Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/scsemi_cv_20261002/pooled/manifest.json +259 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/scsemi_cv_20261002/pooled/rbo.csv +11 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/scsemi_cv_20261002/pooled/repro.json +21 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_extra/immicro/scsemi_cv_20261002/pooled/en.csv +9 -0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/scsemi_cv_20261002/pooled/manifest.json
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| 1 |
+
{
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| 2 |
+
"schema": "paired_ft_contrast_extra.v1",
|
| 3 |
+
"dataset": "giroux2022",
|
| 4 |
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"design": "scored",
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| 5 |
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"unit": "scsemi_cv_20261002/pooled",
|
| 6 |
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"written_utc": "2026-10-08T01:58:48.212788+00:00",
|
| 7 |
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"command": [
|
| 8 |
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"tools/contrast_extra.py",
|
| 9 |
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"--design",
|
| 10 |
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"scored",
|
| 11 |
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"--dataset",
|
| 12 |
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"giroux2022",
|
| 13 |
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"--score-dir",
|
| 14 |
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"scores_nosex/giroux2022/scsemi_cv_20261002/pooled",
|
| 15 |
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"--arms",
|
| 16 |
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"scsemi__raw",
|
| 17 |
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"--unit",
|
| 18 |
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"scsemi_cv_20261002/pooled",
|
| 19 |
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"--threads",
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| 20 |
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"6"
|
| 21 |
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],
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| 22 |
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"threads": 6,
|
| 23 |
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"donors": [
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"450905_d0",
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"450905_d14",
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| 26 |
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"0B943B_d0",
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| 27 |
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"0B943B_d14",
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| 28 |
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"7085CA_d0",
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"7085CA_d7",
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| 30 |
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"7085CA_d14",
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| 31 |
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"2AD75E_d0",
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| 32 |
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"2AD75E_d7",
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| 33 |
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"2AD75E_d14",
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"B85D75_d0",
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| 35 |
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"B85D75_d7",
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| 36 |
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"180E1A_d0",
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| 37 |
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"180E1A_d7",
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| 38 |
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"180E1A_d14",
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| 39 |
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"82CCF5_d0",
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| 40 |
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"82CCF5_d7",
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| 41 |
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"82CCF5_d14",
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| 42 |
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"BAAF62_d0",
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| 43 |
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"BAAF62_d7",
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| 44 |
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"BAAF62_d14",
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| 45 |
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"0BF51C_d0",
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| 46 |
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"0BF51C_d7",
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| 47 |
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"0BF51C_d14"
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| 48 |
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],
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| 49 |
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"n_samples": 24,
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| 50 |
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"contrast": {
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| 51 |
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"case_groups": [
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| 52 |
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"severe"
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| 53 |
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],
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| 54 |
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"control_groups": [
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| 55 |
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"mild"
|
| 56 |
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],
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| 57 |
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"n_case_donors": 11,
|
| 58 |
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"n_control_donors": 13
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| 59 |
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},
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| 60 |
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"calls": {
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| 61 |
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"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/scsemi_cv_20261002/pooled": {
|
| 62 |
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"arms": [
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| 63 |
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"scsemi__raw"
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| 64 |
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],
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| 65 |
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"summary_sha256": "a9aceb5ba082c625923496f45bd317d91b45cf7b888a1c262b979cbb60f58595",
