ACCUMULATE

ACquiring CrUcial Medical information Using LAnguage TEchnology

Aims

ACCUMULATE automatically recognizes crucial information in the free text of clinical reports written in English and Dutch by designing, developing and evaluating advanced language technology for deep semantic processing of the texts which are often morpho-syntactically not well-formed. An extra focus is on easy portability of the technology across domains and languages.

Partners

LIIR coordinates the ACCUMULATE project. The other partners are: KU Leuven ESAT-STADIUS (Prof. Jan Aerts), UZ Leuven (Prof. Bart Van den Bosch), CLiPS Research Center of the University of Antwerp (Prof. Walter Daelemans) and the University Hospital of Antwerp (Dr. Kim Luyckx).

Results

We have built novel deep learning models for recognizing temporal and causal relations between medical events in the natural language texts of clinical records. We are investigating explainable deep learning models for medical decision making in clinical radiology. In addition, we study algorithms for hierarchical classification of clinical reports with ICD (International Classification of Diseases) coding. We have built models for extracting event time lines from clinical reports.



Period From 2016-01-01 to 2020-09-30.
Financed by IWT-SBO 150056
Supervised by Marie-Francine Moens
Staff Abbas Akkasi
Tuur Leeuwenberg
Elias Moons
Graham Spinks
Contact Abbas Akkasi

More information can be found on the project website http://www.accumulate.be/

Publications

  1. Leeuwenberg, Artuur & Moens, Marie-Francine KULeuven-LIIR at SemEval 2016 Task 12: Detecting Narrative Containment in Clinical Records. In Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval 2016). 2016
  2. Leeuwenberg, Artuur & Moens, Marie-Francine Structured Learning for Temporal Relation Extraction from Clinical Records. In Proceedings of the Conference of the European Chapter of the Association for Computational Linguistics. 2017
  3. Leeuwenberg, Tuur & Moens, Marie-Francine KULeuven-LIIR at SemEval-2017 Task 12: Cross-Domain Temporal Information Extraction from Clinical Records. In Proceedings of the International Workshop on Semantic Evaluation 2017. ACL. 2017
  4. Kordjamshidi, P., Rahgooy, T., Moens, M.-F., Pustejovsky, J., Manzoor, U. & Roberts, K. CLEF 2017: Multimodal Spatial Role Labeling (mSpRL) Task Overview. In Proceedings CLEF 2017 (Lecture Notes in Computer Science 10456) (pp. 367-376). Springer. 2017
  5. Spinks, Graham & Moens, Marie-Francine Generating Continuous Representations of Medical Texts. In Proceedings of the 16th Annual Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. ACL. 2018
  6. Heyman, Geert, Vulić, Ivan & Moens, Marie-Francine A Deep Learning Approach to Bilingual Lexicon Induction in the Biomedical Domain. BMC Bioinformatics . 2018
  7. Francis, Sumam, Van Landeghem, Jordy & Moens, Marie-Francine Transfer Learning for Named Entity Recognition in Financial and Biomedical Documents, Information. 2019
  8. Spinks, Graham & Moens, Marie-Francine Justifying Diagnosis Decisions by Deep Neural Networks Journal of Biomedical Informatics. 2019
  9. Leeuwenberg, Tuur & Moens, Marie-Francine A Survey on Temporal Reasoning for Temporal Information Extraction from Text. Journal of Artificial Intelligence Research (JAIR). 2019
  10. Leeuwenberg, Tuur & Moens, Marie-Francine Word-Level Loss Extensions for Neural Temporal Relation Classification In Proceedings of the 27th International Conference on Computational Linguistics (COLING 2018). ACL. 2018
  11. Spinks, Graham & Moens, Marie-Francine Generating Text from Images in a Smooth Representation Space In Proceedings of the Conference and Labs of the Evaluation Forum (CLEF 2018) - Lecture Notes in Computer Science. 2018
  12. Spinks, Graham & Moens, Marie-Francine Evaluating Textual Representations through Image Generation In Proceedings of the EMNLP Workshop: Analyzing and Interpreting Neural Networks for NLP. 2018
  13. Leeuwenberg, Artuur & Moens, Marie-Francine Temporal Information Extraction by Predicting Relative Time-lines In Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing. 2018
  14. Tuur Leeuwenberg and Marie-Francine Moens A Survey on Temporal Reasoning for Temporal Information Extraction from Text. In Proceedings of the International Joint Conference on Artificial Intelligence Pacific Rim International Conference on Artificial Intelligence (IJCAI-PRICAI 2020) - Journal track. 2020
  15. Moons, Elias, Khanna, Aditya, Akkasi, Abbas & Moens, Marie-Francine A Comparison of Deep Learning Methods for ICD Coding of Clinical Records. Applied Sciences 10 (15), 5262. 2020
  16. Moons, Elias & Moens, Marie-Francine Convolutional Attention Models with Post-Processing Heuristics at CLEF eHealth 2020. In Proceedings CLEF eHealth 2020. CEUR. 2020
  17. Leeuwenberg, Tuur & Moens, Marie-Francine Towards extracting absolute event timelines from English clinical reports. IEEE/ACM Transactions on Audio, Speech and Language Processing . 2020
  18. Akkasi, Abbas & Moens, Marie-Francine Causal relationship extraction from biomedical text using deep neural models: A comprehensive survey. Journal of Biomedical Informatics 119. 103820. 2021
  19. Moons, Elias and Moens, Marie-Francine Clinical Report Classification: Continually Learning from User Feedback. In Proceedings of IEEE CBMS Special Track on Clinical & Biomedical Text Mining (6 p.). 2021


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