Archive 4 checkpoints (1-4)

.gitattributes

@@ -100,3 +100,5 @@ paper-releases/pbisc-diffusion/updates/20261006T150859Z-deck-readme-order-step/d
 paper-releases/pbisc-diffusion/updates/20261006T150859Z-deck-readme-order-step/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pptx filter=lfs diff=lfs merge=lfs -text
 paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pdf filter=lfs diff=lfs merge=lfs -text
 paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pptx filter=lfs diff=lfs merge=lfs -text
+paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pdf filter=lfs diff=lfs merge=lfs -text
+paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pptx filter=lfs diff=lfs merge=lfs -text

paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/logs/score-imperial_eskd-scsemi_cv_20261002-pooled_20261008T134742.log

@@ -0,0 +1,11 @@
+13:47:46 imperial_eskd: 157 scored donors, 1 arm(s); fitting the observed reference
+13:47:54 reference: R1 23482 cells, PCA var 0.258, R2 control P/C 0.9673/0.9997; contrast on
+13:47:54 observed top-50 DEG lists: T 50 (sig 1057, 113+34 donors, 262546 cells), B 50 (sig 298, 113+34 donors, 48625 cells), Mono 50 (sig 349, 112+34 donors, 80851 cells), NK 50 (sig 427, 113+34 donors, 72125 cells), DC 50 (sig 341, 113+34 donors, 13572 cells)
+13:47:54 scsemi__raw: loading generated_counts (235500 cells in the NPZ, 235500 scored)
+13:48:08 scsemi__raw: Poisson read-out nnz 30704580 (whole NPZ), median library 1354; annotating
+13:48:21 scsemi__raw: L1 0.5203 (null 0.5047406322420376) P/C 0.3478/0.0823 pb r 0.6171 top1 0.013 mono 14.1% (26.9 s)
+13:48:21 scsemi__raw: top-50 DEG 87/250 (T 26, B 13, Mono 17, NK 20, DC 11); broadcast 84 (0.23 s)
+             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
+scsemi__raw   0.5203                0.5047     0.3478    0.0823        0.4152        0.138       0.6171   0.0127       14.1223       16.9164          1354.0          1349.0                     0.7054                               0.4024                           0.6606                                     0.6049         26.0         13.0            17.0          20.0          11.0           87.0          250.0                 76.0                     84.0     26.9
+13:48:21 done in 38.3 s -> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/pooled
+UNIT_EXIT 0

paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores_contrast/_logs/cx-imperial-scsemi-cv_20261008T134836.log

@@ -0,0 +1,31 @@
+JOB_START 2026-10-08T13:48:36+09:00 --design scored --dataset imperial_eskd --score-dir scores/imperial_eskd/scsemi_cv_20261002/pooled --arms scsemi__raw --unit scsemi_cv_20261002/pooled --threads 6
+13:48:37 imperial_eskd scsemi_cv_20261002/pooled: 157 scored samples (113 case / 34 control), 5927 genes for the disease scores
+13:48:47 split half: 494503 observed cells of the 4 types, 5 seeds; mean r(A,B) T 0.970, B 0.781, Mono 0.900, NK 0.932 (9.6 s; full aggregates rebuilt = cache)
+13:49:04 scsemi__raw: 235500 cells; r mean_cp10k T 0.772/0.632, B 0.628/0.403, Mono 0.656/0.307, NK 0.766/0.412 (Pearson/Spearman); repro PASS (max |d| 8.3e-17) (18 s)
+13:49:14 limma: 22 jobs in 9 s (0 not ok)
+13:49:14 unit scsemi_cv_20261002/pooled of imperial_eskd -> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores_contrast/imperial_eskd/scsemi_cv_20261002/pooled in 37.4 s; reproduction PASS
+	Command being timed: "/home/sj_server_1/miniforge3/envs/cxg_corpus/bin/python tools/contrast_extra.py --design scored --dataset imperial_eskd --score-dir scores/imperial_eskd/scsemi_cv_20261002/pooled --arms scsemi__raw --unit scsemi_cv_20261002/pooled --threads 6"
+	User time (seconds): 39.66
+	System time (seconds): 2.53
+	Percent of CPU this job got: 111%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:37.95
+	Average shared text size (kbytes): 0
+	Average unshared data size (kbytes): 0
+	Average stack size (kbytes): 0
+	Average total size (kbytes): 0
+	Maximum resident set size (kbytes): 10282884
+	Average resident set size (kbytes): 0
+	Major (requiring I/O) page faults: 0
+	Minor (reclaiming a frame) page faults: 519960
+	Voluntary context switches: 460
+	Involuntary context switches: 548
+	Swaps: 0
+	File system inputs: 33400
+	File system outputs: 161456
+	Socket messages sent: 0
+	Socket messages received: 0
+	Signals delivered: 0
+	Page size (bytes): 4096
+	Exit status: 0
+JOB_EXIT 0 38s --design scored --dataset imperial_eskd --score-dir scores/imperial_eskd/scsemi_cv_20261002/pooled --arms scsemi__raw --unit scsemi_cv_20261002/pooled --threads 6
+UNIT_EXIT 0

paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pdf

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paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/presentations/2026-09-30--paper-summary--r00/PBISC-Diffusion_paper_summary_20260930.pptx

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