Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/giroux2022/loco_lora16_K1000/summary.json +531 -0
- paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/giroux2022/zs_K1000/summary.json +531 -0
- paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/immicro/zs_K1000/summary.json +295 -0
- paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/imperial_eskd/zs_K1000/summary.json +1063 -0
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/giroux2022/loco_lora16_K1000/summary.json
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|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_scores.v1",
|
| 3 |
+
"dataset": "giroux2022",
|
| 4 |
+
"written_utc": "2026-10-02T12:02:49.480629+00:00",
|
| 5 |
+
"command": [
|
| 6 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
|
| 7 |
+
"--dataset",
|
| 8 |
+
"giroux2022",
|
| 9 |
+
"--threads",
|
| 10 |
+
"8",
|
| 11 |
+
"--donors",
|
| 12 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/giroux2022/usable_samples.txt",
|
| 13 |
+
"--arm",
|
| 14 |
+
"loco_lora16_K1000=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/generated/giroux2022/ho_giroux2022/K1000_lora16.npz",
|
| 15 |
+
"--case-groups",
|
| 16 |
+
"severe",
|
| 17 |
+
"--control-groups",
|
| 18 |
+
"mild",
|
| 19 |
+
"--out",
|
| 20 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores/giroux2022/loco_lora16_K1000"
|
| 21 |
+
],
|
| 22 |
+
"arms": [
|
| 23 |
+
"loco_lora16_K1000"
|
| 24 |
+
],
|
| 25 |
+
"donors": [
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| 26 |
+
"450905_d0",
|
| 27 |
+
"450905_d14",
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| 28 |
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"0B943B_d0",
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| 29 |
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"0B943B_d14",
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| 30 |
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"7085CA_d0",
|
| 31 |
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"7085CA_d7",
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| 32 |
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"7085CA_d14",
|
| 33 |
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"2AD75E_d0",
|
| 34 |
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"2AD75E_d7",
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| 35 |
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"2AD75E_d14",
|
| 36 |
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"B85D75_d0",
|
| 37 |
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"B85D75_d7",
|
| 38 |
+
"180E1A_d0",
|
| 39 |
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"180E1A_d7",
|
| 40 |
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"180E1A_d14",
|
| 41 |
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"82CCF5_d0",
|
| 42 |
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"82CCF5_d7",
|
| 43 |
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"82CCF5_d14",
|
| 44 |
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"BAAF62_d0",
|
| 45 |
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"BAAF62_d7",
|
| 46 |
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"BAAF62_d14",
|
| 47 |
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"0BF51C_d0",
|
| 48 |
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"0BF51C_d7",
|
| 49 |
+
"0BF51C_d14"
|
| 50 |
+
],
|
| 51 |
+
"n_donors": 24,
|
| 52 |
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"reference": {
|
| 53 |
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"cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022",
|
| 54 |
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"reference_sha256": "dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593",
|
| 55 |
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"features_sha256": "fb41b91617e3ff786d5153c4dc7869d66191ca5947ff28161d24215a24f819e5",
|
| 56 |
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"n_r1_cells": 3600,
|
| 57 |
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"pca": {
|
| 58 |
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"n_components": 50,
|
| 59 |
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"explained_variance_ratio_sum": 0.23158283531665802,
|
| 60 |
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"n_fit_cells": 3600
|
| 61 |
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},
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| 62 |
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"r2_control": {
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| 63 |
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"precision": 0.9980555555555556,
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| 64 |
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"coverage": 1.0,
|
| 65 |
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"density": 3.7886666666666664,
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| 66 |
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"n_query": 3600,
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| 67 |
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"depth_matched": {
|
| 68 |
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"precision": 0.9980555555555556,
|
| 69 |
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"coverage": 1.0,
|
| 70 |
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"density": 3.7033611111111115
|
| 71 |
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}
|
| 72 |
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},
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| 73 |
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"observed_l1_loo_null_mean": 0.30584824369245694
|
| 74 |
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},
|
| 75 |
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"contrast_definition": {
|
| 76 |
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"enabled": true,
|
| 77 |
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"rule": "explicit --case-groups / --control-groups",
|
| 78 |
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"group_source": "features groups",
|
| 79 |
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"case_groups": [
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| 80 |
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"severe"
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| 81 |
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],
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| 82 |
