Publications

Florian Borchert and Matthieu-P. Schapranow. HPI-DHC @ BioASQ DisTEMIST: Spanish Biomedical Entity Linking with Pre-trained Transformers and Cross-lingual Candidate Retrieval. Proceedings of the Working Notes of CLEF 2022 - Conference and Labs of the Evaluation Forum, pp. 244-258. Bologna, Italy. 🏆 1st place DisTEMIST shared task (entity linking subtrack) [Link] [Code]

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]

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]

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

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

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

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]