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"contrast_csv_sha256": "e3b0c7e53990fabea7059d39ab6b9f63bb3d3e91073d9a343a9f2f604a02f6d6"
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| 67 |
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}
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| 68 |
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},
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| 69 |
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"notes": {
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| 70 |
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"source_tree": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex"
|
| 71 |
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},
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| 72 |
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"reference_sha256": "dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593",
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| 73 |
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"deg_reference": {
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| 74 |
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"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022/deg_reference.npz",
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"gene_exclusion": {
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| 78 |
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"file": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/sex_linked_genes/sex_linked_genes_exclude.csv",
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"sha256": "e3a0f3f225d94d7c193d94ea020b1ab097fa657c0601fce4301b9a09a9c243de",
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| 82 |
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| 83 |
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| 84 |
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"applies_to": "group contrast (logFC r generated / broadcast / partial: dropped from each type's detected-gene set) and top-50 DEG (observed, generated and broadcast tests: columns dropped before log1p CPM, Welch and BH); all other metrics use every scoring gene"
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| 85 |
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},
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| 86 |
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"n_genes_disease_scores": 5498,
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| 87 |
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"genes_per_type": {
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"T cell": 2886,
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| 89 |
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| 90 |
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| 92 |
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},
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| 93 |
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"arms": {
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| 94 |
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"scsemi__raw": {
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| 95 |
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"call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/scsemi_cv_20261002/pooled",
|
| 96 |
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"npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled_scsemi_cv_20261002/scsemi__raw.npz",
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| 97 |
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"npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled_scsemi_cv_20261002/scsemi__raw.npz",
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| 98 |
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| 99 |
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| 100 |
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"condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/pooled_scsemi_cv_20261002/conditions_pooled_raw.npz",
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| 101 |
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| 104 |
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"label": "scSemiProfiler, all training pairs (5-fold CV)",
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| 109 |
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| 110 |
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| 111 |
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"inputs_sha256": {
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| 112 |
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"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/cells_panel6k.npz": "7d22c0ff4b3af2b1fd1741421633616b5ab0e679a800ecffb780cc5fd1b507d1",
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"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/cells_obs.parquet": "e2d1c0c490563d0e9858c6e8d3680d702ce14a180ce75101e305e95be572e618"
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|
| 205 |
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| 207 |
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| 208 |
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|
| 209 |
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|
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| 211 |
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| 212 |
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|
| 213 |
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| 214 |
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| 215 |
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|
| 216 |
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|
| 217 |
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|
| 218 |
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|
| 219 |
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| 220 |
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|
| 221 |
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| 222 |
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| 223 |
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| 224 |
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|
| 225 |
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|
| 226 |
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|
| 227 |
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| 228 |
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|
| 229 |
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|
| 230 |
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| 231 |
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|
| 232 |
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|
| 233 |
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|
| 234 |
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|
| 235 |
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| 236 |
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|
| 237 |
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|
| 238 |
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|
| 239 |
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|
| 240 |
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|
| 241 |
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|
| 242 |
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|
| 243 |
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|
