Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261013T144247Z-f01-trunk4x-campaign-launch/diffusion/dataset/server_1/model8/plans/f01_trunk4x_complete_20261013/baseline_records/ye2026_sepsis/fold2/real_lora/RUN.json +148 -0
- paper-releases/pbisc-diffusion/updates/20261013T144247Z-f01-trunk4x-campaign-launch/diffusion/dataset/server_1/model8/plans/f01_trunk4x_complete_20261013/baseline_records/ye2026_sepsis/fold3/real_lora/RUN.json +148 -0
- paper-releases/pbisc-diffusion/updates/20261013T144247Z-f01-trunk4x-campaign-launch/diffusion/dataset/server_1/model8/plans/f01_trunk4x_complete_20261013/baseline_records/ye2026_sepsis/fold4/real_lora/RUN.json +148 -0
- paper-releases/pbisc-diffusion/updates/20261013T144247Z-f01-trunk4x-campaign-launch/diffusion/dataset/server_1/model8/plans/f01_trunk4x_complete_20261013/configs/baseline_1x.json +85 -0
paper-releases/pbisc-diffusion/updates/20261013T144247Z-f01-trunk4x-campaign-launch/diffusion/dataset/server_1/model8/plans/f01_trunk4x_complete_20261013/baseline_records/ye2026_sepsis/fold2/real_lora/RUN.json
ADDED
|
@@ -0,0 +1,148 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"schema": "pbisc_sdd.ft_intradataset.run.v1",
|
| 3 |
+
"source_checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
|
| 4 |
+
"source_checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
|
| 5 |
+
"dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis",
|
| 6 |
+
"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",
|
| 7 |
+
"condition_npz_sha256": "ce8b61d7dcd3e62b9e63d52189cfb5bba881f87a661384277a7949a629231cb4",
|
| 8 |
+
"fold": 2,
|
| 9 |
+
"mode": "lora",
|
| 10 |
+
"trainable": {
|
| 11 |
+
"mode": "lora",
|
| 12 |
+
"lora_layers": [
|
| 13 |
+
"time_encoder.0",
|
| 14 |
+
"time_encoder.2",
|
| 15 |
+
"condition_encoder.0",
|
| 16 |
+
"condition_encoder.3",
|
| 17 |
+
"context_mixer.2",
|
| 18 |
+
"down_blocks.0.input_projection",
|
| 19 |
+
"down_blocks.0.context_projection.1",
|
| 20 |
+
"down_blocks.1.input_projection",
|
| 21 |
+
"down_blocks.1.context_projection.1",
|
| 22 |
+
"down_blocks.2.input_projection",
|
| 23 |
+
"down_blocks.2.context_projection.1",
|
| 24 |
+
"down_blocks.3.input_projection",
|
| 25 |
+
"down_blocks.3.context_projection.1",
|
| 26 |
+
"up_blocks.0.input_projection",
|
| 27 |
+
"up_blocks.0.context_projection.1",
|
| 28 |
+
"up_blocks.1.input_projection",
|
| 29 |
+
"up_blocks.1.context_projection.1",
|
| 30 |
+
"up_blocks.2.input_projection",
|
| 31 |
+
"up_blocks.2.context_projection.1",
|
| 32 |
+
"output_trunk.0",
|
| 33 |
+
"value_head",
|
| 34 |
+
"active_head"
|
| 35 |
+
],
|
| 36 |
+
"lora_rank": 16,
|
| 37 |
+
"lora_alpha": 16.0,
|
| 38 |
+
"n_trainable": 1296224,
