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.
A paper written by Rahmat Mulyana, Lazar Rusu, and Erik Perjons and entitled: “IT Governance Mechanisms that Influence Digital Transformation: A Delphi Study in Indonesian Banking and Insurance” has been published in PACIS 2022 Proceedings, Paper 267, Association for Information Systems (Nominated for the Best Paper (Paper 1160) in PACIS 2022 Detailed Program: https://pacis2022.aisconferences.org/schedule-program/conference-program/)
A paper written by Parisa Aasi, Sebastian Atug, Lorenzo Cermeno, and Lazar Rusu, and entitled: “Digital Transformation Success Through Aligning the Organizational Structure: Case Study of Swedish Public Organizations” has been accepted for publication in AMCIS 2022 Proceedings, Association for Information Systems
A paper written by Gideon Mekonnen Jonathan, Lazar Rusu, and Erik Perjons and entitled: “Digital Transformation in Public Organisations: IT Alignment-Related Success Factors” has been accepted for publication in ISD 2022 Proceedings, Association for Information Systems
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.
We have two new papers accepted to the 13th Language Resources and Evaluation Conference, LREC 2022 that takes place in Marseille the upcoming June!
The first paper is authored by Thomas Vakili, Aron Henriksson, Hercules Dalianis, and me and is called “Downstream Task Performance of BERT Models Pre-Trained Using Automatically De-Identified Clinical Data” with code 412. It evaluates the performance of a language model that is trained using De-identified clinical text in later tasks, and explores the de-identification impact in the development of the language model.
The second paper is authored by Aron Henriksson, Hercules Dalianis, and me and is called “Evaluating Pre-training Strategies for Clinical BERT Models” with code 661. It empirically compares different pre-training strategies for the development of domain-adapted language models in the Swedish clinical text domain.
You can find all the accepted papers including the ones mentioned above here!
The application submitted in this year to Swedish Research School of Management and Information Technology (MIT) for Ph.D. funding for research in IT management and governance at DSV/Stockholm University has been successfully. In the next five years DSV will receive 1.750.000 SEK from MIT for co-financing a Ph.D. position in IT management and governance. For more information about Swedish Research School of Management and Information Technology (MIT) please access the following link: http://www.mit.uu.se/
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.
My name is Yash. I recently started working at DSV as a Research Assistant with Aron Henriksson. I will be working on a project that is aimed at developing Machine Learning models for the outcome prediction of COVID-19 hospitalizations using structured and text data. I will also be working as a Teaching Assistant for the courses BIG DATA and NLP.
I recently completed my Masters degree in Statistics and Machine Learning from Linköping University and hold a Bachelors in Electronics and Telecommunications from the College of Engineering Pune, India.
I am glad to be here and I look forward to meeting you all! 🙂
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!