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/fold2/lora_r4_n5/RUN.json

@@ -0,0 +1,106 @@
+{
+ "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": 2,
+ "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": 5000,
+ "eval_every": 250,
+ "patience": 8,
+ "train_subset": {
+  "train_n": 5,
+  "subset_seed": 1002,
+  "strata_regex": "sepsis",
+  "allocation": {
+   "False": 1,
+   "True": 4
+  }
+ },
+ "train_donors_file": null,
+ "fixed_steps": null,
+ "selected_step": 3000,
+ "selected_inner_val_loss": 0.11457795277237892,
+ "pretrained_inner_val_loss": 0.12508239736780524,
+ "train_rows": [
+  "Abd-PS23",
+  "PIC02",
+  "Res-PS16",
+  "Res-PS22",
+  "Res-S77"
+ ],
+ "inner_val_rows": [
+  "Abd-PS19",
+  "Abd-S98",
+  "HC12",
+  "IC23",
+  "PIC04",
+  "Res-S19",
+  "Uri-S147",
+  "Uri-S157"
+ ],
+ "test_rows_never_loaded_for_training": [
+  "Abd-PS04",
+  "Abd-PS05",
+  "Abd-S57",
+  "Abd-S79",
+  "HC09",
+  "IC10",
+  "IC19",
+  "PHC05",
+  "Res-PS26",
+  "Res-S146",
+  "Res-S150",
+  "Res-S174",
+  "Res-S177",
+  "Res-S40",
+  "Skin-S152",
+  "Skin-S74"
+ ],
+ "max_abs_weight_change": 0.24256370961666107,
+ "n_tensors_changed": 22,
+ "seed": 20260927,
+ "wall_seconds": 205.2,
+ "written_utc": "2026-10-01T08:10:49.709449+00:00",
+ "checkpoint_sha256": "517b1ee04986a5e615ee56292b9ad500a4a5f7c6cc1b25d90a6b44dae4ea75d2",
+ "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/fold2/lora_r4_n5/history.json

@@ -0,0 +1,127 @@
+[
+ {
+  "step": 0,
+  "inner_val_loss": 0.12508239736780524,
+  "train_loss": null
+ },
+ {
+  "step": 250,
+  "inner_val_loss": 0.12456955155357718,
+  "train_loss": 0.10726191705465317,
+  "sec": 9.1
+ },
+ {
+  "step": 500,
+  "inner_val_loss": 0.12288947915658355,
+  "train_loss": 0.10364037123322486,
+  "sec": 18.1
+ },
+ {
+  "step": 750,
+  "inner_val_loss": 0.1206529913470149,
+  "train_loss": 0.10310178181529045,
+  "sec": 28.1
+ },
+ {
+  "step": 1000,
+  "inner_val_loss": 0.1184883201494813,
+  "train_loss": 0.10289984714984894,
+  "sec": 38.3
+ },
+ {
+  "step": 1250,
+  "inner_val_loss": 0.11686129868030548,
+  "train_loss": 0.10351406821608543,
+  "sec": 48.5
+ },
+ {
+  "step": 1500,
+  "inner_val_loss": 0.11578781995922327,
+  "train_loss": 0.10297408828139305,
+  "sec": 58.8
+ },
+ {
+  "step": 1750,
+  "inner_val_loss": 0.11521086189895868,
+  "train_loss": 0.10240336605906486,
+  "sec": 69.1
+ },
+ {
+  "step": 2000,
+  "inner_val_loss": 0.11487724771723151,
+  "train_loss": 0.10244197052717209,
+  "sec": 79.4
+ },
+ {
+  "step": 2250,
+  "inner_val_loss": 0.11469903960824013,
+  "train_loss": 0.10272028347849846,
+  "sec": 89.6
+ },
+ {
+  "step": 2500,
+  "inner_val_loss": 0.11461825389415026,
+  "train_loss": 0.10255571207404136,
+  "sec": 99.8
+ },
+ {
+  "step": 2750,
+  "inner_val_loss": 0.11458344431594014,
+  "train_loss": 0.10205294278264046,
+  "sec": 110.1
+ },
+ {
+  "step": 3000,
+  "inner_val_loss": 0.11457795277237892,
+  "train_loss": 0.10278437837958336,
+  "sec": 120.2
+ },
+ {
+  "step": 3250,
+  "inner_val_loss": 0.11459007347002625,
+  "train_loss": 0.10237908563017845,
+  "sec": 130.4
+ },
+ {
+  "step": 3500,
+  "inner_val_loss": 0.11461076233536005,
