Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw3/limma/versions.txt +3 -0
- paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw3/manifest.json +496 -0
- paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw3/rbo.csv +51 -0
- paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw3/repro.json +53 -0
paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw3/limma/versions.txt
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R version 4.5.2 (2025-10-31)
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limma 3.66.0
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edgeR 4.8.1
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paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw3/manifest.json
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| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_contrast_extra.v1",
|
| 3 |
+
"dataset": "giroux2022",
|
| 4 |
+
"design": "fewshot",
|
| 5 |
+
"unit": "fewshot_n5/draw3",
|
| 6 |
+
"written_utc": "2026-10-02T06:28:08.714949+00:00",
|
| 7 |
+
"command": [
|
| 8 |
+
"tools/contrast_extra.py",
|
| 9 |
+
"--design",
|
| 10 |
+
"fewshot",
|
| 11 |
+
"--dataset",
|
| 12 |
+
"giroux2022",
|
| 13 |
+
"--draws",
|
| 14 |
+
"0,1,2,3,4",
|
| 15 |
+
"--threads",
|
| 16 |
+
"4"
|
| 17 |
+
],
|
| 18 |
+
"threads": 4,
|
| 19 |
+
"donors": [
|
| 20 |
+
"0B943B_d0",
|
| 21 |
+
"0B943B_d14",
|
| 22 |
+
"2AD75E_d0",
|
| 23 |
+
"2AD75E_d7",
|
| 24 |
+
"2AD75E_d14",
|
| 25 |
+
"82CCF5_d0",
|
| 26 |
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"82CCF5_d7",
|
| 27 |
+
"82CCF5_d14",
|
| 28 |
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"0BF51C_d0",
|
| 29 |
+
"0BF51C_d7",
|
| 30 |
+
"0BF51C_d14"
|
| 31 |
+
],
|
| 32 |
+
"n_samples": 11,
|
| 33 |
+
"contrast": {
|
| 34 |
+
"case_groups": [
|
| 35 |
+
"severe"
|
| 36 |
+
],
|
| 37 |
+
"control_groups": [
|
| 38 |
+
"mild"
|
| 39 |
+
],
|
| 40 |
+
"n_case_donors": 6,
|
| 41 |
+
"n_control_donors": 5
|
| 42 |
+
},
|
| 43 |
+
"calls": {
|
| 44 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5/draw3": {
|
| 45 |
+
"arms": [
|
| 46 |
+
"zs_raw",
|
| 47 |
+
"zs_pseudo",
|
| 48 |
+
"zs_cal",
|
| 49 |
+
"lora5"
|
| 50 |
+
],
|
| 51 |
+
"summary_sha256": "9688709239fd5208ab46a44bf406c1eba70619d28c0cf77901903b261b617a66",
|
| 52 |
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"contrast_csv_sha256": "6a5122837d306989db93f12c9303094033e1d36ec245bfcf697cdb01987830c8"
|
| 53 |
+
},
|
| 54 |
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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/fewshot_n5/draw3_scsemi5": {
|
| 55 |
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"arms": [
|
| 56 |
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"scsemi5"
|
| 57 |
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],
|
| 58 |
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"summary_sha256": "ecda2225a61282f4495e071e02cdc52c72ed872b784c6bc8730e20a88501c23d",
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| 59 |
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"contrast_csv_sha256": "957420051ca127e6f760c47a0682f4d01dc7bf6a81ad80998d2a9063a99df9ab"
|
| 60 |
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}
|
| 61 |
+
},
|
| 62 |
+
"notes": {
|
| 63 |
+
"source_tree": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex"
|
| 64 |
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},
|
| 65 |
+
"reference_sha256": "dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593",
|
| 66 |
+
"deg_reference": {
|
| 67 |
+
"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",
|
| 68 |
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"sha256": "412c44bba7481b0b851c3b12e695f1b7ff662163e1f7849d3a64359dfce6d50e"
|
| 69 |
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},
|
| 70 |
+
"gene_exclusion": {
|
| 71 |
+
