twitter searches, Alicia Pérez presented a rule- and key-word-based approach for Spanish ICD-9 coding and Juan Antonio Lossio Ventura presented key-word extraction using the C-value method. A study by Hyunju Lee on a gene search engine, showed the results of the searches by colour coding relevant entities in the retrieved journal abstracts. Kevin Cohen presented a study on how features from topic modelling can be used for improving assertion classification. There was also a keynote speech on the Japanese KEGG database, which contains pharmaceutical drug-related information.

The symposium was held in a very beautiful lecture hall at Tokyo University. Here Kai Hakala (a master student at Turko University), who was awarded best paper for "Hypothesis Generation in Large-Scale Event Networks".

The symposium was held in a very beautiful lecture hall at Tokyo University. Here Kai Hakala from Turku University, who was awarded best paper for “Hypothesis Generation in Large-Scale Event Networks”, presents.

 

Excursion with the other participants to Asakusa.

Excursion with the other participants to Asakusa.

 

 

Annual Symposium of the American Medical Informatics Association (AMIA 2013) in Washington DC

Health Informatics, Presentation

Sumithra Velupillai and Aron Henriksson attended the Annual Symposium of the American Medical Informatics Association (AMIA) in Washington DC (Nov. 17-20). The AMIA symposium is the main medical informatics event in the US, with participants from all states, and around the world, with participants from all continents – there were well over 2,000 participants in total. The symposium thus provided a good overview of current challenges and ongoing research in the world of medical informatics, as well as a great opportunity for networking. Aron presented a paper, Identifying Synonymy between SNOMED Clinical Terms of Varying Length Using Distributional Analysis of Electronic Health Records, co-authored with Mike Conway (UCSD), Martin Duneld (DSV, SU) and Wendy Chapman (University of Utah). We also had a nice reunion dinner with participants in the Interlock project, a two-year (2011-2013) collaboration between Stockholm University and University of California, San Diego.