Master thesis presentation at SHI 2022, Tromsø

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.

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PhD Student Mahbub Ul Alam Received the Best Student Paper Award at the IEEE 35th International Symposium on Computer-Based Medical Systems (CBMS 2022)

Hello Everyone,

Greetings. I hope you are well. I would like to share some very good news with you.

 I recently published a paper with two other co-authors at the IEEE 35th International Symposium on Computer Based Medical Systems (CBMS 2022, July 21-23, 2022, Shenzhen, China, Online Event). CBMS is the premier conference for computer-based medical systems, and one of the main conferences within the fields of medical informatics and biomedical informatics.

The title of my paper is “Exploring LRP and Grad-CAM visualization to interpret multi-label-multi-class pathology prediction using chest radiography“, (Mahbub Ul Alam, Jón Rúnar Baldvinsson and Yuxia Wang)”. In this paper, we tried to explain the decision process of deep neural networks to predict pathology (abnormality) in chest-X ray data using two popular interpretable methods. We investigated whether this explanation matches the clinical diagnosis or not. Interpretability is very crucial and it is emphasized in the recent European Union Artifical Intelligence Act. We hope that this paper will create a positive impact in this aspect.

The paper was received well during the CBMS 2022 symposium presentation time. I am delighted to inform you that the paper received the ‘best student paper award’. The award was provided by the IEEE Technical Committee on Computational Life Science (TCCLS).

I am very honoured and would like to thank DSV for providing me with this opportunity. I am fortunate to be working here to get a second award for my research work. Previously I won the ‘best paper award’ at BIOSTEC HEALTHINF 2020 (you can read more about it here).

Want to know more about the paper? Please check out the following presentation video I made!

An excerpt of the paper
An excerpt of the paper

Abstract:

The area of interpretable deep neural networks has received increased attention in recent years due to the need for transparency in various fields, including medicine, healthcare, stock market analysis, compliance with legislation, and law. Layer-wise Relevance Propagation (LRP) and Gradient-weighted Class Activation Mapping (Grad-CAM) are two widely used algorithms to interpret deep neural networks. In this work, we investigated the applicability of these two algorithms in the sensitive application area of interpreting chest radiography images. In order to get a more nuanced and balanced outcome, we use a multi-label classification-based dataset and analyze the model prediction by visualizing the outcome of LRP and Grad-CAM on the chest radiography images. The results show that LRP provides more granular heatmaps than Grad-CAM when applied to the CheXpert dataset classification model. We posit that this is due to the inherent construction difference of these algorithms (LRP is layer-wise accumulation, whereas Grad-CAM focuses primarily on the final sections in the model’s architecture). Both can be useful for understanding the classification from a micro or macro level to get a superior and interpretable clinical decision support system.

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LREC 2022 in Marseille, France

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.

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Papers published and accepted for publication in Proceedings of Pacific Asia Conference on Information Systems (PACIS) 2022, Americas Conference on Information Systems (AMCIS) 2022, and International Conference on Information Systems Development (ISD) 2022  

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

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Paper at ACL 2022 workshop: BioNLP

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.

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LREC 2022 – Accepted papers

Hello everyone!

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!

 

 

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Ph.D. Funding for Research in IT Management and Governance from Swedish Research School of Management and Information Technology (MIT)

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/

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AAAI Fall Symposium and EMNLP – November 2021

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.

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