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junidude14 commited on
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Archive 4 checkpoints (1-4)

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  1. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/logs/score-giroux2022-scsemi_cv_20261002-f4_20261008T105631.log +13 -0
  2. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/logs/score-giroux2022-scsemi_cv_20261002-pooled_20261008T105647.log +11 -0
  3. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/logs/score-ye2026_sepsis-scsemi_budget_20261002-f0_20261008T110545.log +26 -0
  4. paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/logs/score-ye2026_sepsis-scsemi_budget_20261002-f1_20261008T110618.log +26 -0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/logs/score-giroux2022-scsemi_cv_20261002-f4_20261008T105631.log ADDED
@@ -0,0 +1,13 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 10:56:32 giroux2022: 3 scored donors, 1 arm(s); fitting the observed reference
2
+ 10:56:32 reference: R1 450 cells, PCA var 0.352, R2 control P/C 1.0000/1.0000; contrast off
3
+ 10:56:32 scsemi__raw: loading generated_counts (4500 cells in the NPZ, 4500 scored)
4
+ 10:56:32 scsemi__raw: Poisson read-out nnz 506180 (whole NPZ), median library 460; annotating
5
+ /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py:411: RuntimeWarning: Mean of empty slice
6
+ "l1_obs_loo_null_mean": float(np.nanmean(null)) if S > 1 else None,
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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:412: RuntimeWarning: Mean of empty slice
8
+ "l1_generated_loo_mean_vs_observed_mean": float(np.nanmean(gen_loo)) if S > 1 else None,
9
+ 10:56:35 scsemi__raw: L1 0.1718 (null nan) P/C 1.0000/0.8133 pb r 0.6397 top1 1.000 mono 34.2% (3.5 s)
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+ comp_l1 comp_l1_obs_loo_null precision coverage precision_dm coverage_dm pb_r_median pb_top1 mono_pct_gen mono_pct_obs median_umi_gen median_umi_obs seconds
11
+ scsemi__raw 0.1718 NaN 1.0 0.8133 0.9067 0.6778 0.6397 1.0 34.1778 28.3553 460.0 548.0 3.5
12
+ 10:56:35 done in 3.8 s -> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold4
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+ UNIT_EXIT 0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/logs/score-giroux2022-scsemi_cv_20261002-pooled_20261008T105647.log ADDED
@@ -0,0 +1,11 @@
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 10:56:48 giroux2022: 24 scored donors, 1 arm(s); fitting the observed reference
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+ 10:56:49 reference: R1 3600 cells, PCA var 0.232, R2 control P/C 0.9981/1.0000; contrast on
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+ 10:56:49 observed top-50 DEG lists: T 50 (sig 306, 11+13 donors, 145034 cells), B 9 (sig 9, 11+13 donors, 17383 cells), Mono 7 (sig 7, 11+13 donors, 47311 cells), NK 50 (sig 83, 11+13 donors, 29061 cells), DC 7 (sig 7, 11+13 donors, 4328 cells)
4
+ 10:56:49 scsemi__raw: loading generated_counts (36000 cells in the NPZ, 36000 scored)
5
+ 10:56:51 scsemi__raw: Poisson read-out nnz 4025738 (whole NPZ), median library 472; annotating
6
+ 10:56:55 scsemi__raw: L1 0.2431 (null 0.30584824369245694) P/C 0.8722/0.3542 pb r 0.6256 top1 0.292 mono 23.3% (6.0 s)
7
+ 10:56:55 scsemi__raw: top-50 DEG 6/123 (T 4, B 1, Mono 0, NK 1, DC 0); broadcast 39 (0.04 s)
8
+ comp_l1 comp_l1_obs_loo_null precision coverage precision_dm coverage_dm pb_r_median pb_top1 mono_pct_gen mono_pct_obs median_umi_gen median_umi_obs contrast_mean_cp10k_r_gen contrast_pseudobulk_log1p_cpm_r_gen contrast_mean_cp10k_r_broadcast contrast_pseudobulk_log1p_cpm_r_broadcast deg_top50_T deg_top50_B deg_top50_Mono deg_top50_NK deg_top50_DC deg_top50_sum deg_top50_max deg_top50_sum_4type deg_top50_sum_broadcast seconds
9
