Daniel Thompson commited on
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README.md
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@@ -84,22 +84,30 @@ If the length of the clinical text exceeds 512 tokens, you can use a sliding win
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You can view and run the full example on GitHub here:
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[Sliding Window Example Notebook](https://github.com/dannyt101/AAA_classification/blob/main/Stage_1/bio-clinicalBERT_vasc_class_demo.ipynb)
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## Training and evaluation data
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## Training procedure
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### Training hyperparameters
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The following hyperparameters were used during training:
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### Framework versions
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You can view and run the full example on GitHub here:
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[Sliding Window Example Notebook](https://github.com/dannyt101/AAA_classification/blob/main/Stage_1/bio-clinicalBERT_vasc_class_demo.ipynb)
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## Training and evaluation data
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EHRs were downloaded from [MIMIC-IV clinical notes dataset](https://physionet.org/content/mimic-iv-note/2.2/)
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The EHRs were annotated by a Vascular Surgery Specialist Registrar/Resident and categorized as ‘Vascular’ if there was an acute pathology relevant to vascular surgery during their admission as per [National Health Service (NHS) England Service Specifications for Vascular Services](https://www.google.com/url?sa=t&source=web&rct=j&opi=89978449&url=https://www.england.nhs.uk/wp-content/uploads/2017/06/specialised-vascular-services-service-specification-adults.pdf&ved=2ahUKEwiknoKus4uIAxUFwAIHHaaQCBcQFnoECBMQAQ&usg=AOvVaw3yRyS-Ei1fiTNi6dcP8yOL).
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## Training procedure
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The training was performed using TensorFlow's TPU strategy. Dataset was preprocessed using a sliding window approach to handle text longer than 512 tokens.
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### Training hyperparameters
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The following hyperparameters were used during training:
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- **Optimizer**: Adam
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- **Learning Rate**: 5e-5
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- **Batch Size**: 16
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- **Epochs**: Maximum of 5
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- **Early Stopping**: Triggered if validation loss did not improve for 2 consecutive epochs
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### Training Results
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The Bio-clinicalBERT model achieved the following results on the validation set:
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| Model | Accuracy | Precision (Vascular) | Recall (Vascular) | F1-Score (Vascular) | Precision (Non-Vascular) | Recall (Non-Vascular) | F1-Score (Non-Vascular) |
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|--------------------|----------|----------------------|-------------------|---------------------|--------------------------|-----------------------|-------------------------|
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| **Bio-clinicalBERT** | 0.94 | 0.88 | 0.70 | 0.78 | 0.95 | 0.98 | 0.96 |
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### Framework versions
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