This repository provides the code for the publication Critical Assessment of Transformer-based AI Models for German Clinical Notes. In that study, we assessed the performance of eight published general-purpose and three newly trained transformer-based language models specific to the biomedical domain.

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├── fine-tuning                             # Directory which contains all scripts for fine-tuning
│   ├── bronco
│   │   └── data
│   │       ├── config
│   │       ├── databases
│   │       ├── processed
│   │       └── raw
│   ├── chadl
│   │   ├── data
│   │   │   ├── config
│   │   │   ├── interim
│   │   │   └── raw
│   │   └── helpers
│   ├── ggponc
│   │   └── data
│   │       ├── config
│   │       ├── processed
│   │       └── raw
│   │── jsyncc
│   |   └── data
│   │       └── config
│   └── clef
│       └── data
│           └── config
├── pre-training                            # Directory which contains the scripts to pre-train BioGottBERT and BioELECTRA
└── toolbox                                 # Python module with the code used in the pre-training and fine-tuning scripts
    ├── datasets
    ├── models
    ├── pretraining
    ├── training
    │   ├── ner
    │   └── sequence_classification
    └── utils

Unfortunately, the pre-training and the ChaDL datasets are not publicly available. However, the BRONCO150, CLEF eHealth 2019, GGPONC, and JSynCC datasets can be acquired. The BRONCO150 and GGPONC datasets can be requested by the authors directly, and the JSynCC repository provides code to generate the JSynCC dataset. The CLEF eHealth 2019 dataset can be downloaded directly.

We made our domain-adapted BioGottBERT model available in the Huggingface model hub at https://huggingface.co/SCAI-BIO/bio-gottbert-base.

The following three commands are needed to pre-train BioELECTRA models.

python 0_create_custom_tokenizer.py custom_tokenizer -i test.txt -i test2.txt --vocab-size=15000
python 1_create_pretraining_data.py 512 example -i data/raw/example.txt -v data/processed/vocab.txt --threads 16 --model ELECTRA
python 2_pretrain.py electra-small BioELECTRA data/processed/ELECTRA_example-512_training.pt data/processed/ELECTRA_example-512_validation.pt  data/processed/vocab.txt

The following two commands are needed to run the domain-adaption script:

python 1_create_pretraining_data.py 512 example -i data/raw/example.txt -t ~/git/german-clinical-bert/model_evaluation/bronco/data/external/gottbert-base --threads 16 --model RoBERTa
python 2_pretrain.py domain-adapted-roberta roberta_output data/processed/RoBERTa_example-512_training.pt data/processed/RoBERTa_example-512_validation.pt uklfr/gottbert-base

The relevant files for fine-tuning can be found in the fine-tuning subdirectories. Initially, the data must be preprocessed. For this purpose, a 0_generate_dataset.py file is available in each folder. Subsequently, the 1_train_model.py or 1_run_ncv.py files must be executed specifying a configuration file for each model and, if necessary, for each outer fold.

Please post a GitHub issue if you have any questions.