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Add stability analysis #48

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merged 19 commits into from
May 24, 2024
Merged

Add stability analysis #48

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c948b2f
add bootstrapping component
rcannood May 23, 2024
34913a6
update wf
rcannood May 23, 2024
369582d
add script
rcannood May 23, 2024
e353a42
also allow subsampling the vars
rcannood May 23, 2024
d21f6d0
fix configs
rcannood May 23, 2024
1b5cefc
fill in defaults
rcannood May 23, 2024
216cc09
fix bootstrap method
rcannood May 23, 2024
6a9df5b
fix components & scripts
rcannood May 23, 2024
26081cd
return stability output
rcannood May 23, 2024
1acd4a2
reconvert the h5ad files after bootstrapping
rcannood May 23, 2024
be8c0f3
Merge remote-tracking branch 'origin/main' into add_bootstrapping
rcannood May 23, 2024
6392bd8
fix script
rcannood May 23, 2024
9b687d5
fix revision
rcannood May 23, 2024
fccfa6a
fix missing metadata
rcannood May 24, 2024
a7a52ac
undo escaping
rcannood May 24, 2024
650932a
bump resources
rcannood May 24, 2024
164c2f5
fix script
rcannood May 24, 2024
6419e4f
clean up description for now
rcannood May 24, 2024
bb8845d
decrease max time
rcannood May 24, 2024
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fix script
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@rcannood
rcannood committed May 24, 2024
commit 164c2f5d9299e730dc166904b1a1fa166e12eb3c
6 changes: 1 addition & 5 deletions scripts/run_stability_benchmark_tw.sh
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Expand Up @@ -9,11 +9,7 @@ input_states: s3://openproblems-bio/public/neurips-2023-competition/workflow-res
output_state: "state.yaml"
publish_dir: "$publish_dir"
rename_keys: "de_train:de_train,de_train_h5ad:de_train_h5ad,de_test:de_test,de_test_h5ad:de_test_h5ad,id_map:id_map"
settings:
stability: true
stability_num_replicates: 10
stability_obs_fraction: 0.99
stability_var_fraction: 0.99
settings: '{"stability": true, "stability_obs_fraction": 0.99, "stability_var_fraction": 0.99}'
HERE

tw launch https://github.com/openproblems-bio/task-dge-perturbation-prediction.git \
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