Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261001T145641Z-lora-rank-sweep-calibration-budget/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold4/lora_r4_n5/RUN.json

@@ -0,0 +1,105 @@
+{
+ "schema": "pbisc_sdd.ft_intradataset.run.v1",
+ "source_checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
+ "source_checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis",
+ "condition_npz": "/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",
+ "condition_npz_sha256": "ce8b61d7dcd3e62b9e63d52189cfb5bba881f87a661384277a7949a629231cb4",
+ "fold": 4,
+ "mode": "lora",
+ "trainable": {
+  "mode": "lora",
+  "lora_layers": [
+   "time_encoder.0",
+   "time_encoder.2",
+   "condition_encoder.0",
+   "condition_encoder.3",
+   "context_mixer.2",
+   "down_blocks.0.input_projection",
+   "down_blocks.0.context_projection.1",
+   "down_blocks.1.input_projection",
+   "down_blocks.1.context_projection.1",
+   "down_blocks.2.input_projection",
+   "down_blocks.2.context_projection.1",
+   "down_blocks.3.input_projection",
+   "down_blocks.3.context_projection.1",
+   "up_blocks.0.input_projection",
+   "up_blocks.0.context_projection.1",
+   "up_blocks.1.input_projection",
+   "up_blocks.1.context_projection.1",
+   "up_blocks.2.input_projection",
+   "up_blocks.2.context_projection.1",
+   "output_trunk.0",
+   "value_head",
+   "active_head"
+  ],
+  "lora_rank": 4,
+  "lora_alpha": 4.0,
+  "n_trainable": 324056,
+  "n_total_base": 54185184,
+  "trainable_tensors": 44
+ },
+ "lr": 0.0005,
+ "warmup": 200,
+ "batch_size": 256,
+ "ema_decay": 0.999,
+ "max_steps": 20000,
+ "steps_run": 5500,
+ "eval_every": 250,
+ "patience": 8,
+ "train_subset": {
+  "train_n": 5,
+  "subset_seed": 1004,
+  "strata_regex": "sepsis",
+  "allocation": {
+   "False": 1,
+   "True": 4
+  }
+ },
+ "train_donors_file": null,
+ "fixed_steps": null,
+ "selected_step": 3500,
+ "selected_inner_val_loss": 0.11223910748958588,
+ "pretrained_inner_val_loss": 0.1224389017692634,
+ "train_rows": [
+  "IC23",
+  "Res-S177",
+  "Res-S77",
+  "Skin-S142",
+  "Skin-S74"
+ ],
+ "inner_val_rows": [
+  "Abd-S156",
+  "HC13",
+  "IC22",
+  "Res-PS16",
+  "Res-S174",
+  "Skin-S52",
+  "Uri-S147"
+ ],
+ "test_rows_never_loaded_for_training": [
+  "Abd-PS20",
+  "Abd-PS27",
+  "Abd-S42",
+  "Abd-S54",
+  "Abd-S98",
+  "HC16",
+  "IC15",
+  "PHC02",
+  "PIC02",
+  "Res-PS03",
+  "Res-S127",
+  "Res-S164",
+  "Res-S166",
+  "Res-S87",
+  "Skin-S43",
+  "Uri-S93"
+ ],
+ "max_abs_weight_change": 0.5590962171554565,
+ "n_tensors_changed": 22,
+ "seed": 20260927,
+ "wall_seconds": 207.7,
+ "written_utc": "2026-10-01T08:27:56.648405+00:00",
+ "checkpoint_sha256": "6118559b2f028f7394fe4a3328697eb57dff15968a6c759b873c19bdada72ca6",
+ "reload_forward_max_abs_diff": 0.0
+}

paper-releases/pbisc-diffusion/updates/20261001T145641Z-lora-rank-sweep-calibration-budget/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold4/lora_r4_n5/history.json