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|
| 83 |
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"mild"
|
| 84 |
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],
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| 85 |
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| 86 |
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"n_control_donors": 13,
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| 87 |
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| 88 |
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| 114 |
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| 115 |
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| 116 |
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| 140 |
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| 141 |
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"top50_jaccard_broadcast": 0.3888888888888889,
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| 483 |
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"n_cells_obs": 47311,
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"n_cells_gen": 3736
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| 485 |
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|
| 486 |
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"NK cell": {
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| 487 |
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| 496 |
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| 497 |
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"DC": {
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"deg_scored": true,
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"top50_jaccard": 0.0,
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|
| 507 |
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|
| 508 |
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| 509 |
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"sum": 14,
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| 511 |
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"max": 123,
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"mean": 2.8,
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| 513 |
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"sum_broadcast": 39,
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| 514 |
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| 515 |
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"broadcast_n_significant": 18,
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| 516 |
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"seconds": 0.09
|
| 517 |
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},
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| 518 |
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"seconds": 10.7
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| 519 |
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}
|
| 520 |
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},
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| 521 |
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"code_sha256": {
|
| 522 |
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"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py": "ec5f40b4cea6d5062d0138f3b934abb6465e34cbfeac869c8a0906924c033aec",
|
| 523 |
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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",
|
| 524 |
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"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da",
|
| 525 |
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"/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py": "48b12d794782b840838853e93e0fc55fab00532c4b3698f4588e926b985d2881",
|
| 526 |
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"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/tools/immicro_common.py": "c5c30e917148cc5e664e91ea30c11bbdff9b6d1f53a3e0a13e16b1917eff37e9",
|
| 527 |
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"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/predict_scanvi.py": "482ee5dcf4d72b54bc36cbb6dcff62e5030bc7afc46cb5fb01eca73a82ee45a5",
|
| 528 |
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"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/poisson_readout.py": "8bfa080942fbcdc89ae23b276524a1a83266fb8cbc56b9af279e50f82e6cde38"
|
| 529 |
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},
|
| 530 |
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"seconds": 12.6
|
| 531 |
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}
|
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/giroux2022/zs_K1000/summary.json
ADDED
|
@@ -0,0 +1,531 @@
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|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_scores.v1",
|
| 3 |
+
"dataset": "giroux2022",
|
| 4 |
+
"written_utc": "2026-10-02T11:42:09.311139+00:00",
|
| 5 |
+
"command": [
|
| 6 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
|
| 7 |
+
"--dataset",
|
| 8 |
+
"giroux2022",
|
| 9 |
+
"--threads",
|
| 10 |
+
"8",
|
| 11 |
+
"--donors",
|
| 12 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/giroux2022/usable_samples.txt",
|
| 13 |
+
"--arm",
|
| 14 |
+
"zs_K1000=/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",
|
| 15 |
+
"--case-groups",
|
| 16 |
+
"severe",
|
| 17 |
+
"--control-groups",
|
| 18 |
+
"mild",
|
| 19 |
+
"--out",
|
| 20 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores/giroux2022/zs_K1000"
|
| 21 |
+
],
|
| 22 |
+
"arms": [
|
| 23 |
+
"zs_K1000"
|
| 24 |
+
],
|
| 25 |
+
"donors": [
|
| 26 |
+
"450905_d0",
|
| 27 |
+
"450905_d14",
|
| 28 |
+
"0B943B_d0",
|
| 29 |
+
"0B943B_d14",
|
| 30 |
+
"7085CA_d0",
|
| 31 |
+
"7085CA_d7",
|
| 32 |
+
"7085CA_d14",
|
| 33 |
+
"2AD75E_d0",
|
| 34 |
+
"2AD75E_d7",
|
| 35 |
+
"2AD75E_d14",
|
| 36 |
+
"B85D75_d0",
|
| 37 |
+
"B85D75_d7",
|
| 38 |
+
"180E1A_d0",
|
| 39 |
+
"180E1A_d7",
|
| 40 |
+
"180E1A_d14",
|
| 41 |
+
"82CCF5_d0",
|
| 42 |
+
"82CCF5_d7",
|
| 43 |
+
"82CCF5_d14",
|
| 44 |
+
"BAAF62_d0",
|
| 45 |
+
"BAAF62_d7",
|
| 46 |
+
"BAAF62_d14",
|
| 47 |
+
"0BF51C_d0",
|
| 48 |
+
"0BF51C_d7",
|
| 49 |
+
"0BF51C_d14"
|
| 50 |
+
],
|
| 51 |
+
"n_donors": 24,
|
| 52 |
+
"reference": {
|
| 53 |
+
"cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022",
|
| 54 |
+
"reference_sha256": "dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593",
|
| 55 |
+
"features_sha256": "fb41b91617e3ff786d5153c4dc7869d66191ca5947ff28161d24215a24f819e5",
|
| 56 |
+
"n_r1_cells": 3600,
|
| 57 |
+
"pca": {