+  "train_loss": 0.10202792829275131,
+  "sec": 140.8
+ },
+ {
+  "step": 3750,
+  "inner_val_loss": 0.11462739203125238,
+  "train_loss": 0.10234273418784141,
+  "sec": 151.2
+ },
+ {
+  "step": 4000,
+  "inner_val_loss": 0.1146400785073638,
+  "train_loss": 0.10256657654047012,
+  "sec": 161.5
+ },
+ {
+  "step": 4250,
+  "inner_val_loss": 0.11465602042153478,
+  "train_loss": 0.10230860105156898,
+  "sec": 171.8
+ },
+ {
+  "step": 4500,
+  "inner_val_loss": 0.11468275357037783,
+  "train_loss": 0.10244786003232002,
+  "sec": 182.4
+ },
+ {
+  "step": 4750,
+  "inner_val_loss": 0.1147043015807867,
+  "train_loss": 0.10238796043395997,
+  "sec": 192.8
+ },
+ {
+  "step": 5000,
+  "inner_val_loss": 0.11471399944275618,
+  "train_loss": 0.10246292141079903,
+  "sec": 203.4
+ }
+]

paper-releases/pbisc-diffusion/updates/20261001T145641Z-lora-rank-sweep-calibration-budget/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/runs/ye2026_sepsis/fold2/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": 2,
+ "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": 7000,
+ "eval_every": 250,
+ "patience": 8,
+ "train_subset": null,
+ "train_donors_file": null,
+ "fixed_steps": null,
+ "selected_step": 5000,
+ "selected_inner_val_loss": 0.1129078222438693,
+ "pretrained_inner_val_loss": 0.12508239736780524,
+ "train_rows": [
+  "Abd-PS07",
+  "Abd-PS20",
+  "Abd-PS23",
+  "Abd-PS27",
+  "Abd-S102",
+  "Abd-S103",
+  "Abd-S120",
+  "Abd-S123",
+  "Abd-S156",
+  "Abd-S39",
+  "Abd-S42",
+  "Abd-S47",
+  "Abd-S51",
+  "Abd-S54",
+  "Abd-S66",
+  "Abd-S83",
+  "HC01",
+  "HC05",
+  "HC07",
+  "HC13",
+  "HC16",
+  "IC15",
+  "IC16",
+  "IC22",
+  "PHC01",
+  "PHC02",
+  "PHC03",
+  "PIC01",
+  "PIC02",
+  "PIC05",
+  "Res-PS02",
+  "Res-PS03",
+  "Res-PS12",
+  "Res-PS16",
+  "Res-PS21",
+  "Res-PS22",
+  "Res-PS25",
+  "Res-S10",
+  "Res-S125",
+  "Res-S127",
+  "Res-S136",
+  "Res-S139",
+  "Res-S149",
+  "Res-S164",
+  "Res-S166",
+  "Res-S184",
+  "Res-S26",
+  "Res-S77",
+  "Res-S87",
+  "Skin-S140",
+  "Skin-S142",
+  "Skin-S38",
+  "Skin-S43",
+  "Skin-S46",
+  "Skin-S52",
+  "Uri-S134",
+  "Uri-S20",
+  "Uri-S93"
+ ],
+ "inner_val_rows": [
+  "Abd-PS19",
+  "Abd-S98",
+  "HC12",
+  "IC23",
+  "PIC04",
+  "Res-S19",
+  "Uri-S147",
+  "Uri-S157"
+ ],
+ "test_rows_never_loaded_for_training": [
+  "Abd-PS04",
+  "Abd-PS05",
+  "Abd-S57",
+  "Abd-S79",
+  "HC09",
+  "IC10",
+  "IC19",
+  "PHC05",
+  "Res-PS26",
+  "Res-S146",
+  "Res-S150",
+  "Res-S174",
+  "Res-S177",
+  "Res-S40",
+  "Skin-S152",
+  "Skin-S74"
+ ],
+ "max_abs_weight_change": 1.4288980960845947,
+ "n_tensors_changed": 22,
+ "seed": 20260927,
+ "wall_seconds": 260.5,
+ "written_utc": "2026-10-01T10:03:58.509457+00:00",
+ "checkpoint_sha256": "2f3beea1ced904988194529b656878145d117026d28e72a01626cfa62fdaa8d4",
+ "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/fold2/lora_r64/history.json

@@ -0,0 +1,175 @@
+[
+ {
+  "step": 0,
+  "inner_val_loss": 0.12508239736780524,
+  "train_loss": null
+ },
+ {
+  "step": 250,
+  "inner_val_loss": 0.12387706059962511,
+  "train_loss": 0.11174024283885955,
+  "sec": 9.4
+ },
+ {
+  "step": 500,
+  "inner_val_loss": 0.12146354746073484,