@@ -0,0 +1,139 @@
+[
+ {
+  "step": 0,
+  "inner_val_loss": 0.1224389017692634,
+  "train_loss": null
+ },
+ {
+  "step": 250,
+  "inner_val_loss": 0.12187511899641582,
+  "train_loss": 0.11601920273900032,
+  "sec": 9.1
+ },
+ {
+  "step": 500,
+  "inner_val_loss": 0.120095678206001,
+  "train_loss": 0.11186052119731903,
+  "sec": 17.9
+ },
+ {
+  "step": 750,
+  "inner_val_loss": 0.11795933438198906,
+  "train_loss": 0.11150069800019265,
+  "sec": 26.6
+ },
+ {
+  "step": 1000,
+  "inner_val_loss": 0.1160951592028141,
+  "train_loss": 0.11114801868796348,
+  "sec": 35.2
+ },
+ {
+  "step": 1250,
+  "inner_val_loss": 0.11472002895815032,
+  "train_loss": 0.11167194929718971,
+  "sec": 43.8
+ },
+ {
+  "step": 1500,
+  "inner_val_loss": 0.11377935750143868,
+  "train_loss": 0.11099972236156463,
+  "sec": 52.8
+ },
+ {
+  "step": 1750,
+  "inner_val_loss": 0.11316523275205068,
+  "train_loss": 0.11083015537261963,
+  "sec": 61.7
+ },
+ {
+  "step": 2000,
+  "inner_val_loss": 0.11276086685912949,
+  "train_loss": 0.1109343639910221,
+  "sec": 70.5
+ },
+ {
+  "step": 2250,
+  "inner_val_loss": 0.11251701840332576,
+  "train_loss": 0.1114152390062809,
+  "sec": 79.2
+ },
+ {
+  "step": 2500,
+  "inner_val_loss": 0.11237839556166104,
+  "train_loss": 0.11082016882300377,
+  "sec": 87.9
+ },
+ {
+  "step": 2750,
+  "inner_val_loss": 0.11230294991816793,
+  "train_loss": 0.11038543954491616,
+  "sec": 96.6
+ },
+ {
+  "step": 3000,
+  "inner_val_loss": 0.11225519861493792,
+  "train_loss": 0.11117996022105217,
+  "sec": 105.1
+ },
+ {
+  "step": 3250,
+  "inner_val_loss": 0.11224666237831116,
+  "train_loss": 0.11080500370264053,
+  "sec": 113.8
+ },
+ {
+  "step": 3500,
+  "inner_val_loss": 0.11223910748958588,
+  "train_loss": 0.1104615273475647,
+  "sec": 122.7
+ },
+ {
+  "step": 3750,
+  "inner_val_loss": 0.1122477443090507,
+  "train_loss": 0.11049224218726159,
+  "sec": 133.3
+ },
+ {
+  "step": 4000,
+  "inner_val_loss": 0.11225121627960886,
+  "train_loss": 0.11095672205090523,
+  "sec": 143.7
+ },
+ {
+  "step": 4250,
+  "inner_val_loss": 0.1122648258294378,
+  "train_loss": 0.1108553404211998,
+  "sec": 154.1
+ },
+ {
+  "step": 4500,
+  "inner_val_loss": 0.11227902344294957,
+  "train_loss": 0.1108503535091877,
+  "sec": 164.6
+ },
+ {
+  "step": 4750,
+  "inner_val_loss": 0.11229735027466502,
+  "train_loss": 0.11073792362213135,
+  "sec": 174.9
+ },
+ {
+  "step": 5000,
+  "inner_val_loss": 0.11231059953570366,
+  "train_loss": 0.11090172469615936,
+  "sec": 185.3
+ },
+ {
+  "step": 5250,
+  "inner_val_loss": 0.11231652753693717,
+  "train_loss": 0.11085931015014648,
+  "sec": 195.7
+ },
+ {
+  "step": 5500,
+  "inner_val_loss": 0.11232783432517733,
+  "train_loss": 0.11081701627373695,
+  "sec": 206.0
+ }
+]

paper-releases/pbisc-diffusion/updates/20261001T145641Z-lora-rank-sweep-calibration-budget/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold4/lora_r64/RUN.json

