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News and Events

Master thesis presentation at SHI 2022, Tromsø

Health Informatics, Presentation, Publication, Research Paper, SYSLAB

Alexander Dolk presented his and Hjalmar Davidsen master thesis in form of a scientific paper with the title Evaluation of LIME and SHAP in Explaining Automatic ICD-10 Classifications of Swedish Gastrointestinal Discharge Summaries at the 18th Scandinavian Conference on Health Informatics, SHI 2022, 22-23 Aug, 2022 i Tromsø, Norway, both supervisor Thomas Vakili and I were also part of the paper.

The research work were part of the ClinCode project in Tromsø. At the conference another paper also from the ClinCode project was presented with title The Influence of NegEx on ICD-10 Code Prediction in Swedish: How is the Performance of BERT and SVM Models Affected by Negations? by Andrius Budrionis, Taridzo Chomutare, Therese Olsen Svenning and Hercules Dalianis.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

There is a conference report from SHI 2022 available upon request to Hercules.

LREC 2022 in Marseille, France

Health Informatics, Presentation, Research Paper, SYSLAB

The 13th Language Resources and Evaluation Conference (LREC 2022) was held in Marseille, France with over 1000 participants. Four of us from DSV were there to present our recent findings and learn about the state of the NLP field. Anastasios Lamproudis, Aron Henriksson, Hercules Dalianis and I (Thomas Vakili) had a total of four papers for the conference and its workshops. 

All four of us presented a paper about continued pre-training BERT models using automatically de-identified clinical data. We showed that pre-training with safer de-identified clinical data works just as well as using sensitive data. During the conference, we also received ethical approval to share one of the models with academic researchers.

I also presented two workshop papers co-written with researchers from Linköping University, Linköping University Hospital and RISE. The first paper was about using a clinical BERT model to conduct terminology extraction to find terms associated with medical implants in electronic health records. The other paper investigated how well the de-identification system developed at DSV using the Health Bank performs on data from clinics not present in our datasets.

Anastasios, Aron and Hercules presented a paper in which they evaluated various strategies for creating clinical BERT models. They compared initializing the model from a general-domain model versus pre-training from scratch, and whether adapting the general-domain vocabulary to the clinical domain helps or not. They found that all strategies lead to improvements on clinical tasks, but that all strategies ultimately lead to similarly performing models. However, initializing from a general-domain model decreased the amount of training needed.

We had many fruitful discussions and returned home full of ideas to try out. If you are interested in seeing our posters, then you can find them here and here.

AAAI Fall Symposium and EMNLP – November 2021

Health Informatics, Presentation, Publication, Research Paper, SYSLAB, Visit

Professor Hercules Dalianis and I got a paper about the privacy preserving qualities of BERT accepted to the AAAI Fall Symposium on Human Partnership with Medical Artificial Intelligence! The paper is titled Are Clinical BERT Models Privacy Preserving? The Difficulty of Extracting Patient-Condition Associations. Our results strongly suggest that BERT’s poor generative capabilities makes it resistant to training data extraction attacks. Other models, such as GPT-2, have been shown to be susceptible to these attacks. From a privacy perspective, being a poor generator may be a feature!

Later in the same week, I flew from Stockholm to Punta Cana in the Dominican Republic to participate at EMNLP 2021. Almost 500 participants were there, with the total number of participants exceeding 4,000. There were many interesting presentations regarding NLP in general, but also some that were specifically about the privacy aspects of NLP. It was a great experience to learn where the field is headed and also to get to know many talented researchers. I have written a summary of some of the interesting papers – reach out if you are interested in it.

DSV at the First ClinCode Conference in Tromsø, Norway

Health Informatics, Presentation, SYSLAB, Visit

Professor Hercules Dalianis, Sonja Remmer and myself represented DSV at the First ClinCode Conference. The conference gathered experts in medicine and computer science from across the Nordics and took place at the University Hospital of North Norway (UNN) in Tromsø.

The conference was chaired by Hercules, who is also a guest professor at the Norwegian Centre for E-health Research. Sonja shared her work on automatic ICD-10 classification using BERT and I spoke about the difficulty of extracting training data from clinical BERT models.

Several participants had an industry or medical background. This provided valuable insights into how our research at DSV may be used in practice and what challenges are most important. It also highlighted the great potential that can be unlocked by continuing to investigate ICD-10 classification and other medical NLP problems.

Many excellent ideas were hatched in the discussions, and it was lovely to visit the beautiful polar city of Tromsø. Personally, I really look forward to future iterations of the conference!

Press release

Prof. Anna Dreber talk on (Predicting) replication outcomes, May 12, 2021

Presentation, SYSLAB, Video

Speaker: Anna Dreber, professor, Stockholm School of Economics

Title: (Predicting) replication outcomes

Abstract
Why are there so many false positive results in the published
scientific literature? And what is the actual share of results
that do not replicate in different literatures in the experimental
social sciences? I will discuss several recent large replication
projects, as well as our studies on “wisdom-of-crowds” mechanisms
like prediction markets and forecasting surveys where researchers
attempt to predict replication outcomes as well as new outcomes.

Time: Wednesday May 12, 2021, 13-14.00
Recording

Bio
Anna Dreber is the Johan Björkman Professor of Economics at the
Stockholm School of Economics, as well as a Wallenberg Scholar
and a member of the Royal Swedish Academy of Sciences.
Her research is mainly in meta-science and behavioral economics,
please see https://sites.google.com/site/annadreber/ for more.

Talk by Alberto Blanco Garcés with the title Multi-label deep neural classification of health records in Spanish

Health Informatics, Presentation, SYSLAB, Visit
Alberto Blanco Garcés visitor at DSV/Stockholm university from the University of the Basque country gave today a Zoomtalk with the title Multi-label deep neural classification of health records in Spanish. 
 
Abstract
The seminar is about clinical text mining, a field of Natural Language Processing applied to biomedical informatics. The aim is to classify Electronic Health Records with respect to the International Classification of Diseases, which is the foundation for the identification of international health statistics and the standard for reporting diseases and health conditions. Within the framework of data mining, the goal is the multi-label classification, as each health record has assigned multiple International Classification of Diseases codes. We present our research advances and results by applying Deep Learning methods to EHRs in Spanish, exploring techniques such as Feed-forward Neural Networks, Recurrent Neural Networks and Transformers. 
 
The talk was recorded here
 
The best results using 110 labels gave at most an F-score of 0.40 using as input 2.553 different ICD-10 codes distributed over 22,907 Electronic Health Records, see also Blanco et al 2020.

The Workshop NLP: mining clinical notes in EHR systems in Tromsø

Employee, Health Informatics, Presentation, SYSLAB

Hercules and I recently had the opportunity to attend and present at a workshop in clinical text mining on March 10 in Tromsø. The workshop NLP: mining clinical notes was arranged by The Norwegian Center for E-health Research.

During the workshop, Hercules gave a presentation on why NLP is needed. I gave a presentation on De-identification of text in electronic health records, and the Stockholm University master student Synnøve Bråten presented her current master thesis work on creating a synthetic Norwegian reference standard for de-identification. Sumithra Velupillai and Natalia Viani, from King’s College London, presented different NLP problems for clinical research and how to set up a clinical NLP research study.