+ scsemi__raw 0.2431 0.3058 0.8722 0.3542 0.3442 0.1686 0.6256 0.2917 23.2722 19.2479 472.0 471.0 0.5306 0.3345 0.6381 0.7947 4.0 1.0 0.0 1.0 0.0 6.0 123.0 6.0 39.0 6.0
10
+ 10:56:55 done in 7.3 s -> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/pooled
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+ UNIT_EXIT 0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/logs/score-ye2026_sepsis-scsemi_budget_20261002-f0_20261008T110545.log ADDED
@@ -0,0 +1,26 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 11:05:45 ye2026_sepsis: 17 scored donors, 4 arm(s); fitting the observed reference
2
+ 11:05:46 reference: R1 2550 cells, PCA var 0.360, R2 control P/C 0.9969/1.0000; contrast on
3
+ 11:05:46 observed top-50 DEG lists: T 50 (sig 113, 12+5 donors, 61162 cells), B 50 (sig 164, 12+5 donors, 21022 cells), Mono 50 (sig 932, 12+5 donors, 31471 cells), NK 50 (sig 122, 12+5 donors, 10457 cells), DC 50 (sig 152, 12+5 donors, 1035 cells)
4
+ 11:05:46 scsemi_n5__raw: loading generated_counts (25500 cells in the NPZ, 25500 scored)
5
+ 11:05:48 scsemi_n5__raw: Poisson read-out nnz 2862952 (whole NPZ), median library 2282; annotating
6
+ 11:05:52 scsemi_n5__raw: L1 0.5395 (null 0.5132314215340571) P/C 0.9447/0.1176 pb r 0.5988 top1 0.118 mono 25.3% (5.8 s)
7
+ 11:05:52 scsemi_n5__raw: top-50 DEG 0/250 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
8
+ 11:05:52 scsemi_n10__raw: loading generated_counts (25500 cells in the NPZ, 25500 scored)
9
+ 11:05:54 scsemi_n10__raw: Poisson read-out nnz 2924919 (whole NPZ), median library 2063; annotating
10
+ 11:05:58 scsemi_n10__raw: L1 0.5480 (null 0.5132314215340571) P/C 0.8937/0.1341 pb r 0.6121 top1 0.118 mono 19.2% (5.8 s)
11
+ 11:05:58 scsemi_n10__raw: top-50 DEG 0/250 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
12
+ 11:05:58 scsemi_n20__raw: loading generated_counts (25500 cells in the NPZ, 25500 scored)
13
+ 11:06:00 scsemi_n20__raw: Poisson read-out nnz 2997021 (whole NPZ), median library 2118; annotating
14
+ 11:06:04 scsemi_n20__raw: L1 0.4851 (null 0.5132314215340571) P/C 0.9000/0.1325 pb r 0.6379 top1 0.059 mono 21.8% (6.0 s)
15
+ 11:06:04 scsemi_n20__raw: top-50 DEG 0/250 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
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+ 11:06:04 scsemi_n40__raw: loading generated_counts (25500 cells in the NPZ, 25500 scored)
17
+ 11:06:07 scsemi_n40__raw: Poisson read-out nnz 3002033 (whole NPZ), median library 1985; annotating
18
+ 11:06:11 scsemi_n40__raw: L1 0.4802 (null 0.5132314215340571) P/C 0.8973/0.1286 pb r 0.6239 top1 0.059 mono 20.9% (7.3 s)
19
+ 11:06:11 scsemi_n40__raw: top-50 DEG 0/250 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
20
+ comp_l1 comp_l1_obs_loo_null precision coverage precision_dm coverage_dm pb_r_median pb_top1 mono_pct_gen mono_pct_obs median_umi_gen median_umi_obs contrast_mean_cp10k_r_gen contrast_pseudobulk_log1p_cpm_r_gen contrast_mean_cp10k_r_broadcast contrast_pseudobulk_log1p_cpm_r_broadcast deg_top50_T deg_top50_B deg_top50_Mono deg_top50_NK deg_top50_DC deg_top50_sum deg_top50_max deg_top50_sum_4type deg_top50_sum_broadcast seconds
21
+ scsemi_n5__raw 0.5395 0.5132 0.9447 0.1176 0.7059 0.2545 0.5988 0.1176 25.2706 24.6001 2282.0 2022.0 0.3438 0.1400 0.4815 0.4503 0.0 0.0 0.0 0.0 0.0 0.0 250.0 0.0 0.0 5.8
22
+ scsemi_n10__raw 0.5480 0.5132 0.8937 0.1341 0.6639 0.2714 0.6121 0.1176 19.1608 24.6001 2063.0 2022.0 0.4127 0.1535 0.4815 0.4503 0.0 0.0 0.0 0.0 0.0 0.0 250.0 0.0 0.0 5.8
23
+ scsemi_n20__raw 0.4851 0.5132 0.9000 0.1325 0.6294 0.2584 0.6379 0.0588 21.7882 24.6001 2118.0 2022.0 0.4121 0.2014 0.4815 0.4503 0.0 0.0 0.0 0.0 0.0 0.0 250.0 0.0 0.0 6.0
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+ scsemi_n40__raw 0.4802 0.5132 0.8973 0.1286 0.6059 0.2525 0.6239 0.0588 20.9412 24.6001 1985.0 2022.0 0.4557 0.2047 0.4815 0.4503 0.0 0.0 0.0 0.0 0.0 0.0 250.0 0.0 0.0 7.3