"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",
|
| 72 |
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"sha256": "e3a0f3f225d94d7c193d94ea020b1ab097fa657c0601fce4301b9a09a9c243de",
|
| 73 |
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"n_listed": 196,
|
| 74 |
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"n_scoring_genes": 5563,
|
| 75 |
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"n_dropped_from_scoring_genes": 65,
|
| 76 |
+
"n_scoring_genes_kept": 5498,
|
| 77 |
+
"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"
|
| 78 |
+
},
|
| 79 |
+
"n_genes_disease_scores": 5498,
|
| 80 |
+
"genes_per_type": {
|
| 81 |
+
"T cell": 2885,
|
| 82 |
+
"B cell": 3018,
|
| 83 |
+
"Monocyte": 3038,
|
| 84 |
+
"NK cell": 2926
|
| 85 |
+
},
|
| 86 |
+
"arms": {
|
| 87 |
+
"zs_raw": {
|
| 88 |
+
"call": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_nosex/giroux2022/fewshot_n5/draw3",
|
| 89 |
+
"npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/fewshot_n5/zs__raw_all.npz",
|
| 90 |
+
"npz_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/fewshot_n5/zs__raw_all.npz",
|
| 91 |
+
"npz_sha256": "16b110e1effd23cdcdaaa55a28ef83e9a91035e74cdea69dc7706a03552fef5e",
|
| 92 |
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"receipt_verified": true,
|
| 93 |
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"condition": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fewshot_n5/all_usable_raw.npz",
|
| 94 |
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"condition_sha256": "ac755a41a900fac61df07f3a95be029353cfd4869439fa19612e599527d37665",
|
| 95 |
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"condition_label": "all_usable_raw.npz@ac755a41",
|
| 96 |
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"condition_read_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/giroux2022/fewshot_n5/all_usable_raw.npz",
|
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paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw3/rbo.csv
ADDED
|
@@ -0,0 +1,51 @@
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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
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| 22 |
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| 23 |
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| 24 |
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| 25 |
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| 26 |
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| 27 |
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| 28 |
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| 29 |
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| 30 |
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| 31 |
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| 32 |
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| 33 |
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| 34 |
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| 35 |
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| 36 |
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| 37 |
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giroux2022,fewshot,fewshot_n5/draw3,lora5,broadcast:test_raw.npz@4efbb07e,Monocyte,0.98,0.22313444465516005,0.26228482218432514,0.2427096334197426,True,5105,5466
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|
| 39 |
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| 40 |
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|
| 41 |
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|
| 42 |
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giroux2022,fewshot,fewshot_n5/draw3,scsemi5,generated:scsemi5,T cell,0.98,0.09705249980759094,0.06342272885640275,0.08023761433199685,True,5225,2022
|
| 43 |