|
| 39 |
+
"n_total_base": 54185184,
|
| 40 |
+
"trainable_tensors": 44
|
| 41 |
+
},
|
| 42 |
+
"lr": 0.0005,
|
| 43 |
+
"warmup": 200,
|
| 44 |
+
"batch_size": 256,
|
| 45 |
+
"ema_decay": 0.999,
|
| 46 |
+
"max_steps": 20000,
|
| 47 |
+
"steps_run": 15000,
|
| 48 |
+
"eval_every": 250,
|
| 49 |
+
"patience": 8,
|
| 50 |
+
"selected_step": 13000,
|
| 51 |
+
"selected_inner_val_loss": 0.11297935340553522,
|
| 52 |
+
"pretrained_inner_val_loss": 0.12508239736780524,
|
| 53 |
+
"train_rows": [
|
| 54 |
+
"Abd-PS07",
|
| 55 |
+
"Abd-PS20",
|
| 56 |
+
"Abd-PS23",
|
| 57 |
+
"Abd-PS27",
|
| 58 |
+
"Abd-S102",
|
| 59 |
+
"Abd-S103",
|
| 60 |
+
"Abd-S120",
|
| 61 |
+
"Abd-S123",
|
| 62 |
+
"Abd-S156",
|
| 63 |
+
"Abd-S39",
|
| 64 |
+
"Abd-S42",
|
| 65 |
+
"Abd-S47",
|
| 66 |
+
"Abd-S51",
|
| 67 |
+
"Abd-S54",
|
| 68 |
+
"Abd-S66",
|
| 69 |
+
"Abd-S83",
|
| 70 |
+
"HC01",
|
| 71 |
+
"HC05",
|
| 72 |
+
"HC07",
|
| 73 |
+
"HC13",
|
| 74 |
+
"HC16",
|
| 75 |
+
"IC15",
|
| 76 |
+
"IC16",
|
| 77 |
+
"IC22",
|
| 78 |
+
"PHC01",
|
| 79 |
+
"PHC02",
|
| 80 |
+
"PHC03",
|
| 81 |
+
"PIC01",
|
| 82 |
+
"PIC02",
|
| 83 |
+
"PIC05",
|
| 84 |
+
"Res-PS02",
|
| 85 |
+
"Res-PS03",
|
| 86 |
+
"Res-PS12",
|
| 87 |
+
"Res-PS16",
|
| 88 |
+
"Res-PS21",
|
| 89 |
+
"Res-PS22",
|
| 90 |
+
"Res-PS25",
|
| 91 |
+
"Res-S10",
|
| 92 |
+
"Res-S125",
|
| 93 |
+
"Res-S127",
|
| 94 |
+
"Res-S136",
|
| 95 |
+
"Res-S139",
|
| 96 |
+
"Res-S149",
|
| 97 |
+
"Res-S164",
|
| 98 |
+
"Res-S166",
|
| 99 |
+
"Res-S184",
|
| 100 |
+
"Res-S26",
|
| 101 |
+
"Res-S77",
|
| 102 |
+
"Res-S87",
|
| 103 |
+
"Skin-S140",
|
| 104 |
+
"Skin-S142",
|
| 105 |
+
"Skin-S38",
|
| 106 |
+
"Skin-S43",
|
| 107 |
+
"Skin-S46",
|
| 108 |
+
"Skin-S52",
|
| 109 |
+
"Uri-S134",
|
| 110 |
+
"Uri-S20",
|
| 111 |
+
"Uri-S93"
|
| 112 |
+
],
|
| 113 |
+
"inner_val_rows": [
|
| 114 |
+
"Abd-PS19",
|
| 115 |
+
"Abd-S98",
|
| 116 |
+
"HC12",
|
| 117 |
+
"IC23",
|
| 118 |
+
"PIC04",
|
| 119 |
+
"Res-S19",
|
| 120 |
+
"Uri-S147",
|
| 121 |
+
"Uri-S157"
|
| 122 |
+
],
|
| 123 |
+
"test_rows_never_loaded_for_training": [
|
| 124 |
+
"Abd-PS04",
|
| 125 |
+
"Abd-PS05",
|
| 126 |
+
"Abd-S57",
|
| 127 |
+
"Abd-S79",
|
| 128 |
+
"HC09",
|
| 129 |
+
"IC10",
|
| 130 |
+
"IC19",
|
| 131 |
+
"PHC05",
|
| 132 |
+
"Res-PS26",
|
| 133 |
+
"Res-S146",
|
| 134 |
+
"Res-S150",
|
| 135 |
+
"Res-S174",
|
| 136 |
+
"Res-S177",
|
| 137 |
+
"Res-S40",
|
| 138 |
+
"Skin-S152",
|
| 139 |
+
"Skin-S74"
|
| 140 |
+
],
|
| 141 |
+
"max_abs_weight_change": 1.5520620346069336,
|
| 142 |
+
"n_tensors_changed": 22,
|
| 143 |
+
"seed": 20260927,
|
| 144 |
+
"wall_seconds": 639.6,
|
| 145 |
+
"written_utc": "2026-09-27T12:32:06.257301+00:00",
|
| 146 |
