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Version 1.0 of the GGPONC medical text corpus is now available to researchers: Link
Our paper describing version 1.0 of the GGPONC corpus will be presented at the LOUHI workshop at EMNLP.
We have published an article in the German Digital Health magazine “Gesundhyte.de” about the role of NLP in evidence-based medicine and our GGPONC corpus.
Our paper “Knowledge bases and software support for variant interpretation in precision oncology” has been published in Briefings in Bioinformatics! Thanks to all collaborators from the HiGHmed consortium.
Our paper “Controversial Trials First: Identifying Disagreement Between Clinical Guidelines and New Evidence” featuring the Next Generation Evidence Browser will be presented at the AMIA Annual Symposium in November ‘21.
I am excited that our paper “Controversial Trials First: Identifying Disagreement Between Clinical Guidelines and New Evidence”, presented at the AMIA Annual Symposium received a Distinguished Paper Award.
I have organized a workshop with experts from both the German clinical NLP and the clinical guideline communities, to deepen the dialogue that we have started with our GGPONC project. Check out the event website for details.
Our paper for the new release of GGPONC 2.0 has been accepted at LREC! The new dataset is currently the largest, freely distributable annotated corpus of German medical text (1.87M tokens, 250K annotations). We also created baseline NER models with HuggingFace transformers.
Prediction of defects in continuous steel casting
Predictive Business Process Monitoring
Development of interactive XR applications for HoloLens and other HMDs / mobile devices
Weakly supervised information extraction from multilingual biomedical text
German Guideline Program in Oncology NLP Corpus
Published in LOUHI@EMNLP, 2020
Recommended citation: Florian Borchert*, Christina Lohr*, Luise Modersohn*, Thomas Langer, Markus Follmann, Jan Philipp Sachs, Udo Hahn, Matthieu-P. Schapranow. GGPONC: A Corpus of German Medical Text with Rich Metadata Based on Clinical Practice Guidelines. In Proceedings of the 11th International Workshop on Health Text Mining and Information Analysis, pp. 38–48. Online: Association for Computational Linguistics, 2020. (* equal contribution) [Data Access] [Code]
Published in Briefings in Bioinformatics, 2021
Recommended citation: Florian Borchert*, Andreas Mock*, Aurelie Tomczak*, Jonas Hügel, Samer Alkarkoukly, Alexander Knurr, Anna-Lena Volckmar, Albrecht Stenzinger, Peter Schirmacher, Jürgen Debus, Dirk Jäger, Thomas Longerich, Stefan Fröhling, Roland Eils, Nina Bougatf, Ulrich Sax, Matthieu-P Schapranow. Knowledge Bases and Software Support for Variant Interpretation in Precision Oncology, Briefings in Bioinformatics, Volume 22, Issue 6, November 2021, bbab134 (* equal contribution) IF = 11.6 https://doi.org/10.1093/bib/bbab134.
Published in 1st Conference on ICT for Health, Accessibility and Wellbeing, 2021
Recommended citation: Richard Henkenjohann, Benjamin Bergner, Florian Borchert, Nina Bougatf, Hauke Hund, Roland Eils, and Matthieu-P. Schapranow. An Engineering Approach towards Multi-Site Virtual Molecular Tumor Board Software Support. Proceedings of the 1st Conference on ICT for Health, Accessibility and Wellbeing. Springer International Publishing, 2021
Published in IEEE International Conference on Bioinformatics and Biomedicine, 2021
Recommended citation: Aadil Rasheed, Florian Borchert, Lasse Kohlmeyer, Richard Henkenjohann, and Matthieu-P. Schapranow. A Comparison of Concept Embeddings for German Clinical Corpora. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 2314-2321, Online, 2021
Published in AMIA 2021 Annual Symposium, 2021
Recommended citation: Florian Borchert, Laura Meister, Thomas Langer, Markus Follmann, Bert Arnrich, and Matthieu-P. Schapranow. Controversial Trials First: Identifying Disagreement Between Clinical Guidelines and New Evidence, Proceedings of the AMIA Annual Symposium, pp. 237-246, San Diego, USA, 2021 🏆 Distinguished Paper Award [Link]
GGPONC 2.0 - The German Clinical Guideline Corpus for Oncology: Curation Workflow, Annotation Policy, Baseline NER Taggers
Published in LREC, 2022
Recommended citation: Florian Borchert, Christina Lohr, Luise Modersohn, Jonas Witt, Thomas Langer, Markus Follmann, Matthias Gietzelt, Bert Arnrich, Udo Hahn and Matthieu-P. Schapranow. GGPONC 2.0 - The German Clinical Guideline Corpus for Oncology: Curation Workflow, Annotation Policy, Baseline NER Taggers. LREC 2022 — Proceedings of the Language Resources and Evaluation Conference, pp. 3650‑3660. Marseille, France, European Language Resources Association, 2022 [Data Access] [Code]
HPI-DHC @ BioASQ DisTEMIST: Spanish Biomedical Entity Linking with Pre-trained Transformers and Cross-lingual Candidate Retrieval
Published in CLEF, 2022
Recommended citation: Florian Borchert and Matthieu-P. Schapranow. HPI-DHC @ BioASQ DisTEMIST: Spanish Biomedical Entity Linking with Pre-trained Transformers and Cross-lingual Candidate Retrieval (To appear at CLEF 2022 / BioASQ Lab). 🏆 1st place DisTEMIST shared task (entity linking subtrack) [Link] [Code]