Implementation Kronos 2 for Multiplex - #181
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heavenduck wants to merge 12 commits into
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heavenduck wants to merge 12 commits into
heavenduck wants to merge 12 commits into
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s1787956
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Sep 10, 2026
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| ```text | ||
| /mnt/nova-curie/arndtwagner/stamp_multiplex_implementation/data/results/Vorversuche_2_Tumorpanel/kronos2/per_marker_v1/ |
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please remove paths related to your workspaces
s1787956
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Looks really good, thank you very much! Just remove the paths of your workspace and we can merge
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| ```text | ||
| /mnt/nova-curie/arndtwagner/stamp_multiplex_implementation/data/results/Vorversuche_2_Tumorpanel/kronos2/per_marker_v1/ | ||
| preprocess/ # shared by smoke and cohort extraction | ||
| crossval/splits.json # copied from the existing crossval_v2 baseline | ||
| crossval/split-{0,1,2}/model.ckpt | ||
| explainability/split-{0,1,2}/ # each checkpoint explains only its held-out slides | ||
| ``` | ||
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| The target remains `Her2`, with three folds and seed 42. Training uses seven ViT | ||
| branches (192 hidden units, two layers) and batch size 4, with 512 tiles per bag. | ||
| Batch size was reduced from 32 to accommodate the seven branches; GPU memory and | ||
| runtime for full-cohort training have not yet been measured. | ||
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| ## Run next | ||
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| From the workspace: | ||
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| ```bash | ||
| cd /mnt/nova-curie/arndtwagner/stamp_multiplex_implementation/data/slurm_files |
| patches, model_marker_names, coords = SPImage( | ||
| slide, | ||
| markers=marker_names, | ||
| mpp=1.0, |
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Why is mpp here hardcoded to 1.0?
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