German Medical Named Entity Recognition Model and Data Set Creation Using Machine Translation and Word Alignment: Algorithm Development and Validation
Bibliographic record
Abstract
BACKGROUND: Data mining in the field of medical data analysis often needs to rely solely on the processing of unstructured data to retrieve relevant data. For German natural language processing, few open medical neural named entity recognition (NER) models have been published before this work. A major issue can be attributed to the lack of German training data. OBJECTIVE: We developed a synthetic data set and a novel German medical NER model for public access to demonstrate the feasibility of our approach. In order to bypass legal restrictions due to potential data leaks through model analysis, we did not make use of internal, proprietary data sets, which is a frequent veto factor for data set publication. METHODS: The underlying German data set was retrieved by translation and word alignment of a public English data set. The data set served as a foundation for model training and evaluation. For demonstration purposes, our NER model follows a simple network architecture that is designed for low computational requirements. RESULTS: score of 0.82 on the test set after training across 7 different NER types. Artifacts in the synthesized data set with regard to translation and alignment induced by the proposed method were exposed. The annotation performance was evaluated on an external data set and measured in comparison with an existing baseline model that has been trained on a dedicated German data set in a traditional fashion. We discussed the drop in annotation performance on an external data set for our simple NER model. Our model is publicly available. CONCLUSIONS: We demonstrated the feasibility of obtaining a data set and training a German medical NER model by the exclusive use of public training data through our suggested method. The discussion on the limitations of our approach includes ways to further mitigate remaining problems in future work.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.005 | 0.010 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.003 | 0.002 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".