@@ -0,0 +1,151 @@
+{
+ "schema": "pbisc_sdd.ft_intradataset.run.v1",
+ "source_checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
+ "source_checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
+ "dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis",
+ "condition_npz": "/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",
+ "condition_npz_sha256": "ce8b61d7dcd3e62b9e63d52189cfb5bba881f87a661384277a7949a629231cb4",
+ "fold": 4,
+ "mode": "lora",
+ "trainable": {
+  "mode": "lora",
+  "lora_layers": [
+   "time_encoder.0",
+   "time_encoder.2",
+   "condition_encoder.0",
+   "condition_encoder.3",
+   "context_mixer.2",
+   "down_blocks.0.input_projection",
+   "down_blocks.0.context_projection.1",
+   "down_blocks.1.input_projection",
+   "down_blocks.1.context_projection.1",
+   "down_blocks.2.input_projection",
+   "down_blocks.2.context_projection.1",
+   "down_blocks.3.input_projection",
+   "down_blocks.3.context_projection.1",
+   "up_blocks.0.input_projection",
+   "up_blocks.0.context_projection.1",
+   "up_blocks.1.input_projection",
+   "up_blocks.1.context_projection.1",
+   "up_blocks.2.input_projection",
+   "up_blocks.2.context_projection.1",
+   "output_trunk.0",
+   "value_head",
+   "active_head"
+  ],
+  "lora_rank": 64,
+  "lora_alpha": 64.0,
+  "n_trainable": 5184896,
+  "n_total_base": 54185184,
+  "trainable_tensors": 44
+ },
+ "lr": 0.0005,
+ "warmup": 200,
+ "batch_size": 256,
+ "ema_decay": 0.999,
+ "max_steps": 20000,
+ "steps_run": 6250,
+ "eval_every": 250,
+ "patience": 8,
+ "train_subset": null,
+ "train_donors_file": null,
+ "fixed_steps": null,
+ "selected_step": 4250,
+ "selected_inner_val_loss": 0.11092884625707354,
+ "pretrained_inner_val_loss": 0.1224389017692634,
+ "train_rows": [
+  "Abd-PS04",
+  "Abd-PS05",
+  "Abd-PS07",
+  "Abd-PS19",
+  "Abd-PS23",
+  "Abd-S102",
+  "Abd-S103",
+  "Abd-S120",
+  "Abd-S123",
+  "Abd-S39",
+  "Abd-S47",
+  "Abd-S51",
+  "Abd-S57",
+  "Abd-S66",
+  "Abd-S79",
+  "Abd-S83",
+  "HC01",
+  "HC05",
+  "HC07",
+  "HC09",
+  "HC12",
+  "IC10",
+  "IC16",
+  "IC19",
+  "IC23",
+  "PHC01",
+  "PHC03",
+  "PHC05",
+  "PIC01",
+  "PIC04",
+  "PIC05",
+  "Res-PS02",
+  "Res-PS12",
+  "Res-PS21",
+  "Res-PS22",
+  "Res-PS25",
+  "Res-PS26",
+  "Res-S10",
+  "Res-S125",
+  "Res-S136",
+  "Res-S139",
+  "Res-S146",
+  "Res-S149",
+  "Res-S150",
+  "Res-S177",
+  "Res-S184",
+  "Res-S19",
+  "Res-S26",
+  "Res-S40",
+  "Res-S77",
+  "Skin-S140",
+  "Skin-S142",
+  "Skin-S152",
+  "Skin-S38",
+  "Skin-S46",
+  "Skin-S74",
+  "Uri-S134",
+  "Uri-S157",
+  "Uri-S20"
+ ],
+ "inner_val_rows": [
+  "Abd-S156",
+  "HC13",
+  "IC22",
+  "Res-PS16",
+  "Res-S174",
+  "Skin-S52",
+  "Uri-S147"
+ ],
+ "test_rows_never_loaded_for_training": [
+  "Abd-PS20",
+  "Abd-PS27",
+  "Abd-S42",
+  "Abd-S54",
+  "Abd-S98",
+  "HC16",
+  "IC15",
+  "PHC02",
+  "PIC02",
+  "Res-PS03",
+  "Res-S127",
+  "Res-S164",
+  "Res-S166",
+  "Res-S87",
+  "Skin-S43",
+  "Uri-S93"
+ ],
+ "max_abs_weight_change": 1.5259108543395996,
+ "n_tensors_changed": 22,
+ "seed": 20260927,
+ "wall_seconds": 235.2,
+ "written_utc": "2026-10-01T10:32:08.389684+00:00",
+ "checkpoint_sha256": "01f60e5bb5420f7a8cb57c2a575b1cdfa0a413d1570a6f3341e1b60c08722d98",
+ "reload_forward_max_abs_diff": 0.0
+}

paper-releases/pbisc-diffusion/updates/20261001T145641Z-lora-rank-sweep-calibration-budget/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold4/lora_r64/history.json

