Prof. Dr. Christoph Lippert

Florian Borchert, M.Sc.

Research Assistant, PhD Candidate

Phone:+49 (331) 5509-4839
Fax:+49 (331) 5509-163
Room:G-2.2.15 (Campus III)
Personal Website:florianborchert.de

Research Interests

  • Clinical Natural Language Processing
  • Weakly Supervised Machine Learning
  • Medical Knowledge Synthesis

Awards & Competitions



  • 1.
    Bressem, K.K., Papaioannou, J.-M., Grundmann, P., Borchert, F., Adams, L.C., Liu, L., Busch, F., Xu, L., Loyen, J.P., Niehues, S.M., Augustin, M., Grosser, L., Makowski, M.R., Aerts, H.J., Löser, A.: medBERT.de: A Comprehensive German BERT Model for the Medical Domain. Expert Systems with Applications. 121598 (2023).
  • 2.
    Schapranow, M.-P., Borchert, F., Bougatf, N., Hund, H., Eils, R.: Software-Tool Support for Collaborative, Virtual, Multi-Site Molecular Tumor Boards. SN Computer Science. 4, 358 (2023).
  • 3.
    Borchert, F., Llorca, I., Schapranow, M.-P.: Cross-Lingual Candidate Retrieval and Re-ranking for Biomedical Entity Linking. In: Arampatzis, A., Kanoulas, E., Tsikrika, T., Vrochidis, S., Giachanou, A., Li, D., Aliannejadi, M., Vlachos, M., Faggioli, G., en Ferro, N. (reds.) Experimental IR Meets Multilinguality, Multimodality, and Interaction. bll. 135–147. Springer Nature Switzerland, Cham (2023).
  • 4.
    Ladas, N., Borchert, F., Franz, S., Rehberg, A., Strauch, N., Sommer, K.K., Marschollek, M., Gietzelt, M.: Programming techniques for improving rule readability for rule-based information extraction natural language processing pipelines of unstructured and semi-structured medical texts. Health Informatics Journal. 29, 14604582231164696 (2023).
  • 5.
    Steinwand, S., Borchert, F., Winkler, S., Schapranow, M.-P.: GGTWEAK: Gene Tagging with Weak Supervision for German Clinical Text. In: Juarez, J.M., Marcos, M., Stiglic, G., en Tucker, A. (reds.) Artificial Intelligence in Medicine. bll. 183–192. Springer Nature Switzerland, Cham (2023).
  • 6.
    Hugo, J., Ibing, S., Borchert, F., Sachs, J.P., Cho, J., Ungaro, R.C., Böttinger, E.P.: Machine Learning Based Prediction of Incident Cases of Crohn’s Disease Using Electronic Health Records from a Large Integrated Health System. In: Juarez, J.M., Marcos, M., Stiglic, G., en Tucker, A. (reds.) Artificial Intelligence in Medicine. bll. 293–302. Springer Nature Switzerland, Cham (2023).
  • 7.
    Kämmer, N., and Borchert, F., and Winkler, S., and de Melo, G., and Schapranow, M.-P.: Resolving Elliptical Compounds in German Medical Text. The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks. bll. 292–305. Association for Computational Linguistics, Toronto, Canada (2023).
  • 8.
    Llorca, I., Borchert, F., Schapranow, M.-P.: A Meta-dataset of German Medical Corpora: Harmonization of Annotations and Cross-corpus NER Evaluation. Proceedings of the 5th Clinical Natural Language Processing Workshop. bll. 171–181. Association for Computational Linguistics, Toronto, Canada (2023).
  • 9.
    Richter-Pechanski, P., Wiesenbach, P., Schwab, D.M., Kiriakou, C., He, M., Allers, M.M., Tiefenbacher, A.S., Kunz, N., Martynova, A., Spiller, N., Mierisch, J., Borchert, F., Schwind, C., Frey, N., Dieterich, C., Geis, N.A.: A Distributable German Clinical Corpus Containing Cardiovascular Clinical Routine Doctor’s Letters. Scientific Data. 10, 207 (2023).


  • 1.
    Borchert, F., Schapranow, M.-P.: 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. bll. 244–258. , Bologna, Italy (2022).
  • 2.
    Borchert, F., Lohr, C., Modersohn, L., Witt, J., Langer, T., Follmann, M., Gietzelt, M., Arnrich, B., Hahn, U., Schapranow, M.-P.: GGPONC 2.0 - The German Clinical Guideline Corpus for Oncology: Curation Workflow, Annotation Policy, Baseline NER Taggers. Proceedings of the Language Resources and Evaluation Conference. bll. 3650–3660. European Language Resources Association, Marseille, France (2022).
  • 3.
    Henkenjohann, R., Bergner, B., Borchert, F., Bougatf, N., Hund, H., Eils, R., Schapranow, M.-P.: An Engineering Approach towards Multi-Site Virtual Molecular Tumor Board Software Support. In: Pissaloux, E., Papadopoulos, G., Achilleos, A., en Velázquez, R. (reds.) ICT for Health, Accessibility and Wellbeing. IHAW 2021. bll. 156–170. Springer, Cham (2022).


  • 1.
    Rasheed, A., Borchert, F., Kohlmeyer, L., Henkenjohann, R., Schapranow, M.-P.: A Comparison of Concept Embeddings for German Clinical Corpora. 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). bll. 2314–2321 (2021).
  • 2.
    Borchert, F., Meister, L., Langer, T., Follmann, M., Arnrich, B., Schapranow, M.-P.: Controversial Trials First: Identifying Disagreement Between Clinical Guidelines and New Evidence. AMIA Annual Symposium Proceedings. bll. 237–246. American Medical Informatics Association (2021).
  • 3.
    Borchert, F., Mock, A., Tomczak, A., Hügel, J., Alkarkoukly, S., Knurr, A., Volckmar, A.-L., Stenzinger, A., Schirmacher, P., Debus, J., Jäger, D., Longerich, T., Fröhling, S., Eils, R., Bougatf, N., Sax, U., Schapranow, M.-P.: Knowledge bases and software support for variant interpretation in precision oncology. Briefings in Bioinformatics. 22, (2021).


  • 1.
    Borchert, F., Lohr, C., Modersohn, L., Hahn, U., Langer, T., Wenzel, G., Follmann, M., Schapranow, M.-P.: "Herr Doktor, verstehen Sie mich?“: Wie lernende Systeme helfen medizinische Fachsprache zu verstehen und welche Rolle klinische Leitlinien dabei spielen. gesundhyte.de: Das Magazin für Digitale Gesundheit in Deutschland. 13, 19–22 (2020).
  • 2.
    Borchert, F., Lohr, C., Modersohn, L., Langer, T., Follmann, M., Sachs, J.P., Hahn, U., Schapranow, M.-P.: GGPONC: A Corpus of German Medical Text with Rich Metadata Based on Clinical Practice Guidelines. Proceedings of the 11th International Workshop on Health Text Mining and Information Analysis. bll. 38–48. Association for Computational Linguistics, Online (2020).