tatonetti-lab / tnm-stage-classifier

Extract TNM cancer staging from pathology notes.

Extract TNM cancer staging from pathology notes.

Models generated by this study can be found on Hugging Face:

https://huggingface.co/jkefeli/CancerStage_Classifier_T
https://huggingface.co/jkefeli/CancerStage_Classifier_N
https://huggingface.co/jkefeli/CancerStage_Classifier_M

We have included a small dataset, the T14 TCGA pathology report held-out test set, to demonstrate the utility and ease-of-use of the trained models. Please see the Demo folder for data and code.

The following python package versions were used in model training and testing:

numpy==1.19.5
pandas==1.2.4
scikit-learn==0.24.2
scipy==1.6.3
seaborn==0.11.2
transformers==4.12.5
torch==1.7.1

To apply one of the TNM models to an external dataset, use the code provided in the Demo jupyter notebook. Replace the dataset and ensure that the target labels in the new dataset are the same as those for the trained models (T14, N03, M01). Ensure that the python packages used locally are the same as those outlined above.