+
"checkpoint_sha256": "6313cb928e2ed70b82c00d92cec114d8e77ce6aa813bab8bf142846af1452e3c",
|
| 147 |
+
"reload_forward_max_abs_diff": 0.0
|
| 148 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261013T144247Z-f01-trunk4x-campaign-launch/diffusion/dataset/server_1/model8/plans/f01_trunk4x_complete_20261013/baseline_records/ye2026_sepsis/fold3/real_lora/RUN.json
ADDED
|
@@ -0,0 +1,148 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"schema": "pbisc_sdd.ft_intradataset.run.v1",
|
| 3 |
+
"source_checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
|
| 4 |
+
"source_checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
|
| 5 |
+
"dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis",
|
| 6 |
+
"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",
|
| 7 |
+
"condition_npz_sha256": "ce8b61d7dcd3e62b9e63d52189cfb5bba881f87a661384277a7949a629231cb4",
|
| 8 |
+
"fold": 3,
|
| 9 |
+
"mode": "lora",
|
| 10 |
+
"trainable": {
|
| 11 |
+
"mode": "lora",
|
| 12 |
+
"lora_layers": [
|
| 13 |
+
"time_encoder.0",
|
| 14 |
+
"time_encoder.2",
|
| 15 |
+
"condition_encoder.0",
|
| 16 |
+
"condition_encoder.3",
|
| 17 |
+
"context_mixer.2",
|
| 18 |
+
"down_blocks.0.input_projection",
|
| 19 |
+
"down_blocks.0.context_projection.1",
|
| 20 |
+
"down_blocks.1.input_projection",
|
| 21 |
+
"down_blocks.1.context_projection.1",
|
| 22 |
+
"down_blocks.2.input_projection",
|
| 23 |
+
"down_blocks.2.context_projection.1",
|
| 24 |
+
"down_blocks.3.input_projection",
|
| 25 |
+
"down_blocks.3.context_projection.1",
|
| 26 |
+
"up_blocks.0.input_projection",
|
| 27 |
+
"up_blocks.0.context_projection.1",
|
| 28 |
+
"up_blocks.1.input_projection",
|
| 29 |
+
"up_blocks.1.context_projection.1",
|
| 30 |
+
"up_blocks.2.input_projection",
|
| 31 |
+
"up_blocks.2.context_projection.1",
|
| 32 |
+
"output_trunk.0",
|
| 33 |
+
"value_head",
|
| 34 |
+
"active_head"
|
| 35 |
+
],
|
| 36 |
+
"lora_rank": 16,
|
| 37 |
+
"lora_alpha": 16.0,
|
| 38 |
+
"n_trainable": 1296224,
|
| 39 |
+
"n_total_base": 54185184,
|
| 40 |
+
"trainable_tensors": 44
|
| 41 |
+
},
|
| 42 |
+
"lr": 0.0005,
|
| 43 |
+
"warmup": 200,
|
| 44 |
+
"batch_size": 256,
|
| 45 |
+
"ema_decay": 0.999,
|
| 46 |
+
"max_steps": 20000,
|
| 47 |
+
"steps_run": 8250,
|
| 48 |
+
"eval_every": 250,
|
| 49 |
+
"patience": 8,
|
| 50 |
+
"selected_step": 6250,
|
| 51 |
+
"selected_inner_val_loss": 0.10772703029215336,
|
| 52 |
+
"pretrained_inner_val_loss": 0.11872250866144896,
|
| 53 |
+
"train_rows": [
|
| 54 |
+
"Abd-PS04",
|
| 55 |
+
"Abd-PS05",
|
| 56 |
+
"Abd-PS07",
|
| 57 |
+
"Abd-PS19",
|
| 58 |
+
"Abd-PS23",
|
| 59 |
+
"Abd-PS27",
|
| 60 |
+
"Abd-S120",
|
| 61 |
+
"Abd-S123",
|
| 62 |
+
