# GERNERMED -- An Open German Medical NER Model

arXiv: https://arxiv.org/abs/2109.12104 · HTML: https://mlsanity.com/paper/2109.12104/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 10 of its 44 references that are in the map.
- First posted on arXiv 24 Sep 2021.

## Builds on (most cited first, 10 of 10)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [fairseq: A Fast, Extensible Toolkit for Sequence Modeling](https://mlsanity.com/paper/1904.01038/) (2019)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction](https://mlsanity.com/paper/2005.12833/) (2020)
- [Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets](https://mlsanity.com/paper/1906.05474/) (2019)
- [Relation extraction from clinical texts using domain invariant convolutional neural network](https://mlsanity.com/paper/1606.09370/) (2016)
- [GGPONC: A Corpus of German Medical Text with Rich Metadata Based on Clinical Practice Guidelines](https://mlsanity.com/paper/2007.06400/) (2020)
- [From Witch's Shot to Music Making Bones -- Resources for Medical Laymen to Technical Language and Vice Versa](https://mlsanity.com/paper/2005.11494/) (2020)

## Abstract (arXiv)

The current state of adoption of well-structured electronic health records and integration of digital methods for storing medical patient data in structured formats can often considered as inferior compared to the use of traditional, unstructured text based patient data documentation. Data mining in the field of medical data analysis often needs to rely solely on processing of unstructured data to retrieve relevant data. In natural language processing (NLP), statistical models have been shown successful in various tasks like part-of-speech tagging, relation extraction (RE) and named entity recognition (NER). In this work, we present GERNERMED, the first open, neural NLP model for NER tasks dedicated to detect medical entity types in German text data. Here, we avoid the conflicting goals of protection of sensitive patient data from training data extraction and the publication of the statistical model weights by training our model on a custom dataset that was translated from publicly available datasets in foreign language by a pretrained neural machine translation model. The sample code and the statistical model is available at: https://github.com/frankkramer-lab/GERNERMED