|
| 58 |
+
"n_components": 50,
|
| 59 |
+
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"code_sha256": {
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"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/umap/cell_immicro_5arm/tools/stage_b_embed.py": "d056cfdf38fb0e5f478756f370174e993b75d0c973c48e02e21749175a4ca2da",
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|
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|
| 529 |
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},
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| 530 |
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"seconds": 15.6
|
| 531 |
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}
|
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/immicro/zs_K1000/summary.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_scores.v1",
|
| 3 |
+
"dataset": "immicro",
|
| 4 |
+
"written_utc": "2026-10-02T11:39:27.562279+00:00",
|
| 5 |
+
"command": [
|
| 6 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
|
| 7 |
+
"--dataset",
|
| 8 |
+
"immicro",
|
| 9 |
+
"--threads",
|
| 10 |
+
"8",
|
| 11 |
+
"--donors",
|
| 12 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/immicro/usable_samples.txt",
|
| 13 |
+
"--arm",
|
| 14 |
+
"zs_K1000=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/immicro/fewshot_n5/zs__raw_all.npz",
|
| 15 |
+
"--out",
|
| 16 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores/immicro/zs_K1000"
|
| 17 |
+
],
|
| 18 |
+
"arms": [
|
| 19 |
+
"zs_K1000"
|
| 20 |
+
],
|
| 21 |
+
"donors": [
|
| 22 |
+
"HS1",
|
| 23 |
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"HS2",
|
| 24 |
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"HS3",
|
| 25 |
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"HS4",
|
| 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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|
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|
| 33 |
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|
| 35 |
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|
| 36 |
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|
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|
| 40 |
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| 43 |
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|
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|
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|
| 56 |
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|
| 57 |
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|
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| 59 |
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|
| 60 |
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|
| 64 |
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|
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|
| 66 |
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|
| 67 |
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|
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|
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|
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|
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|
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|
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|
| 77 |
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|
| 78 |
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|
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|
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|
| 81 |
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|
| 82 |
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|
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|
| 84 |
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|
| 85 |
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|
| 86 |
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|
| 87 |
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|
| 88 |
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|
| 89 |
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|
| 90 |
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|
| 91 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/imperial_eskd/zs_K1000/summary.json
ADDED
|
@@ -0,0 +1,1063 @@
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|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_scores.v1",
|
| 3 |
+
"dataset": "imperial_eskd",
|
| 4 |
+
"written_utc": "2026-10-02T11:41:52.789824+00:00",
|
| 5 |
+
"command": [
|
| 6 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
|
| 7 |
+
"--dataset",
|
| 8 |
+
"imperial_eskd",
|
| 9 |
+
"--threads",
|
| 10 |
+
"8",
|
| 11 |
+
"--donors",
|
| 12 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/data/imperial_eskd/usable_samples.txt",
|
| 13 |
+
"--arm",
|
| 14 |
+
"zs_K1000=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/inputs_server2/imperial_eskd/zs__raw_all.npz",
|
| 15 |
+
"--case-groups",
|
| 16 |
+
"covid_positive",
|
| 17 |
+
"--control-groups",
|
| 18 |
+
"covid_negative",
|
| 19 |
+
"--out",
|
| 20 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_crosscohort_20261002/scores/imperial_eskd/zs_K1000"
|
| 21 |
+
],
|
| 22 |
+
"arms": [
|
| 23 |
+
"zs_K1000"
|
| 24 |
+
],
|
| 25 |
+
"donors": [
|
| 26 |
+
"C20_1004",
|
| 27 |
+
"C20_1404",
|
| 28 |
+
"C21_1004",
|
| 29 |
+
"C21_1704",
|
| 30 |
+
"C21_2504",
|
| 31 |
+
"C23_2204",
|
| 32 |
+
"C31_1304",
|
| 33 |
+
"C31_2004",
|
| 34 |
+
"C31_2704",
|
| 35 |
+
"C33_1401",
|
| 36 |
+
"C33_1601",
|
| 37 |
+
"C33_1901",
|
| 38 |
+
"C34_1404",
|
| 39 |
+
"C34_2104",
|
| 40 |
+
"C34_2504",
|
| 41 |
+
"C36_1504",
|
| 42 |
+
"C36_1704",
|
| 43 |
+
"C36_2104",
|
| 44 |
+
"C40_1504",
|
| 45 |
+
"C40_2204",
|
| 46 |
+
"C40_0105",
|
| 47 |
+
"C42_1504",
|
| 48 |
+
"C42_2204",
|
| 49 |
+
"C42_2704",
|
| 50 |
+
"C58_1604",
|
| 51 |
+
"C58_2501",
|
| 52 |
+
"C58_2901",
|
| 53 |
+
"C58_0102",
|
| 54 |
+
"C58_0402",
|
| 55 |
+
"C58_1003",
|
| 56 |
+
"C60_2504",
|
| 57 |
+
"C63_1704",
|
| 58 |
+
"C63_2404",
|
| 59 |
+
"C63_2904",
|
| 60 |
+
"C65_1704",
|
| 61 |
+
"C65_2104",
|
| 62 |
+
"C65_2504",
|
| 63 |
+
"C69_1804",
|
| 64 |
+
"C82_2504",
|
| 65 |
+
"C85_2004",
|
| 66 |
+
"C93_2104",
|
| 67 |
+
"C93_2704",
|
| 68 |
+
"C93_0405",
|
| 69 |
+
"C101_0601",
|
| 70 |
+
"C101_1101",
|
| 71 |
+
"C101_1301",
|
| 72 |
+
"C101_1801",
|
| 73 |
+
"C101_2001",
|
| 74 |
+
"C101_2502",
|
| 75 |
+
"C103_2204",
|
| 76 |
+
"C104_2204",
|
| 77 |
+
"C106_2204",
|
| 78 |
+
"C108_2204",
|
| 79 |
+
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