Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/smoke/scratch_init_20261005/run/RUN.json

@@ -0,0 +1,139 @@
+{
+ "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": 0,
+ "mode": "full",
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+  "trainable_tensors": 64
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+ "lr": 0.0002,
+ "warmup": 200,
+ "batch_size": 32,
+ "ema_decay": 0.999,
+ "max_steps": 20,
+ "steps_run": 20,
+ "eval_every": 5,
+ "patience": 8,
+ "train_subset": null,
+ "init": "random",
+ "init_seed": 20260627,
+ "n_tensors": 64,
+ "kept_from_checkpoint": [
+  "model_config",
+  "diffusion_config",
+  "gene panel",
+  "value_scaler",
+  "conditioner z-score constants"
+ ],
+ "augmentation": {
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+  "recipe_frac": 0.0,
+  "recipe_cells_per_step": 0,
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+ "selected_step": 20,
+ "selected_inner_val_loss": 1.7770713567733765,
+ "pretrained_inner_val_loss": 1.782603451183864,
+ "train_rows": [
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+  "Abd-PS05",
+  "Abd-PS07",
+  "Abd-PS20",
+  "Abd-PS27",
+  "Abd-S102",
+  "Abd-S103",
+  "Abd-S120",
+  "Abd-S156",
+  "Abd-S42",
+  "Abd-S51",
+  "Abd-S54",
+  "Abd-S57",
+  "Abd-S79",
+  "Abd-S83",
+  "Abd-S98",
+  "HC05",
+  "HC09",
+  "HC12",
+  "HC13",
+  "IC10",
+  "IC15",
+  "IC16",
+  "IC22",
+  "PHC01",
+  "PHC02",
+  "PHC05",
+  "PIC01",
+  "PIC02",
+  "PIC05",
+  "Res-PS02",
+  "Res-PS03",
+  "Res-PS12",
+  "Res-PS16",
+  "Res-PS21",
+  "Res-PS22",
+  "Res-S125",
+  "Res-S146",
+  "Res-S149",
+  "Res-S150",
+  "Res-S164",
+  "Res-S166",
+  "Res-S174",
+  "Res-S177",
+  "Res-S184",
+  "Res-S19",
+  "Res-S40",
+  "Res-S87",
+  "Skin-S142",
+  "Skin-S152",
+  "Skin-S38",
+  "Skin-S46",
+  "Skin-S52",
+  "Skin-S74",
+  "Uri-S134",
+  "Uri-S157",
+  "Uri-S20",
+  "Uri-S93"
+ ],
+ "inner_val_rows": [
+  "HC16",
+  "IC19",
+  "Res-PS26",
+  "Res-S10",
+  "Res-S127",
+  "Res-S136",
+  "Skin-S43"
+ ],
+ "test_rows_never_loaded_for_training": [
+  "Abd-PS19",
+  "Abd-PS23",
+  "Abd-S123",
+  "Abd-S39",
+  "Abd-S47",
+  "Abd-S66",
+  "HC01",
+  "HC07",
+  "IC23",
+  "PHC03",
+  "PIC04",
+  "Res-PS25",
+  "Res-S139",
+  "Res-S26",
+  "Res-S77",
+  "Skin-S140",
+  "Uri-S147"
+ ],
+ "max_abs_weight_change": 17.885892868041992,
+ "n_tensors_changed": 64,
+ "seed": 20260927,
+ "wall_seconds": 4.4,
+ "written_utc": "2026-10-05T00:52:46.910096+00:00",
+ "checkpoint_sha256": "aba9c698f969d060349b304c51ca270b2113b5e5f2b16f666e4511c68f957459",
+ "reload_forward_max_abs_diff": 0.0
+}

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/smoke/scratch_init_20261005/run/checkpoint_ft.pt.deleted

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+20-step CPU smoke checkpoint of --init random deleted 2026-10-05 (throwaway; RUN.json/history kept)

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/smoke/scratch_init_20261005/run/history.json

@@ -0,0 +1,31 @@
+[
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+ {
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+ {
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+ {
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+  "inner_val_loss": 1.7797346455710275,
+  "train_loss": 1.6044066905975343,
+  "sec": 3.1
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+ {
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+  "inner_val_loss": 1.7770713567733765,
+  "train_loss": 1.5238935470581054,
+  "sec": 4.3
+ }
+]

paper-releases/pbisc-diffusion/updates/20261005T063808Z-no-pretraining-ablation-f0/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/smoke/scratch_init_20261005/smoke.log

@@ -0,0 +1,8 @@
+2026-10-05T09:52:36 random init of every denoiser weight (seed 20260627); no pretrained weights used
+2026-10-05T09:52:42 mode=full trainable=54,185,184 rows train/inner/test=58/7/17 cells(train)=413,130
+2026-10-05T09:52:42 step 0 inner-val loss 1.78260 (random init)
+2026-10-05T09:52:43 step 5 train 1.75746 inner-val 1.78240 best 1.78240@5 (1s)
+2026-10-05T09:52:44 step 10 train 1.68606 inner-val 1.78151 best 1.78151@10 (2s)
+2026-10-05T09:52:45 step 15 train 1.60441 inner-val 1.77973 best 1.77973@15 (3s)
+2026-10-05T09:52:46 step 20 train 1.52389 inner-val 1.77707 best 1.77707@20 (4s)
+2026-10-05T09:52:47 saved /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/smoke/scratch_init_20261005/run/checkpoint_ft.pt (selected step 20, inner-val 1.77707 vs pretrained 1.78260); sha aba9c698f969