"Abd-S156",
|
| 63 |
+
"Abd-S39",
|
| 64 |
+
"Abd-S42",
|
| 65 |
+
"Abd-S47",
|
| 66 |
+
"Abd-S54",
|
| 67 |
+
"Abd-S57",
|
| 68 |
+
"Abd-S66",
|
| 69 |
+
"Abd-S79",
|
| 70 |
+
"Abd-S98",
|
| 71 |
+
"HC05",
|
| 72 |
+
"HC07",
|
| 73 |
+
"HC09",
|
| 74 |
+
"HC13",
|
| 75 |
+
"HC16",
|
| 76 |
+
"IC10",
|
| 77 |
+
"IC15",
|
| 78 |
+
"IC16",
|
| 79 |
+
"IC19",
|
| 80 |
+
"PHC02",
|
| 81 |
+
"PHC03",
|
| 82 |
+
"PHC05",
|
| 83 |
+
"PIC02",
|
| 84 |
+
"PIC04",
|
| 85 |
+
"PIC05",
|
| 86 |
+
"Res-PS03",
|
| 87 |
+
"Res-PS12",
|
| 88 |
+
"Res-PS22",
|
| 89 |
+
"Res-PS25",
|
| 90 |
+
"Res-PS26",
|
| 91 |
+
"Res-S10",
|
| 92 |
+
"Res-S139",
|
| 93 |
+
"Res-S146",
|
| 94 |
+
"Res-S164",
|
| 95 |
+
"Res-S166",
|
| 96 |
+
"Res-S174",
|
| 97 |
+
"Res-S177",
|
| 98 |
+
"Res-S184",
|
| 99 |
+
"Res-S19",
|
| 100 |
+
"Res-S26",
|
| 101 |
+
"Res-S77",
|
| 102 |
+
"Res-S87",
|
| 103 |
+
"Skin-S140",
|
| 104 |
+
"Skin-S142",
|
| 105 |
+
"Skin-S152",
|
| 106 |
+
"Skin-S43",
|
| 107 |
+
"Skin-S46",
|
| 108 |
+
"Skin-S74",
|
| 109 |
+
"Uri-S147",
|
| 110 |
+
"Uri-S157",
|
| 111 |
+
"Uri-S93"
|
| 112 |
+
],
|
| 113 |
+
"inner_val_rows": [
|
| 114 |
+
"Abd-PS20",
|
| 115 |
+
"HC01",
|
| 116 |
+
"IC23",
|
| 117 |
+
"PHC01",
|
| 118 |
+
"Res-S127",
|
| 119 |
+
"Res-S150",
|
| 120 |
+
"Res-S40",
|
| 121 |
+
"Skin-S52"
|
| 122 |
+
],
|
| 123 |
+
"test_rows_never_loaded_for_training": [
|
| 124 |
+
"Abd-S102",
|
| 125 |
+
"Abd-S103",
|
| 126 |
+
"Abd-S51",
|
| 127 |
+
"Abd-S83",
|
| 128 |
+
"HC12",
|
| 129 |
+
"IC22",
|
| 130 |
+
"PIC01",
|
| 131 |
+
"Res-PS02",
|
| 132 |
+
"Res-PS16",
|
| 133 |
+
"Res-PS21",
|
| 134 |
+
"Res-S125",
|
| 135 |
+
"Res-S136",
|
| 136 |
+
"Res-S149",
|
| 137 |
+
"Skin-S38",
|
| 138 |
+
"Uri-S134",
|
| 139 |
+
"Uri-S20"
|
| 140 |
+
],
|
| 141 |
+
"max_abs_weight_change": 1.2607972621917725,
|
| 142 |
+
"n_tensors_changed": 22,
|
| 143 |
+
"seed": 20260927,
|
| 144 |
+
"wall_seconds": 350.8,
|
| 145 |
+
"written_utc": "2026-09-27T13:20:35.335727+00:00",
|
| 146 |
+
"checkpoint_sha256": "b503c24e4898abd88517883ddcb6f8835470aa3c633bc635cb5d5b027dfe491c",
|
| 147 |
+
"reload_forward_max_abs_diff": 0.0
|
| 148 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261013T144247Z-f01-trunk4x-campaign-launch/diffusion/dataset/server_1/model8/plans/f01_trunk4x_complete_20261013/baseline_records/ye2026_sepsis/fold4/real_lora/RUN.json
ADDED
|
@@ -0,0 +1,148 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"schema": "pbisc_sdd.ft_intradataset.run.v1",
|
| 3 |
+
"source_checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
|
| 4 |
+
"source_checkpoint_sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
|
| 5 |
+
