sapbert-pubmedbert-ddxplus-50k

Model Details

Model Description

This model is a fine-tuned version of cambridgeltl/SapBERT-from-PubMedBERT-fulltext on the DDXPlus dataset (50,000 samples) for medical diagnosis tasks.

This is the model card of a 🤗 transformers model that has been pushed on the Hub. This model card has been automatically generated.

• Developed by: Aashish Acharya
• Model type: sapBERT-BioMedBERT
• Language(s): English
• License: MIT
• Finetuned from model: cambridgeltl/SapBERT-from-PubMedBERT-fulltext

Model Sources

• Repository: cambridgeltl/SapBERT-from-PubMedBERT-fulltext
• Dataset: aai530-group6/ddxplus

Training Dataset

The model was trained on DDXPlus dataset (50,000 samples) containing:

• Patient cases with comprehensive medical information
• Differential diagnosis annotations
• 49 distinct medical conditions
• Evidence-based symptom-condition relationships

Performance

Final Metrics

• Test Precision: 0.8159
• Test Recall: 0.7948
• Test F1 Score: 0.7420

Training Evolution

• Best Validation Loss: 1.4600
• Stopped at Epoch 4 (Early stopping triggered)

<img src="https://cdn-uploads.huggingface.co/production/uploads/662757230601587f0be9781b/tHpbTt7ZyXSR2Lq2wqRAv.png" width="400" alt="image"> <img src="https://cdn-uploads.huggingface.co/production/uploads/662757230601587f0be9781b/3-WA0SZKYQRXnjafLsFTr.png" width="400" alt="image">

Intended Use

This model is designed for:

• Medical diagnosis support
• Symptom analysis
• Disease classification
• Differential diagnosis generation

Out-of-Scope Use

The model should NOT be used for:

• Direct medical diagnosis without professional oversight
• Critical healthcare decisions without human validation
• Clinical applications without proper testing and validation

Training Details

Training Procedure

• Optimizer: AdamW with weight decay (0.01)
• Learning Rate: 1e-5
• Loss Function: Combined loss (0.8 × Focal Loss + 0.2 × KL Divergence)
• Batch Size: 32
• Gradient Clipping: 1.0
• Early Stopping: Patience of 3 epochs
• Training Strategy: Cross-validation with 5 folds

Model Architecture

• Base Model: cambridgeltl/SapBERT-from-PubMedBERT-fulltext
• Hidden Size: 768
• Attention Heads: 12
• Dropout Rate: 0.5
• Added classification layers for diagnostic tasks
• Layer normalization and dropout for regularization

Example Usage

<pre> from transformers import AutoTokenizer, AutoModel # Load model and tokenizer model_name = "acharya-jyu/sapbert-pubmedbert-ddxplus-10k" tokenizer = AutoTokenizer.from_pretrained(model_name) model = AutoModel.from_pretrained(model_name) # Example input structure input_data = { 'age': 45, # Patient age 'sex': 'M', # Patient sex: 'M' or 'F' 'initial_evidence': 'E_91', # Initial evidence code (e.g., E_91 for fever) 'evidences': [ 'E_91', # Fever 'E_77', # Cough 'E_89' # Fatigue ] } # Process demographic data and evidence codes outputs = model(**input_data) # Outputs will include: # - Main diagnosis prediction # - Differential diagnosis probabilities # - Confidence scores </pre>

<b>Note: Evidence codes (E_XX) correspond to specific symptoms and conditions defined in the release_evidences.json file. The model expects these standardized codes rather than raw text input.</b>

Citation

  @misc{acharya2024sapbert,
  title={SapBERT-PubMedBERT Fine-tuned on DDXPlus Dataset},
  author={Acharya, Aashish},
  year={2024},
  publisher={Hugging Face Model Hub}
}

Model Card Contact

Aashish Acharya