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---
license: afl-3.0
datasets:
- bigbio/muchmore
language:
- de
---
---
### Model Description
<!-- Provide a longer summary of what this model is. -->
- **Finetuned from model: bert-base-german-cased
### Model Sources [optional]
<!-- Provide the basic links for the model. -->
- **Repository: https://github.com/sitingGZ/bert-sner
- **Paper : [BERT-SNER](https://aclanthology.org/2023.clinicalnlp-1.31/)
- **Demo (Coming soon)
## Uses
import sys
sys.path.append('modules')
import torch
from transformers import AutoConfig, AutoTokenizer, AutoModelForMaskedLM, EncoderDecoderConfig
from BERT2span_semantic_disam import BERT2span
from helpers import load_config, set_seed
from inference import final_label_results_rescaled
base_name = "bert-base-german-cased"
configs = load_config('configs/step3_gpu_span_semantic_group.yaml')
tokenizer = AutoTokenizer.from_pretrained(base_name)
bertMLM = AutoModelForMaskedLM.from_pretrained(base_name)
bert_sner = BERT2span(configs, bertMLM, tokenizer)
checkpoint_path = "checkpoints/german_bert_ex4cds_500_semantic_term.ckpt"
state_dict = torch.load(checkpoint_path, map_location=torch.device('cpu'))
bert_sner.load_state_dict(state_dict)
bert_sner.eval()
suggested_terms = {'Condition': 'Zeichen oder Symptom',
'DiagLab': 'Diagnostisch und Laborverfahren',
'LabValues': 'Klinisches Attribut',
'HealthState': 'Gesunder Zustand',
'Measure': 'Quantitatives Konzept',
'Medication': 'Pharmakologische Substanz',
'Process': 'Physiologische Funktion',
'TimeInfo': 'Zeitliches Konzept'}
words = "Aktuell Infekt mit Nachweis von E Coli und Pseudomonas im TBS- CRP 99mg/dl".split()
words_list = [words]
heatmaps, ner_results = final_label_results_rescaled(words_list, tokenizer, bert_sner, suggested_terms, threshold=0.5)
<!-- Address questions around how the model is intended to be used, including the foreseeable users of the model and those affected by the model. -->
### Direct Use
<!-- This section is for the model use without fine-tuning or plugging into a larger ecosystem/app. -->
[More Information Needed]
### Downstream Use [optional]
<!-- This section is for the model use when fine-tuned for a task, or when plugged into a larger ecosystem/app -->
[More Information Needed]
## Bias, Risks, and Limitations
<!-- This section is meant to convey both technical and sociotechnical limitations. -->
[More Information Needed]
### Recommendations
<!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->
Users (both direct and downstream) should be made aware of the risks, biases and limitations of the model. More information needed for further recommendations.
## How to Get Started with the Model
[More Information Needed]
## Training Details
### Training Data
<!-- This should link to a Data Card, perhaps with a short stub of information on what the training data is all about as well as documentation related to data pre-processing or additional filtering. -->
[More Information Needed]
### Training Procedure
<!-- This relates heavily to the Technical Specifications. Content here should link to that section when it is relevant to the training procedure. -->
#### Preprocessing [optional]
[More Information Needed]
#### Training Hyperparameters
- **Training regime:** [More Information Needed] <!--fp32, fp16 mixed precision, bf16 mixed precision, bf16 non-mixed precision, fp16 non-mixed precision, fp8 mixed precision -->
#### Speeds, Sizes, Times [optional]
<!-- This section provides information about throughput, start/end time, checkpoint size if relevant, etc. -->
[More Information Needed]
## Evaluation
<!-- This section describes the evaluation protocols and provides the results. -->
### Testing Data, Factors & Metrics
#### Testing Data
<!-- This should link to a Data Card if possible. -->
[More Information Needed]
#### Factors
<!-- These are the things the evaluation is disaggregating by, e.g., subpopulations or domains. -->
[More Information Needed]
#### Metrics
<!-- These are the evaluation metrics being used, ideally with a description of why. -->
[More Information Needed]
### Results
[More Information Needed]
#### Summary
## Model Examination [optional]
<!-- Relevant interpretability work for the model goes here -->
[More Information Needed]
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