"dataset_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/ye2026_sepsis",
|
| 6 |
+
"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",
|
| 7 |
+
"condition_npz_sha256": "ce8b61d7dcd3e62b9e63d52189cfb5bba881f87a661384277a7949a629231cb4",
|
| 8 |
+
"fold": 4,
|
| 9 |
+
"mode": "lora",
|
| 10 |
+
"trainable": {
|
| 11 |
+
"mode": "lora",
|
| 12 |
+
"lora_layers": [
|
| 13 |
+
"time_encoder.0",
|
| 14 |
+
"time_encoder.2",
|
| 15 |
+
"condition_encoder.0",
|
| 16 |
+
"condition_encoder.3",
|
| 17 |
+
"context_mixer.2",
|
| 18 |
+
"down_blocks.0.input_projection",
|
| 19 |
+
"down_blocks.0.context_projection.1",
|
| 20 |
+
"down_blocks.1.input_projection",
|
| 21 |
+
"down_blocks.1.context_projection.1",
|
| 22 |
+
"down_blocks.2.input_projection",
|
| 23 |
+
"down_blocks.2.context_projection.1",
|
| 24 |
+
"down_blocks.3.input_projection",
|
| 25 |
+
"down_blocks.3.context_projection.1",
|
| 26 |
+
"up_blocks.0.input_projection",
|
| 27 |
+
"up_blocks.0.context_projection.1",
|
| 28 |
+
"up_blocks.1.input_projection",
|
| 29 |
+
"up_blocks.1.context_projection.1",
|
| 30 |
+
"up_blocks.2.input_projection",
|
| 31 |
+
"up_blocks.2.context_projection.1",
|
| 32 |
+
"output_trunk.0",
|
| 33 |
+
"value_head",
|
| 34 |
+
"active_head"
|
| 35 |
+
],
|
| 36 |
+
"lora_rank": 16,
|
| 37 |
+
"lora_alpha": 16.0,
|
| 38 |
+
"n_trainable": 1296224,
|
| 39 |
+
"n_total_base": 54185184,
|
| 40 |
+
"trainable_tensors": 44
|
| 41 |
+
},
|
| 42 |
+
"lr": 0.0005,
|
| 43 |
+
"warmup": 200,
|
| 44 |
+
"batch_size": 256,
|
| 45 |
+
"ema_decay": 0.999,
|
| 46 |
+
"max_steps": 20000,
|
| 47 |
+
"steps_run": 8750,
|
| 48 |
+
"eval_every": 250,
|
| 49 |
+
"patience": 8,
|
| 50 |
+
"selected_step": 6750,
|
| 51 |
+
"selected_inner_val_loss": 0.11102822955165591,
|
| 52 |
+
"pretrained_inner_val_loss": 0.1224389017692634,
|
| 53 |
+
"train_rows": [
|
| 54 |
+
"Abd-PS04",
|
| 55 |
+
"Abd-PS05",
|
| 56 |
+
"Abd-PS07",
|
| 57 |
+
"Abd-PS19",
|
| 58 |
+
"Abd-PS23",
|
| 59 |
+
"Abd-S102",
|
| 60 |
+
"Abd-S103",
|
| 61 |
+
"Abd-S120",
|
| 62 |
+
"Abd-S123",
|
| 63 |
+
"Abd-S39",
|
| 64 |
+
"Abd-S47",
|
| 65 |
+
"Abd-S51",
|
| 66 |
+
"Abd-S57",
|
| 67 |
+
"Abd-S66",
|
| 68 |
+
"Abd-S79",
|
| 69 |
+
"Abd-S83",
|
| 70 |
+
"HC01",
|
| 71 |
+
"HC05",
|
| 72 |
+
"HC07",
|
| 73 |
+
"HC09",
|
| 74 |
+
"HC12",
|
| 75 |
+
"IC10",
|
| 76 |
+
"IC16",
|
| 77 |
+
"IC19",
|
| 78 |
+
"IC23",
|
| 79 |
+
"PHC01",
|
| 80 |
+
"PHC03",
|
| 81 |
+
"PHC05",
|
| 82 |
+
"PIC01",
|
| 83 |
+
"PIC04",
|
| 84 |
+
"PIC05",
|
| 85 |
+
"Res-PS02",
|
| 86 |
+
"Res-PS12",
|
| 87 |
+
"Res-PS21",
|
| 88 |
+
"Res-PS22",
|
| 89 |
+
"Res-PS25",
|
| 90 |
+
"Res-PS26",
|
| 91 |
+
"Res-S10",
|
| 92 |
+
"Res-S125",
|
| 93 |
+
"Res-S136",
|
| 94 |