| 244 |
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|
| 245 |
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|
| 246 |
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|
| 247 |
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|
| 248 |
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|
| 249 |
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|
| 250 |
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"fetched_from_server2": [],
|
| 251 |
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"code_sha256": {
|
| 252 |
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|
| 253 |
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|
| 254 |
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"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/ft_common.py": "4a6366b0f22208cd58714fc0261b8840c643b9d4569704d560cfd93534cbc747",
|
| 255 |
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|
| 256 |
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"/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881"
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| 257 |
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|
| 258 |
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|
| 259 |
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|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/scsemi_cv_20261002/pooled/rbo.csv
ADDED
|
@@ -0,0 +1,11 @@
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
dataset,design,unit,arm,predictor,celltype,p,rbo_ext_t_desc,rbo_ext_t_asc,rbo_ext_mean_up_down,pred_defined,len_obs,len_pred
|
| 2 |
+
giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,generated:scsemi__raw,T cell,0.98,0.1554853382534696,0.024570700909473688,0.09002801958147165,True,5295,2590
|
| 3 |
+
giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,broadcast:conditions_pooled_raw.npz@1370617c,T cell,0.98,0.21091520406003963,0.08253009973543636,0.146722651897738,True,5295,5471
|
| 4 |
+
giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,generated:scsemi__raw,B cell,0.98,0.058303244150327886,0.10067843195306608,0.07949083805169699,True,5087,1217
|
| 5 |
+
giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,broadcast:conditions_pooled_raw.npz@1370617c,B cell,0.98,0.15782803844824106,0.038997750761943416,0.09841289460509224,True,5087,5471
|
| 6 |
+
giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,generated:scsemi__raw,Monocyte,0.98,0.012029713677077405,0.15080830988811506,0.08141901178259622,True,5239,1756
|
| 7 |
+
giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,broadcast:conditions_pooled_raw.npz@1370617c,Monocyte,0.98,0.26291333119473204,0.225742147827788,0.24432773951126002,True,5239,5471
|
| 8 |
+
giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,generated:scsemi__raw,NK cell,0.98,0.050824303461465166,0.13260282703895002,0.09171356525020759,True,5103,1451
|
| 9 |
+
giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,broadcast:conditions_pooled_raw.npz@1370617c,NK cell,0.98,0.10956028837936926,0.13174158853092305,0.12065093845514616,True,5103,5471
|
| 10 |
+
giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,generated:scsemi__raw,DC,0.98,0.02716879045214357,0.13579805808498852,0.08148342426856604,True,4914,596
|
| 11 |
+
giroux2022,scored,scsemi_cv_20261002/pooled,scsemi__raw,broadcast:conditions_pooled_raw.npz@1370617c,DC,0.98,0.1075485867109752,0.08492881857024795,0.09623870264061157,True,4914,5471
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/scsemi_cv_20261002/pooled/repro.json
ADDED
|
@@ -0,0 +1,21 @@
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|
|
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|
|
|
|
|
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|
| 1 |
+
{
|
| 2 |
+
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|
| 3 |
+
"scsemi__raw": {
|
| 4 |
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|
| 5 |
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|
| 6 |
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|
| 7 |
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|
| 8 |
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|
| 9 |
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|
| 10 |
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}
|
| 11 |
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|
| 12 |
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"observed_split_half_full_aggregates": {
|
| 13 |
+
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|
| 14 |
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|
| 15 |
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"sum_equal_float32": true,
|
| 16 |
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"cp10k_max_abs_diff_float32": 0.0,
|
| 17 |
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|
| 18 |
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},
|
| 19 |
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"comparable_with_scorer": true,
|
| 20 |
+
"all_pass": true
|
| 21 |
+
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|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_extra/immicro/scsemi_cv_20261002/pooled/en.csv
ADDED
|
@@ -0,0 +1,9 @@
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|
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|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
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|
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|
| 1 |
+
dataset,design,unit,set,cellset,distance,n_samples,n_cells_real,n_cells_gen,n_pcs,lb,ub,dif_mean,en,lb_exact,lb_queries,n_representative_rows,en_reps_at_lb,seconds
|
| 2 |
+
immicro,scored,scsemi_cv_20261002/pooled,real_R2,pc,sq,107,16050,16050,100,145.6455721037472,208.2099790357781,177.8870914002398,0.515333252203914,True,"[16050, 16050]",,,8.5
|
| 3 |
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immicro,scored,scsemi_cv_20261002/pooled,real_R2,pc,l2,107,16050,16050,100,11.941195267314077,14.253822358646222,13.16770358926964,0.5303528297115367,True,"[16050, 16050]",,,8.5
|
| 4 |
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immicro,scored,scsemi_cv_20261002/pooled,real_R2,all,sq,107,196097,196154,100,125.54778826527738,174.69075410630884,144.3846684462183,0.38330776050177373,False,"[20000, 20000]",,,36.5
|
| 5 |
+
immicro,scored,scsemi_cv_20261002/pooled,real_R2,all,l2,107,196097,196154,100,11.087498062731683,13.083721612602794,11.88104390628869,0.39752353568228554,False,"[20000, 20000]",,,36.5
|
| 6 |
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immicro,scored,scsemi_cv_20261002/pooled,scsemi__raw,pc,sq,107,16050,16050,100,116.15699843240971,198.41734217082242,358.13275790299554,2.9415845895328006,True,"[16050, 16050]",,,9.0
|
| 7 |
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immicro,scored,scsemi_cv_20261002/pooled,scsemi__raw,pc,l2,107,16050,16050,100,10.531065927753703,13.896006746242644,18.6751754098303,2.420283125732293,True,"[16050, 16050]",,,9.0
|
| 8 |
+
immicro,scored,scsemi_cv_20261002/pooled,scsemi__raw,all,sq,107,392251,160500,100,104.29436866492185,163.0175128852596,325.4356219214395,3.7658278723421823,False,"[20000, 20000]",,,49.2
|
| 9 |
+
immicro,scored,scsemi_cv_20261002/pooled,scsemi__raw,all,l2,107,392251,160500,100,9.977237276702361,12.624148223019573,17.789152662018843,2.951332909853132,False,"[20000, 20000]",,,49.2
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