Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/queues/ye2026_sepsis_lora_rank_s2.txt

@@ -0,0 +1,61 @@
+# ye2026_sepsis LoRA rank sweep (2026-10-01): r in {4,64}, alpha = r; sizes 5 20 all; all else as the r 16 arms (real_lora, lora_n*)
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/lora_r4_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|0|lora|5e-4|--lora-rank|4|--lora-alpha|4|--train-n|5|--subset-seed|1000|--strata-regex|sepsis
+sample|ye2_f0_lora_r4_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/lora_r4_n5/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold0/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold0/lora_r4_n5__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/lora_r64_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|0|lora|5e-4|--lora-rank|64|--lora-alpha|64|--train-n|5|--subset-seed|1000|--strata-regex|sepsis
+sample|ye2_f0_lora_r64_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/lora_r64_n5/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold0/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold0/lora_r64_n5__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold1/lora_r4_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|1|lora|5e-4|--lora-rank|4|--lora-alpha|4|--train-n|5|--subset-seed|1001|--strata-regex|sepsis
+sample|ye2_f1_lora_r4_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold1/lora_r4_n5/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold1/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold1/lora_r4_n5__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold1/lora_r64_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|1|lora|5e-4|--lora-rank|64|--lora-alpha|64|--train-n|5|--subset-seed|1001|--strata-regex|sepsis
+sample|ye2_f1_lora_r64_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold1/lora_r64_n5/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold1/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold1/lora_r64_n5__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold2/lora_r4_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|2|lora|5e-4|--lora-rank|4|--lora-alpha|4|--train-n|5|--subset-seed|1002|--strata-regex|sepsis
+sample|ye2_f2_lora_r4_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold2/lora_r4_n5/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold2/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold2/lora_r4_n5__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold2/lora_r64_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|2|lora|5e-4|--lora-rank|64|--lora-alpha|64|--train-n|5|--subset-seed|1002|--strata-regex|sepsis
+sample|ye2_f2_lora_r64_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold2/lora_r64_n5/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold2/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold2/lora_r64_n5__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold3/lora_r4_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|3|lora|5e-4|--lora-rank|4|--lora-alpha|4|--train-n|5|--subset-seed|1003|--strata-regex|sepsis
+sample|ye2_f3_lora_r4_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold3/lora_r4_n5/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold3/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold3/lora_r4_n5__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold3/lora_r64_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|3|lora|5e-4|--lora-rank|64|--lora-alpha|64|--train-n|5|--subset-seed|1003|--strata-regex|sepsis
+sample|ye2_f3_lora_r64_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold3/lora_r64_n5/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold3/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold3/lora_r64_n5__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold4/lora_r4_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|4|lora|5e-4|--lora-rank|4|--lora-alpha|4|--train-n|5|--subset-seed|1004|--strata-regex|sepsis
+sample|ye2_f4_lora_r4_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold4/lora_r4_n5/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold4/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold4/lora_r4_n5__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold4/lora_r64_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|4|lora|5e-4|--lora-rank|64|--lora-alpha|64|--train-n|5|--subset-seed|1004|--strata-regex|sepsis
+sample|ye2_f4_lora_r64_n5|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold4/lora_r64_n5/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold4/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold4/lora_r64_n5__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/lora_r4_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|0|lora|5e-4|--lora-rank|4|--lora-alpha|4|--train-n|20|--subset-seed|1000|--strata-regex|sepsis
+sample|ye2_f0_lora_r4_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/lora_r4_n20/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold0/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold0/lora_r4_n20__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/lora_r64_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|0|lora|5e-4|--lora-rank|64|--lora-alpha|64|--train-n|20|--subset-seed|1000|--strata-regex|sepsis
+sample|ye2_f0_lora_r64_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold0/lora_r64_n20/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold0/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold0/lora_r64_n20__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold1/lora_r4_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|1|lora|5e-4|--lora-rank|4|--lora-alpha|4|--train-n|20|--subset-seed|1001|--strata-regex|sepsis
+sample|ye2_f1_lora_r4_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold1/lora_r4_n20/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold1/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold1/lora_r4_n20__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold1/lora_r64_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|1|lora|5e-4|--lora-rank|64|--lora-alpha|64|--train-n|20|--subset-seed|1001|--strata-regex|sepsis
+sample|ye2_f1_lora_r64_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold1/lora_r64_n20/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold1/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold1/lora_r64_n20__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold2/lora_r4_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|2|lora|5e-4|--lora-rank|4|--lora-alpha|4|--train-n|20|--subset-seed|1002|--strata-regex|sepsis
+sample|ye2_f2_lora_r4_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold2/lora_r4_n20/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold2/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold2/lora_r4_n20__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold2/lora_r64_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|2|lora|5e-4|--lora-rank|64|--lora-alpha|64|--train-n|20|--subset-seed|1002|--strata-regex|sepsis
+sample|ye2_f2_lora_r64_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold2/lora_r64_n20/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold2/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold2/lora_r64_n20__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold3/lora_r4_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|3|lora|5e-4|--lora-rank|4|--lora-alpha|4|--train-n|20|--subset-seed|1003|--strata-regex|sepsis
+sample|ye2_f3_lora_r4_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold3/lora_r4_n20/checkpoint_ft.pt|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/fold3/test_raw.npz|20260927|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fold3/lora_r4_n20__raw.npz
+train|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold3/lora_r64_n20|/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis/conditions_raw_fixed.npz|3|lora|5e-4|--lora-rank|64|--lora-alpha|64|--train-n|20|--subset-seed|1003|--strata-regex|sepsis
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paper-releases/pbisc-diffusion/updates/20261001T023742Z-deck-calibration-giroux-sexgenes/diffusion/metadata/NOTE.md

@@ -0,0 +1,5 @@
+# PBISC-diffusion update 20261001T023742Z-deck-calibration-giroux-sexgenes
+
+2026-10-01. Deck: paired gene-wise calibration comparator restored as 'Zero-shot + calibration' next to raw zero-shot (sec07/08/09; sc-only control fed calibrated bulk); Giroux disease metrics rescored with 196 sex-linked genes excluded (chrY non-PAR + Tukiainen 2017 X-escape) because severity is confounded with sex (4F/0M vs 0F/5M scored). Benchmark: score_ft.py --exclude-genes/--reuse-labels, scores_nosex + scores_nochrY, sex-gene list; prepared (not yet run) LoRA rank sweep r4/r64 and equal-pair-budget calibration conditions (alpha_n*, test_cal_n*). CPU only; rank-sweep runs excluded until finished.
+
+Payload states are recorded as supplied. Inference locations are pointers, not archived generated outputs.