@@ -0,0 +1,157 @@
+[
+ {
+  "step": 0,
+  "inner_val_loss": 0.1224389017692634,
+  "train_loss": null
+ },
+ {
+  "step": 250,
+  "inner_val_loss": 0.12124371847936086,
+  "train_loss": 0.11368696215748787,
+  "sec": 9.6
+ },
+ {
+  "step": 500,
+  "inner_val_loss": 0.11885616715465273,
+  "train_loss": 0.11118523308634758,
+  "sec": 19.0
+ },
+ {
+  "step": 750,
+  "inner_val_loss": 0.11626332732183593,
+  "train_loss": 0.11051533880829811,
+  "sec": 28.4
+ },
+ {
+  "step": 1000,
+  "inner_val_loss": 0.11413515891347613,
+  "train_loss": 0.11079668408632279,
+  "sec": 37.6
+ },
+ {
+  "step": 1250,
+  "inner_val_loss": 0.11274602956005506,
+  "train_loss": 0.11094267615675926,
+  "sec": 46.9
+ },
+ {
+  "step": 1500,
+  "inner_val_loss": 0.11197845371706146,
+  "train_loss": 0.11045618948340416,
+  "sec": 56.3
+ },
+ {
+  "step": 1750,
+  "inner_val_loss": 0.11156066826411656,
+  "train_loss": 0.1104977563917637,
+  "sec": 65.7
+ },
+ {
+  "step": 2000,
+  "inner_val_loss": 0.11133320842470441,
+  "train_loss": 0.11003549993038178,
+  "sec": 75.1
+ },
+ {
+  "step": 2250,
+  "inner_val_loss": 0.11120471411517688,
+  "train_loss": 0.11048181217908859,
+  "sec": 84.4
+ },
+ {
+  "step": 2500,
+  "inner_val_loss": 0.11111460413251605,
+  "train_loss": 0.11007247221469879,
+  "sec": 93.8
+ },
+ {
+  "step": 2750,
+  "inner_val_loss": 0.11105701593416077,
+  "train_loss": 0.10991898280382156,
+  "sec": 103.2
+ },
+ {
+  "step": 3000,
+  "inner_val_loss": 0.11101693393928665,
+  "train_loss": 0.11049250382184982,
+  "sec": 112.4
+ },
+ {
+  "step": 3250,
+  "inner_val_loss": 0.11098004984004158,
+  "train_loss": 0.11039231762290001,
+  "sec": 121.6
+ },
+ {
+  "step": 3500,
+  "inner_val_loss": 0.11095164130840983,
+  "train_loss": 0.10979100286960602,
+  "sec": 131.1
+ },
+ {
+  "step": 3750,
+  "inner_val_loss": 0.1109371403498309,
+  "train_loss": 0.11012905582785606,
+  "sec": 140.6
+ },
+ {
+  "step": 4000,
+  "inner_val_loss": 0.11093152261206082,
+  "train_loss": 0.11013320976495743,
+  "sec": 150.0
+ },
+ {
+  "step": 4250,
+  "inner_val_loss": 0.11092884625707354,
+  "train_loss": 0.11017714688181877,
+  "sec": 159.3
+ },
+ {
+  "step": 4500,
+  "inner_val_loss": 0.11093101490821157,
+  "train_loss": 0.11002462714910508,
+  "sec": 168.7
+ },
+ {
+  "step": 4750,
+  "inner_val_loss": 0.11093520532761302,
+  "train_loss": 0.10995236721634864,
+  "sec": 178.0
+ },
+ {
+  "step": 5000,
+  "inner_val_loss": 0.11093777098825999,
+  "train_loss": 0.1100825243294239,
+  "sec": 187.3
+ },
+ {
+  "step": 5250,
+  "inner_val_loss": 0.11093946386660848,
+  "train_loss": 0.1099860551059246,
+  "sec": 196.5
+ },
+ {
+  "step": 5500,
+  "inner_val_loss": 0.1109483220747539,
+  "train_loss": 0.10978265517950057,
+  "sec": 205.7
+ },
+ {
+  "step": 5750,
+  "inner_val_loss": 0.11095432351742472,
+  "train_loss": 0.10968660420179367,
+  "sec": 215.1
+ },
+ {
+  "step": 6000,
+  "inner_val_loss": 0.11095764062234334,
+  "train_loss": 0.11003204521536827,
+  "sec": 224.5
+ },
+ {
+  "step": 6250,
+  "inner_val_loss": 0.11096370273402759,
+  "train_loss": 0.10975685647130012,
+  "sec": 233.7
+ }
+]