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+ 11:06:11 done in 26.3 s -> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_budget_20261002/fold0
26
+ UNIT_EXIT 0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/logs/score-ye2026_sepsis-scsemi_budget_20261002-f1_20261008T110618.log ADDED
@@ -0,0 +1,26 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 11:06:19 ye2026_sepsis: 17 scored donors, 4 arm(s); fitting the observed reference
2
+ 11:06:20 reference: R1 2550 cells, PCA var 0.340, R2 control P/C 0.9980/1.0000; contrast on
3
+ 11:06:20 observed top-50 DEG lists: T 0 (sig 0, 12+5 donors, 67325 cells), B 3 (sig 3, 12+5 donors, 21250 cells), Mono 1 (sig 1, 12+5 donors, 21940 cells), NK 36 (sig 36, 12+5 donors, 11270 cells), DC 5 (sig 5, 11+5 donors, 654 cells)
4
+ 11:06:20 scsemi_n5__raw: loading generated_counts (25500 cells in the NPZ, 25500 scored)
5
+ 11:06:22 scsemi_n5__raw: Poisson read-out nnz 2833135 (whole NPZ), median library 1909; annotating
6
+ 11:06:27 scsemi_n5__raw: L1 0.4046 (null 0.5310296453390433) P/C 0.9510/0.1357 pb r 0.5569 top1 0.235 mono 21.5% (6.9 s)
7
+ 11:06:27 scsemi_n5__raw: top-50 DEG 0/45 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
8
+ 11:06:27 scsemi_n10__raw: loading generated_counts (25500 cells in the NPZ, 25500 scored)
9
+ 11:06:29 scsemi_n10__raw: Poisson read-out nnz 2884835 (whole NPZ), median library 1878; annotating
10
+ 11:06:33 scsemi_n10__raw: L1 0.4162 (null 0.5310296453390433) P/C 0.9529/0.1549 pb r 0.6049 top1 0.235 mono 21.6% (5.9 s)
11
+ 11:06:33 scsemi_n10__raw: top-50 DEG 0/45 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
12
+ 11:06:33 scsemi_n20__raw: loading generated_counts (25500 cells in the NPZ, 25500 scored)
13
+ 11:06:35 scsemi_n20__raw: Poisson read-out nnz 2976810 (whole NPZ), median library 1899; annotating
14
+ 11:06:38 scsemi_n20__raw: L1 0.4982 (null 0.5310296453390433) P/C 0.9557/0.1545 pb r 0.5845 top1 0.235 mono 21.9% (5.7 s)
15
+ 11:06:38 scsemi_n20__raw: top-50 DEG 0/45 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
16
+ 11:06:38 scsemi_n40__raw: loading generated_counts (25500 cells in the NPZ, 25500 scored)
17
+ 11:06:40 scsemi_n40__raw: Poisson read-out nnz 3008327 (whole NPZ), median library 1935; annotating
18
+ 11:06:44 scsemi_n40__raw: L1 0.3977 (null 0.5310296453390433) P/C 0.9749/0.1545 pb r 0.5817 top1 0.118 mono 22.7% (6.2 s)
19
+ 11:06:44 scsemi_n40__raw: top-50 DEG 0/45 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.04 s)
20
+ comp_l1 comp_l1_obs_loo_null precision coverage precision_dm coverage_dm pb_r_median pb_top1 mono_pct_gen mono_pct_obs median_umi_gen median_umi_obs contrast_mean_cp10k_r_gen contrast_pseudobulk_log1p_cpm_r_gen contrast_mean_cp10k_r_broadcast contrast_pseudobulk_log1p_cpm_r_broadcast deg_top50_T deg_top50_B deg_top50_Mono deg_top50_NK deg_top50_DC deg_top50_sum deg_top50_max deg_top50_sum_4type deg_top50_sum_broadcast seconds
21
+ scsemi_n5__raw 0.4046 0.531 0.9510 0.1357 0.6204 0.1882 0.5569 0.2353 21.4863 18.641 1909.0 1949.0 0.3324 0.1407 0.2208 0.2547 0.0 0.0 0.0 0.0 0.0 0.0 45.0 0.0 0.0 6.9
22
+ scsemi_n10__raw 0.4162 0.531 0.9529 0.1549 0.6522 0.2294 0.6049 0.2353 21.6314 18.641 1878.0 1949.0 0.3863 0.1662 0.2208 0.2547 0.0 0.0 0.0 0.0 0.0 0.0 45.0 0.0 0.0 5.9
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+ scsemi_n20__raw 0.4982 0.531 0.9557 0.1545 0.6157 0.2302 0.5845 0.2353 21.9176 18.641 1899.0 1949.0 0.2598 0.1254 0.2208 0.2547 0.0 0.0 0.0 0.0 0.0 0.0 45.0 0.0 0.0 5.7
24
+ scsemi_n40__raw 0.3977 0.531 0.9749 0.1545 0.6475 0.2671 0.5817 0.1176 22.6784 18.641 1935.0 1949.0 0.1789 0.0853 0.2208 0.2547 0.0 0.0 0.0 0.0 0.0 0.0 45.0 0.0 0.0 6.2
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+ 11:06:44 done in 26.2 s -> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/ye2026_sepsis/scsemi_budget_20261002/fold1
26
+ UNIT_EXIT 0