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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-ye2026_sepsis-scsemi_budget_20261002-f2_20261008T110651.log +26 -0
  2. 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-f3_20261008T110724.log +26 -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-f4_20261008T110757.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-pooled_20261008T110903.log +26 -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-f2_20261008T110651.log ADDED
@@ -0,0 +1,26 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 11:06:52 ye2026_sepsis: 16 scored donors, 4 arm(s); fitting the observed reference
2
+ 11:06:53 reference: R1 2400 cells, PCA var 0.347, R2 control P/C 0.9971/1.0000; contrast on
3
+ 11:06:53 observed top-50 DEG lists: T 0 (sig 0, 12+4 donors, 62381 cells), B 0 (sig 0, 12+4 donors, 16254 cells), Mono 1 (sig 1, 12+4 donors, 19357 cells), NK 5 (sig 5, 12+4 donors, 8525 cells), DC 0 (sig 0, 11+4 donors, 697 cells)
4
+ 11:06:53 scsemi_n5__raw: loading generated_counts (24000 cells in the NPZ, 24000 scored)
5
+ 11:06:56 scsemi_n5__raw: Poisson read-out nnz 2847276 (whole NPZ), median library 1943; annotating
6
+ 11:07:00 scsemi_n5__raw: L1 0.4797 (null 0.5047317525565007) P/C 0.9554/0.1317 pb r 0.6102 top1 0.125 mono 21.8% (6.5 s)
7
+ 11:07:00 scsemi_n5__raw: top-50 DEG 0/6 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
8
+ 11:07:00 scsemi_n10__raw: loading generated_counts (24000 cells in the NPZ, 24000 scored)
9
+ 11:07:02 scsemi_n10__raw: Poisson read-out nnz 2856409 (whole NPZ), median library 1933; annotating
10
+ 11:07:06 scsemi_n10__raw: L1 0.4709 (null 0.5047317525565007) P/C 0.9454/0.1408 pb r 0.6025 top1 0.125 mono 20.6% (6.4 s)
11
+ 11:07:06 scsemi_n10__raw: top-50 DEG 0/6 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
12
+ 11:07:06 scsemi_n20__raw: loading generated_counts (24000 cells in the NPZ, 24000 scored)
13
+ 11:07:08 scsemi_n20__raw: Poisson read-out nnz 2850323 (whole NPZ), median library 1990; annotating
14
+ 11:07:13 scsemi_n20__raw: L1 0.4635 (null 0.5047317525565007) P/C 0.9279/0.1350 pb r 0.5988 top1 0.125 mono 18.6% (6.3 s)
15
+ 11:07:13 scsemi_n20__raw: top-50 DEG 0/6 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
16
+ 11:07:13 scsemi_n40__raw: loading generated_counts (24000 cells in the NPZ, 24000 scored)
17
+ 11:07:15 scsemi_n40__raw: Poisson read-out nnz 2934879 (whole NPZ), median library 1968; annotating
18
+ 11:07:19 scsemi_n40__raw: L1 0.4340 (null 0.5047317525565007) P/C 0.9496/0.1400 pb r 0.6136 top1 0.250 mono 26.0% (5.9 s)
19
+ 11:07:19 scsemi_n40__raw: top-50 DEG 0/6 (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 0.4797 0.5047 0.9554 0.1317 0.5662 0.2962 0.6102 0.125 21.8250 19.6079 1943.0 1977.0 0.4785 0.1937 0.3326 0.3162 0.0 0.0 0.0 0.0 0.0 0.0 6.0 0.0 0.0 6.5
22
+ scsemi_n10__raw 0.4709 0.5047 0.9454 0.1408 0.5604 0.2971 0.6025 0.125 20.5875 19.6079 1933.0 1977.0 0.5036 0.2078 0.3326 0.3162 0.0 0.0 0.0 0.0 0.0 0.0 6.0 0.0 0.0 6.4
23
+ scsemi_n20__raw 0.4635 0.5047 0.9279 0.1350 0.5292 0.2754 0.5988 0.125 18.5958 19.6079 1990.0 1977.0 0.5011 0.2429 0.3326 0.3162 0.0 0.0 0.0 0.0 0.0 0.0 6.0 0.0 0.0 6.3