+
"Res-S139",
|
| 95 |
+
"Res-S146",
|
| 96 |
+
"Res-S149",
|
| 97 |
+
"Res-S150",
|
| 98 |
+
"Res-S177",
|
| 99 |
+
"Res-S184",
|
| 100 |
+
"Res-S19",
|
| 101 |
+
"Res-S26",
|
| 102 |
+
"Res-S40",
|
| 103 |
+
"Res-S77",
|
| 104 |
+
"Skin-S140",
|
| 105 |
+
"Skin-S142",
|
| 106 |
+
"Skin-S152",
|
| 107 |
+
"Skin-S38",
|
| 108 |
+
"Skin-S46",
|
| 109 |
+
"Skin-S74",
|
| 110 |
+
"Uri-S134",
|
| 111 |
+
"Uri-S157",
|
| 112 |
+
"Uri-S20"
|
| 113 |
+
],
|
| 114 |
+
"inner_val_rows": [
|
| 115 |
+
"Abd-S156",
|
| 116 |
+
"HC13",
|
| 117 |
+
"IC22",
|
| 118 |
+
"Res-PS16",
|
| 119 |
+
"Res-S174",
|
| 120 |
+
"Skin-S52",
|
| 121 |
+
"Uri-S147"
|
| 122 |
+
],
|
| 123 |
+
"test_rows_never_loaded_for_training": [
|
| 124 |
+
"Abd-PS20",
|
| 125 |
+
"Abd-PS27",
|
| 126 |
+
"Abd-S42",
|
| 127 |
+
"Abd-S54",
|
| 128 |
+
"Abd-S98",
|
| 129 |
+
"HC16",
|
| 130 |
+
"IC15",
|
| 131 |
+
"PHC02",
|
| 132 |
+
"PIC02",
|
| 133 |
+
"Res-PS03",
|
| 134 |
+
"Res-S127",
|
| 135 |
+
"Res-S164",
|
| 136 |
+
"Res-S166",
|
| 137 |
+
"Res-S87",
|
| 138 |
+
"Skin-S43",
|
| 139 |
+
"Uri-S93"
|
| 140 |
+
],
|
| 141 |
+
"max_abs_weight_change": 1.386544108390808,
|
| 142 |
+
"n_tensors_changed": 22,
|
| 143 |
+
"seed": 20260927,
|
| 144 |
+
"wall_seconds": 357.6,
|
| 145 |
+
"written_utc": "2026-09-27T14:09:33.250418+00:00",
|
| 146 |
+
"checkpoint_sha256": "10addff3dffb72d3438713123b5577f3f009e5466b09d65949b869fad71f4c4b",
|
| 147 |
+
"reload_forward_max_abs_diff": 0.0
|
| 148 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261013T144247Z-f01-trunk4x-campaign-launch/diffusion/dataset/server_1/model8/plans/f01_trunk4x_complete_20261013/configs/baseline_1x.json
ADDED
|
@@ -0,0 +1,85 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"data": {
|
| 3 |
+
"coverage_audit_sha256": "3904c5b4026f3a5358d6553948f0d4456c80494eab941ab2f7c2975f459d24c5",
|
| 4 |
+
"coverage_audit_summary": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/full_recipe_allcells_6k_broad_20260909/coverage_v1/summary.json",
|
| 5 |
+
"gene_positions_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/6k/gene_positions.npy",
|
| 6 |
+
"gene_positions_sha256": "653ffa45ac519000baa41086c52408009391d6e68cfb218bc6a50d34163fcb24",
|
| 7 |
+
"gene_selection": "explicit_train_only_hvg_manifest",
|
| 8 |
+
"gene_selection_manifest": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/6k/legacy_selection_manifest.v1.json",
|
| 9 |
+
"gene_selection_manifest_sha256": "1a6090d312df7d0071b3adaa59bb686a915b996a6c555a9aef9cab151905900a",
|
| 10 |
+
"include_availability_in_condition": true,
|
| 11 |
+
"include_bulk_measurement_in_condition": true,
|
| 12 |
+
"n_genes": 6000,
|
| 13 |
+
