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mahmoodlab / Patch-GCN

Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks - MICCAI 2021
http://mahmoodlab.org
GNU General Public License v3.0
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I want to run MI-FCN. However, I don't know how to get the 'fast_cluster_ids.pkl' file? #20

Closed genhao3 closed 2 years ago

genhao3 commented 2 years ago

I want to run MI-FCN. However, I don't know how to get the 'fast_cluster_ids.pkl' file?

Originally posted by @genhao3 in https://github.com/mahmoodlab/Patch-GCN/issues/17#issuecomment-1197883796

Richarizardd commented 2 years ago

Hi @genhao3 - the fast_cluster_ids.pkl is a dictionary that I load for each cancer type, which maps case_id to [M x 1]-dim array of cluster assignments ${1 \cdots C}$, where $M$ is the number of patches and the indices correspond to the cluster assignment of a given patch embedding. You can use packages like faiss to generate these cluster assignments for running MI-FCN / DeepAttnMISL comparisons.

tangluyu commented 2 years ago

can you give an fast_cluster_ids.pkl as a example?

Raymvp commented 1 year ago

can you give an fast_cluster_ids.pkl as a example?