What is immune class?

[zdipath]

Hello,

I noticed that the immune_class task is provided in the CPTAC dataset of Patho-Bench. Could you please share more detailed information or documentation about this task?

Thank you for your valuable contribution to advancing the computational pathology community.

[aspartate]

Hi @zdipath,

Thank you for your question. Immune_class is a recently added set of tasks for the CPTAC cohorts that aims to predict the fraction of stromal and immune cells in a tumor sample. The ground truth labels are created using the ESTIMATE algorithm applied to the gene expression data (https://www.nature.com/articles/ncomms3612). A high ESTIMATE score means more stromal/immune infiltration in a tumor. Our goal is to predict the ESTIMATE score (binned into low/medium/high) from only the histopathology image.

Hope this helps! Thank you for using Patho-Bench.