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giroux2022,fewshot,fewshot_n5/draw3,scsemi5,broadcast:test_raw.npz@4efbb07e,T cell,0.98,0.2941233983642887,0.199938495184023,0.24703094677415585,True,5225,5466
|
| 44 |
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giroux2022,fewshot,fewshot_n5/draw3,scsemi5,generated:scsemi5,B cell,0.98,0.03571975336425455,0.06434068111319051,0.05003021723872253,True,4979,875
|
| 45 |
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giroux2022,fewshot,fewshot_n5/draw3,scsemi5,broadcast:test_raw.npz@4efbb07e,B cell,0.98,0.09480039661057928,0.07569068099264725,0.08524553880161326,True,4979,5466
|
| 46 |
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giroux2022,fewshot,fewshot_n5/draw3,scsemi5,generated:scsemi5,Monocyte,0.98,0.03578447571484127,0.03477868540128513,0.0352815805580632,True,5105,1281
|
| 47 |
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giroux2022,fewshot,fewshot_n5/draw3,scsemi5,broadcast:test_raw.npz@4efbb07e,Monocyte,0.98,0.22313444465516005,0.26228482218432514,0.2427096334197426,True,5105,5466
|
| 48 |
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giroux2022,fewshot,fewshot_n5/draw3,scsemi5,generated:scsemi5,NK cell,0.98,0.07116858967091103,0.14930341732269983,0.11023600349680543,True,4907,1094
|
| 49 |
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giroux2022,fewshot,fewshot_n5/draw3,scsemi5,broadcast:test_raw.npz@4efbb07e,NK cell,0.98,0.18719259638967384,0.1458913784981807,0.1665419874439273,True,4907,5466
|
| 50 |
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giroux2022,fewshot,fewshot_n5/draw3,scsemi5,generated:scsemi5,DC,0.98,0.004694703302083373,0.06127859252635437,0.03298664791421887,True,4646,291
|
| 51 |
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giroux2022,fewshot,fewshot_n5/draw3,scsemi5,broadcast:test_raw.npz@4efbb07e,DC,0.98,0.11241895782504246,0.08006139179281113,0.0962401748089268,True,4646,5466
|
paper-releases/pbisc-diffusion/updates/20261002T085943Z-deck-restructure-contrast-metrics-zeroshot-len/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/giroux2022/fewshot_n5/draw3/repro.json
ADDED
|
@@ -0,0 +1,53 @@
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|
| 1 |
+
{
|
| 2 |
+
"arms": {
|
| 3 |
+
"zs_raw": {
|
| 4 |
+
"contrast_max_abs_diff": 9.71445146547012e-17,
|
| 5 |
+
"contrast_all_equal": true,
|
| 6 |
+
"n_genes_equal": true,
|
| 7 |
+
"welch_lists_equal": true,
|
| 8 |
+
"welch_counts_equal": true,
|
| 9 |
+
"pass": true
|
| 10 |
+
},
|
| 11 |
+
"zs_pseudo": {
|
| 12 |
+
"contrast_max_abs_diff": 8.326672684688674e-17,
|
| 13 |
+
"contrast_all_equal": true,
|
| 14 |
+
"n_genes_equal": true,
|
| 15 |
+
"welch_lists_equal": true,
|
| 16 |
+
"welch_counts_equal": true,
|
| 17 |
+
"pass": true
|
| 18 |
+
},
|
| 19 |
+
"zs_cal": {
|
| 20 |
+
"contrast_max_abs_diff": 9.71445146547012e-17,
|
| 21 |
+
"contrast_all_equal": true,
|
| 22 |
+
"n_genes_equal": true,
|
| 23 |
+
"welch_lists_equal": true,
|
| 24 |
+
"welch_counts_equal": true,
|
| 25 |
+
"pass": true
|
| 26 |
+
},
|
| 27 |
+
"lora5": {
|
| 28 |
+
"contrast_max_abs_diff": 9.367506770274758e-17,
|
| 29 |
+
"contrast_all_equal": true,
|
| 30 |
+
"n_genes_equal": true,
|
| 31 |
+
"welch_lists_equal": true,
|
| 32 |
+
"welch_counts_equal": true,
|
| 33 |
+
"pass": true
|
| 34 |
+
},
|
| 35 |
+
"scsemi5": {
|
| 36 |
+
"contrast_max_abs_diff": 8.326672684688674e-17,
|
| 37 |
+
"contrast_all_equal": true,
|
| 38 |
+
"n_genes_equal": true,
|
| 39 |
+
"welch_lists_equal": true,
|
| 40 |
+
"welch_counts_equal": true,
|
| 41 |
+
"pass": true
|
| 42 |
+
}
|
| 43 |
+
},
|
| 44 |
+
"observed_split_half_full_aggregates": {
|
| 45 |
+
"n_equal": true,
|
| 46 |
+
"det_equal": true,
|
| 47 |
+
"sum_equal_float32": true,
|
| 48 |
+
"cp10k_max_abs_diff_float32": 0.0,
|
| 49 |
+
"cp10k_equal_float32": true
|
| 50 |
+
},
|
| 51 |
+
"comparable_with_scorer": true,
|
| 52 |
+
"all_pass": true
|
| 53 |
+
}
|