24
+ scsemi_n40__raw 0.4340 0.5047 0.9496 0.1400 0.5679 0.2888 0.6136 0.250 26.0000 19.6079 1968.0 1977.0 0.3550 0.1723 0.3326 0.3162 0.0 0.0 0.0 0.0 0.0 0.0 6.0 0.0 0.0 5.9
25
+ 11:07:19 done in 27.2 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/fold2
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-f3_20261008T110724.log ADDED
@@ -0,0 +1,26 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 11:07:25 ye2026_sepsis: 16 scored donors, 4 arm(s); fitting the observed reference
2
+ 11:07:26 reference: R1 2400 cells, PCA var 0.372, R2 control P/C 0.9967/1.0000; contrast on
3
+ 11:07:26 observed top-50 DEG lists: T 50 (sig 97, 13+3 donors, 48746 cells), B 50 (sig 122, 13+3 donors, 20084 cells), Mono 5 (sig 5, 13+3 donors, 19536 cells), NK 30 (sig 30, 13+3 donors, 7787 cells), DC 50 (sig 63, 12+3 donors, 284 cells)
4
+ 11:07:26 scsemi_n5__raw: loading generated_counts (24000 cells in the NPZ, 24000 scored)
5
+ 11:07:28 scsemi_n5__raw: Poisson read-out nnz 2862783 (whole NPZ), median library 1821; annotating
6
+ 11:07:32 scsemi_n5__raw: L1 0.6383 (null 0.5743329400790451) P/C 0.9213/0.1400 pb r 0.5742 top1 0.188 mono 13.1% (6.0 s)
7
+ 11:07:32 scsemi_n5__raw: top-50 DEG 0/185 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
8
+ 11:07:32 scsemi_n10__raw: loading generated_counts (24000 cells in the NPZ, 24000 scored)
9
+ 11:07:34 scsemi_n10__raw: Poisson read-out nnz 2819215 (whole NPZ), median library 1926; annotating
10
+ 11:07:38 scsemi_n10__raw: L1 0.6968 (null 0.5743329400790451) P/C 0.9563/0.1392 pb r 0.5699 top1 0.250 mono 10.9% (6.0 s)
11
+ 11:07:38 scsemi_n10__raw: top-50 DEG 0/185 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
12
+ 11:07:38 scsemi_n20__raw: loading generated_counts (24000 cells in the NPZ, 24000 scored)
13
+ 11:07:40 scsemi_n20__raw: Poisson read-out nnz 2775838 (whole NPZ), median library 1939; annotating
14
+ 11:07:44 scsemi_n20__raw: L1 0.6229 (null 0.5743329400790451) P/C 0.9721/0.1442 pb r 0.5743 top1 0.188 mono 15.5% (6.1 s)
15
+ 11:07:44 scsemi_n20__raw: top-50 DEG 0/185 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
16
+ 11:07:44 scsemi_n40__raw: loading generated_counts (24000 cells in the NPZ, 24000 scored)
17
+ 11:07:46 scsemi_n40__raw: Poisson read-out nnz 2718054 (whole NPZ), median library 1962; annotating
18
+ 11:07:50 scsemi_n40__raw: L1 0.6030 (null 0.5743329400790451) P/C 0.9821/0.1404 pb r 0.5821 top1 0.125 mono 20.4% (5.8 s)
19
+ 11:07:50 scsemi_n40__raw: top-50 DEG 0/185 (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 0.6383 0.5743 0.9212 0.1400 0.6308 0.3633 0.5742 0.1875 13.0583 23.1778 1821.0 1947.0 0.3617 0.0710 0.3761 0.3541 0.0 0.0 0.0 0.0 0.0 0.0 185.0 0.0 0.0 6.0
22
+ scsemi_n10__raw 0.6968 0.5743 0.9562 0.1392 0.5242 0.3350 0.5699 0.2500 10.9292 23.1778 1926.0 1947.0 0.4160 0.1654 0.3761 0.3541 0.0 0.0 0.0 0.0 0.0 0.0 185.0 0.0 0.0 6.0
23
+ scsemi_n20__raw 0.6229 0.5743 0.9721 0.1442 0.5654 0.3575 0.5743 0.1875 15.5333 23.1778 1939.0 1947.0 0.3157 0.0814 0.3761 0.3541 0.0 0.0 0.0 0.0 0.0 0.0 185.0 0.0 0.0 6.1
24
+ scsemi_n40__raw 0.6030 0.5743 0.9821 0.1404 0.6538 0.4000 0.5821 0.1250 20.3625 23.1778 1962.0 1947.0 0.1867 0.0455 0.3761 0.3541 0.0 0.0 0.0 0.0 0.0 0.0 185.0 0.0 0.0 5.8