+  "train_loss": 0.10962238684296607,
+  "sec": 18.8
+ },
+ {
+  "step": 750,
+  "inner_val_loss": 0.11881799250841141,
+  "train_loss": 0.10893619260191917,
+  "sec": 28.0
+ },
+ {
+  "step": 1000,
+  "inner_val_loss": 0.11653099302202463,
+  "train_loss": 0.10927691227197647,
+  "sec": 37.1
+ },
+ {
+  "step": 1250,
+  "inner_val_loss": 0.11500958958640695,
+  "train_loss": 0.10925282523036003,
+  "sec": 46.3
+ },
+ {
+  "step": 1500,
+  "inner_val_loss": 0.11416704161092639,
+  "train_loss": 0.1087804001569748,
+  "sec": 55.5
+ },
+ {
+  "step": 1750,
+  "inner_val_loss": 0.11369966855272651,
+  "train_loss": 0.1087512598335743,
+  "sec": 64.8
+ },
+ {
+  "step": 2000,
+  "inner_val_loss": 0.11344958376139402,
+  "train_loss": 0.10838844287395477,
+  "sec": 74.0
+ },
+ {
+  "step": 2250,
+  "inner_val_loss": 0.11327882343903184,
+  "train_loss": 0.10892075872421264,
+  "sec": 83.2
+ },
+ {
+  "step": 2500,
+  "inner_val_loss": 0.11316394247114658,
+  "train_loss": 0.1084488745033741,
+  "sec": 92.5
+ },
+ {
+  "step": 2750,
+  "inner_val_loss": 0.11309813614934683,
+  "train_loss": 0.10843250933289528,
+  "sec": 101.7
+ },
+ {
+  "step": 3000,
+  "inner_val_loss": 0.11304228473454714,
+  "train_loss": 0.109078280210495,
+  "sec": 110.7
+ },
+ {
+  "step": 3250,
+  "inner_val_loss": 0.11300191283226013,
+  "train_loss": 0.10838411661982536,
+  "sec": 119.8
+ },
+ {
+  "step": 3500,
+  "inner_val_loss": 0.1129836868494749,
+  "train_loss": 0.10819609892368316,
+  "sec": 129.2
+ },
+ {
+  "step": 3750,
+  "inner_val_loss": 0.11295688571408391,
+  "train_loss": 0.1082827320098877,
+  "sec": 138.5
+ },
+ {
+  "step": 4000,
+  "inner_val_loss": 0.11293692979961634,
+  "train_loss": 0.10850531390309334,
+  "sec": 147.7
+ },
+ {
+  "step": 4250,
+  "inner_val_loss": 0.11292296089231968,
+  "train_loss": 0.10828396138548851,
+  "sec": 156.9
+ },
+ {
+  "step": 4500,
+  "inner_val_loss": 0.11291939439252019,
+  "train_loss": 0.10839773771166801,
+  "sec": 166.4
+ },
+ {
+  "step": 4750,
+  "inner_val_loss": 0.11291933013126254,
+  "train_loss": 0.10843981635570527,
+  "sec": 175.8
+ },
+ {
+  "step": 5000,
+  "inner_val_loss": 0.1129078222438693,
+  "train_loss": 0.10854557672142982,
+  "sec": 185.3
+ },
+ {
+  "step": 5250,
+  "inner_val_loss": 0.11290856543928385,
+  "train_loss": 0.10834546819329262,
+  "sec": 194.4
+ },
+ {
+  "step": 5500,
+  "inner_val_loss": 0.11291530495509505,
+  "train_loss": 0.10811698004603386,
+  "sec": 203.6
+ },
+ {
+  "step": 5750,
+  "inner_val_loss": 0.11291626654565334,
+  "train_loss": 0.10828837418556213,
+  "sec": 213.1
+ },
+ {
+  "step": 6000,
+  "inner_val_loss": 0.11292401468381286,
+  "train_loss": 0.10847036889195442,
+  "sec": 222.3
+ },
+ {
+  "step": 6250,
+  "inner_val_loss": 0.11292129661887884,
+  "train_loss": 0.1081531733572483,
+  "sec": 231.4
+ },
+ {
+  "step": 6500,
+  "inner_val_loss": 0.11291974829509854,
+  "train_loss": 0.1079951774775982,
+  "sec": 240.7
+ },
+ {
+  "step": 6750,
+  "inner_val_loss": 0.11291340459138155,
+  "train_loss": 0.1079777328968048,
+  "sec": 249.9
+ },
+ {
+  "step": 7000,
+  "inner_val_loss": 0.11292165471240878,
+  "train_loss": 0.10825670692324639,
+  "sec": 259.1
+ }
+]