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Pytorch implementation of 'Histo-Genomic Knowledge Distillation For Cancer Prognosis From Histopathology Whole Slide Images'

Requirements

Installation

Please refer to Patch-GCN

Dataset Preparation

Please download the official TCGA datasets of BRCA, BLCA, GBMLGG, LUAD, and UCEC. For more details on pre-processing, please refer to CLAM and Patch-GCN.

Model training and testing

before training and testing, please update the configs. Generally, we train the model with one 24 GB memory GPU. You can adjust the 'num_instances_maximum' to sample the number of instances in accordance with your GPU power.
Testing will be performed after each training epoch, and the last model will be employed for the final evaluation.

  e.g., python main.py

Contact

If you have any questions, please don't hesitate to contact us. E-mail: [email protected]

Acknowledgement

This work was built upon the Patch-GCN and CLAM.

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