25
+ 11:07:50 done in 25.7 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/fold3
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-f4_20261008T110757.log ADDED
@@ -0,0 +1,26 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 11:07:58 ye2026_sepsis: 16 scored donors, 4 arm(s); fitting the observed reference
2
+ 11:07:59 reference: R1 2400 cells, PCA var 0.355, R2 control P/C 0.9975/1.0000; contrast on
3
+ 11:07:59 observed top-50 DEG lists: T 35 (sig 35, 12+4 donors, 58503 cells), B 3 (sig 3, 12+4 donors, 21119 cells), Mono 1 (sig 1, 12+4 donors, 18965 cells), NK 0 (sig 0, 12+4 donors, 9793 cells), DC 0 (sig 0, 11+4 donors, 630 cells)
4
+ 11:07:59 scsemi_n5__raw: loading generated_counts (24000 cells in the NPZ, 24000 scored)
5
+ 11:08:01 scsemi_n5__raw: Poisson read-out nnz 2759927 (whole NPZ), median library 2041; annotating
6
+ 11:08:05 scsemi_n5__raw: L1 0.5519 (null 0.5309673683527368) P/C 0.9354/0.1667 pb r 0.6330 top1 0.250 mono 24.7% (6.2 s)
7
+ 11:08:05 scsemi_n5__raw: top-50 DEG 0/39 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
8
+ 11:08:05 scsemi_n10__raw: loading generated_counts (24000 cells in the NPZ, 24000 scored)
9
+ 11:08:07 scsemi_n10__raw: Poisson read-out nnz 2777060 (whole NPZ), median library 2100; annotating
10
+ 11:08:11 scsemi_n10__raw: L1 0.5528 (null 0.5309673683527368) P/C 0.9221/0.1646 pb r 0.6340 top1 0.188 mono 24.4% (5.9 s)
11
+ 11:08:11 scsemi_n10__raw: top-50 DEG 0/39 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
12
+ 11:08:11 scsemi_n20__raw: loading generated_counts (24000 cells in the NPZ, 24000 scored)
13
+ 11:08:13 scsemi_n20__raw: Poisson read-out nnz 2865570 (whole NPZ), median library 2075; annotating
14
+ 11:08:17 scsemi_n20__raw: L1 0.5933 (null 0.5309673683527368) P/C 0.9554/0.1708 pb r 0.6226 top1 0.062 mono 27.1% (5.8 s)
15
+ 11:08:17 scsemi_n20__raw: top-50 DEG 0/39 (T 0, B 0, Mono 0, NK 0, DC 0); broadcast 0 (0.03 s)
16
+ 11:08:17 scsemi_n40__raw: loading generated_counts (24000 cells in the NPZ, 24000 scored)
17
+ 11:08:19 scsemi_n40__raw: Poisson read-out nnz 2796965 (whole NPZ), median library 2007; annotating
18
+ 11:08:23 scsemi_n40__raw: L1 0.6754 (null 0.5309673683527368) P/C 0.9446/0.1787 pb r 0.6208 top1 0.000 mono 18.6% (5.7 s)
19
+ 11:08:23 scsemi_n40__raw: top-50 DEG 0/39 (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 0.5519 0.531 0.9354 0.1667 0.5629 0.2775 0.6330 0.2500 24.7375 17.958 2041.0 1935.0 0.3442 0.1415 0.4527 0.3163 0.0 0.0 0.0 0.0 0.0 0.0 39.0 0.0 0.0 6.2
22
+ scsemi_n10__raw 0.5528 0.531 0.9221 0.1646 0.5562 0.2462 0.6340 0.1875 24.4167 17.958 2100.0 1935.0 0.3831 0.1444 0.4527 0.3163 0.0 0.0 0.0 0.0 0.0 0.0 39.0 0.0 0.0 5.9
23
+ scsemi_n20__raw 0.5933 0.531 0.9554 0.1708 0.6112 0.2725 0.6226 0.0625 27.1375 17.958 2075.0 1935.0 0.5323 0.2054 0.4527 0.3163 0.0 0.0 0.0 0.0 0.0 0.0 39.0 0.0 0.0 5.8
24
+ scsemi_n40__raw 0.6754 0.531 0.9446 0.1788 0.6617 0.2883 0.6208 0.0000 18.6042 17.958 2007.0 1935.0 0.5986 0.2115 0.4527 0.3163 0.0 0.0 0.0 0.0 0.0 0.0 39.0 0.0 0.0 5.7
25
+ 11:08:23 done in 25.2 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/fold4