"priming_policy": "all-train-first-then-validation-v1",
|
| 14 |
+
"profile_worst_k": false,
|
| 15 |
+
"progress": false,
|
| 16 |
+
"test_cells_per_block": 64,
|
| 17 |
+
"test_recipes": 192,
|
| 18 |
+
"topup_manifest": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/full_recipe_allcells_6k_broad_20260909/topup_v1/manifest.json",
|
| 19 |
+
"topup_manifest_sha256": "df300a6f7f758c865209c6640e51abcbec10bab9726ee48c3bc3434936316da1",
|
| 20 |
+
"train_cells_per_block": 4000,
|
| 21 |
+
"train_recipes": 8192,
|
| 22 |
+
"validation_cells_per_block": 64,
|
| 23 |
+
"validation_recipes": 192
|
| 24 |
+
},
|
| 25 |
+
"diffusion": {
|
| 26 |
+
"center_values": true,
|
| 27 |
+
"clip_denoised": true,
|
| 28 |
+
"cosine_offset": 0.008,
|
| 29 |
+
"log_snr_clip": 20.0,
|
| 30 |
+
"max_log1p_value": 8.0,
|
| 31 |
+
"self_condition_probability": 0.5,
|
| 32 |
+
"support_loss_weight": 1.0,
|
| 33 |
+
"support_scale": 1.0,
|
| 34 |
+
"value_loss_mode": "all_measured",
|
| 35 |
+
"value_loss_weight": 1.0
|
| 36 |
+
},
|
| 37 |
+
"experiment_id": "f01_6k_1x_seed20260627",
|
| 38 |
+
"model": {
|
| 39 |
+
"context_dim": 512,
|
| 40 |
+
"dropout": 0.0,
|
| 41 |
+
"hidden_dims": [
|
| 42 |
+
1024,
|
| 43 |
+
1024,
|
| 44 |
+
512,
|
| 45 |
+
256
|
| 46 |
+
],
|
| 47 |
+
"time_embedding_dim": 128
|
| 48 |
+
},
|
| 49 |
+
"paths": {
|
| 50 |
+
"conditioner_cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/runs/E2_full_no_annotation_4epoch_seed20260627/conditioner_cache.pt",
|
| 51 |
+
"model7_root": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang",
|
| 52 |
+
"output_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627"
|
| 53 |
+
},
|
| 54 |
+
"sampling": {
|
| 55 |
+
"active_logit_threshold": 0.0,
|
| 56 |
+
"eta": 0.0,
|
| 57 |
+
"preview_cells": 256,
|
| 58 |
+
"steps": 50
|
| 59 |
+
},
|
| 60 |
+
"schema_version": "pbisc_sdd.train.v1",
|
| 61 |
+
"training": {
|
| 62 |
+
"amp": "bf16",
|
| 63 |
+
"batch_size": 256,
|
| 64 |
+
"device": "cuda",
|
| 65 |
+
"ema_decay": 0.999,
|
| 66 |
+
"ema_update_every": 1,
|
| 67 |
+
"epochs": 16,
|
| 68 |
+
"grad_clip": 5.0,
|
| 69 |
+
"gradient_accumulation_steps": 1,
|
| 70 |
+
"heartbeat_every_steps": 100,
|
| 71 |
+
"lr": 0.0002,
|
| 72 |
+
"max_cuda_memory_gib": 8.0,
|
| 73 |
+
"max_cuda_temperature_c_at_start": 75.0,
|
| 74 |
+
"max_cuda_utilization_percent_at_start": 10.0,
|
| 75 |
+
"max_train_steps": 0,
|
| 76 |
+
"max_validation_steps": 0,
|
| 77 |
+
"min_cuda_memory_available_gib": 0.0,
|
| 78 |
+
"min_system_memory_available_gib": 32.0,
|
| 79 |
+
"num_workers": 4,
|
| 80 |
+
"pin_memory": true,
|
| 81 |
+
"prefetch_factor": 32,
|
| 82 |
+
"seed": 20260627,
|
| 83 |
+
"weight_decay": 0.0
|
| 84 |
+
}
|
| 85 |
+
}
|