|
--- |
|
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, berst_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] |
|
|
|
|