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-pooled_20261008T110903.log ADDED
@@ -0,0 +1,26 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 11:09:10 ye2026_sepsis: 82 scored donors, 4 arm(s); fitting the observed reference
2
+ 11:09:16 reference: R1 12300 cells, PCA var 0.335, R2 control P/C 0.9805/0.9997; contrast on
3
+ 11:09:16 observed top-50 DEG lists: T 50 (sig 1578, 61+21 donors, 298117 cells), B 50 (sig 1102, 61+21 donors, 99729 cells), Mono 50 (sig 2459, 61+21 donors, 111269 cells), NK 50 (sig 1235, 61+21 donors, 47832 cells), DC 50 (sig 1572, 57+21 donors, 3300 cells)
4
+ 11:09:16 scsemi_n5__raw: loading generated_counts (123000 cells in the NPZ, 123000 scored)
5
+ 11:09:23 scsemi_n5__raw: Poisson read-out nnz 14165905 (whole NPZ), median library 1957; annotating
6
+ 11:09:32 scsemi_n5__raw: L1 0.5215 (null 0.515468004498372) P/C 0.7518/0.0969 pb r 0.6061 top1 0.037 mono 21.3% (16.7 s)
7
+ 11:09:32 scsemi_n5__raw: top-50 DEG 2/250 (T 1, B 1, Mono 0, NK 0, DC 0); broadcast 21 (0.13 s)
8
+ 11:09:32 scsemi_n10__raw: loading generated_counts (123000 cells in the NPZ, 123000 scored)
9
+ 11:09:41 scsemi_n10__raw: Poisson read-out nnz 14262062 (whole NPZ), median library 1961; annotating
10
+ 11:09:50 scsemi_n10__raw: L1 0.5358 (null 0.515468004498372) P/C 0.7480/0.1030 pb r 0.6063 top1 0.037 mono 19.3% (17.8 s)
11
+ 11:09:50 scsemi_n10__raw: top-50 DEG 3/250 (T 2, B 1, Mono 0, NK 0, DC 0); broadcast 21 (0.12 s)
12
+ 11:09:50 scsemi_n20__raw: loading generated_counts (123000 cells in the NPZ, 123000 scored)
13
+ 11:09:58 scsemi_n20__raw: Poisson read-out nnz 14465206 (whole NPZ), median library 1997; annotating
14
+ 11:10:07 scsemi_n20__raw: L1 0.5319 (null 0.515468004498372) P/C 0.7529/0.1006 pb r 0.6122 top1 0.012 mono 21.0% (16.5 s)
15
+ 11:10:07 scsemi_n20__raw: top-50 DEG 2/250 (T 0, B 1, Mono 1, NK 0, DC 0); broadcast 21 (0.16 s)
16
+ 11:10:07 scsemi_n40__raw: loading generated_counts (123000 cells in the NPZ, 123000 scored)
17
+ 11:10:15 scsemi_n40__raw: Poisson read-out nnz 14460654 (whole NPZ), median library 1971; annotating
18
+ 11:10:25 scsemi_n40__raw: L1 0.5165 (null 0.515468004498372) P/C 0.7591/0.0960 pb r 0.6119 top1 0.012 mono 21.7% (18.1 s)
19
+ 11:10:25 scsemi_n40__raw: top-50 DEG 6/250 (T 0, B 2, Mono 2, NK 0, DC 2); broadcast 21 (0.16 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 0.5215 0.5155 0.7518 0.0969 0.5286 0.2102 0.6061 0.0366 21.3472 20.8171 1957.0 1967.0 0.5274 0.2630 0.3159 0.291 1.0 1.0 0.0 0.0 0.0 2.0 250.0 2.0 21.0 16.7
22
+ scsemi_n10__raw 0.5358 0.5155 0.7480 0.1030 0.5156 0.2214 0.6063 0.0366 19.3423 20.8171 1961.0 1967.0 0.5611 0.2815 0.3159 0.291 2.0 1.0 0.0 0.0 0.0 3.0 250.0 3.0 21.0 17.8
23
+ scsemi_n20__raw 0.5319 0.5155 0.7529 0.1006 0.5168 0.2132 0.6122 0.0122 21.0390 20.8171 1997.0 1967.0 0.5820 0.2697 0.3159 0.291 0.0 1.0 1.0 0.0 0.0 2.0 250.0 2.0 21.0 16.5
24
+ scsemi_n40__raw 0.5165 0.5155 0.7591 0.0960 0.5263 0.2082 0.6119 0.0122 21.7220 20.8171 1971.0 1967.0 0.5210 0.2151 0.3159 0.291 0.0 2.0 2.0 0.0 2.0 6.0 250.0 4.0 21.0 18.1
25
+ 11:10:25 done in 81.1 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/pooled
26
+ UNIT_EXIT 0