Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw0/score/arms/lora/labels/labels.manifest.json +156 -0
- paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/metadata/NOTE.md +5 -0
- paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/metadata/inference_locations.json +156 -0
- paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/metadata/request.json +318 -0
paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw0/score/arms/lora/labels/labels.manifest.json
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| 1 |
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{
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"dataset_id": "Giroux2022",
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"split": "generated",
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"input_h5ad": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw0/score/arms/lora/query.h5ad",
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"method": "lora",
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"out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/draw0/score/arms/lora/labels/labels.parquet",
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| 7 |
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"training_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/reference/aifi_reference_f01common.h5ad",
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| 8 |
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"target_truth_used_for_fitting": false,
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| 9 |
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"classifier": "aifi_scanvi_rebuild_20260916_frozen_predict[aifi_scanvi_f01common_v1]",
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"labels": [
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"T cell",
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"B cell",
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"Monocyte",
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"NK cell",
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"DC",
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"Other"
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],
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"l2_labels": [
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"ASDC",
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"CD14 monocyte",
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"CD16 monocyte",
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"CD56bright NK cell",
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"CD56dim NK cell",
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"CD8aa",
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"DN T cell",
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"Effector B cell",
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| 27 |
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"Erythrocyte",
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"ILC",
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"Intermediate monocyte",
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| 30 |
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"MAIT",
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| 31 |
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"Memory B cell",
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| 32 |
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"Memory CD4 T cell",
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| 33 |
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"Memory CD8 T cell",
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| 34 |
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"Naive B cell",
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| 35 |
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"Naive CD4 T cell",
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| 36 |
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"Naive CD8 T cell",
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| 37 |
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"Plasma cell",
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| 38 |
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"Platelet",
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| 39 |
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"Progenitor cell",
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| 40 |
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"Proliferating NK cell",
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| 41 |
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"Proliferating T cell",
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"Transitional B cell",
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"Treg",
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"cDC1",
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"cDC2",
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| 46 |
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"gdT",
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"pDC"
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],
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| 49 |
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"n_cells": 16500,
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| 50 |
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"n_genes": 1005,
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| 51 |
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"note": "Evaluation-only annotation with a frozen AIFI scANVI (zero query-training epochs); L1 outside PBMC5 -> Other, never dropped.",
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| 52 |
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"label_source_column": "AIFI_L2 (reference) -> AIFI_L2_TO_L1 -> PBMC5 + Other",
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| 53 |
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"query_train_epochs": 0,
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| 54 |
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"confidence_threshold": 0.0,
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| 55 |
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"subset": false,
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| 56 |
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"evaluator_aligned": true,
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| 57 |
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"gene_space": {
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| 58 |
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"join_key": "ensembl_id",
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| 59 |
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"model_genes": 1005,
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| 60 |
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"query_genes": 1006,
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| 61 |
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"model_genes_missing_from_query_zero_padded": 0,
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| 62 |
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"query_genes_outside_model_dropped": 1,
|
| 63 |
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"rule": "query is subset/reordered to the model's gene list; zero-padding of absent model genes is refused unless --allow-missing-genes"
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| 64 |
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},
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| 65 |
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"readout": null,
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| 66 |
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"query_build": {
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| 67 |
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"kind": "generated_npz",
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| 68 |
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"poisson_note": "one draw over the whole NPZ, then the scored donors' rows",
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| 69 |
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"readout": "poisson",
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| 70 |
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"seed": 20260916,
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| 71 |
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"set": "lora",
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| 72 |
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"source_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw0/lora.npz",
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| 73 |
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"source_sha256": "765845e9a73b40470b9d94fded33c190ccb8d73529f732ae5bc0fc2cea9cda6e"
|
| 74 |
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},
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| 75 |
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"model": {
|
| 76 |
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"scanvi_model_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_model",
|
| 77 |
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"model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
|
| 78 |
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"model_manifest": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/MODEL_MANIFEST.json",
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| 79 |
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"held_out_summary": {
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| 80 |
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"l2_accuracy": 0.8692869740488788,
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| 81 |
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"l2_macro_f1": 0.8500925599737216,
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| 82 |
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"l1_accuracy": 0.9918367346938776,
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| 83 |
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"l1_macro_f1": 0.9715232379009036,
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| 84 |
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"pbmc5_other_accuracy": 0.9920886873267826,
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| 85 |
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"pbmc5_other_macro_f1": 0.9812088972148597
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| 86 |
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}
|
| 87 |
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},
|
| 88 |
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"label_counts": {
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| 89 |
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"celltype_l1_pred": {
|
| 90 |
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"T cell": 10828,
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| 91 |
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"Monocyte": 2983,
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| 92 |
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"NK cell": 1009,
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| 93 |
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"B cell": 765,
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| 94 |
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"Other": 543,
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| 95 |
+
"DC": 372
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| 96 |
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},
|
| 97 |
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"aifi_l1": {
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| 98 |
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"T cell": 10828,
|
| 99 |
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"Monocyte": 2983,
|
| 100 |
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"NK cell": 1009,
|
| 101 |
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"B cell": 765,
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| 102 |
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"DC": 372,
|
| 103 |
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"Erythrocyte": 284,
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| 104 |
+
"ILC": 149,
|
| 105 |
+
"Platelet": 99,
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| 106 |
+
"Progenitor cell": 11
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| 107 |
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},
|
| 108 |
+
"aifi_l2": {
|
| 109 |
+
"DN T cell": 2122,
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| 110 |
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"Naive CD4 T cell": 2033,
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| 111 |
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"Memory CD4 T cell": 1681,
|
| 112 |
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"Intermediate monocyte": 1411,
|
| 113 |
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"Memory CD8 T cell": 1391,
|
| 114 |
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"Naive CD8 T cell": 1229,
|
| 115 |
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"CD14 monocyte": 1108,
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| 116 |
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"Treg": 756,
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| 117 |
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"CD56dim NK cell": 636,
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| 118 |
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"gdT": 626,
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| 119 |
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"CD16 monocyte": 464,
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| 120 |
+
"CD8aa": 455,
|
| 121 |
+
"MAIT": 443,
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| 122 |
+
"Naive B cell": 313,
|
| 123 |
+
"Memory B cell": 313,
|
| 124 |
+
"Erythrocyte": 284,
|
| 125 |
+
"cDC2": 279,
|
| 126 |
+
"CD56bright NK cell": 217,
|
| 127 |
+
"Proliferating NK cell": 156,
|
| 128 |
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"ILC": 149,
|
| 129 |
+
"Effector B cell": 103,
|
| 130 |
+
"Platelet": 99,
|
| 131 |
+
"Proliferating T cell": 92,
|
| 132 |
+
"pDC": 78,
|
| 133 |
+
"Plasma cell": 28,
|
| 134 |
+
"Progenitor cell": 11,
|
| 135 |
+
"cDC1": 10,
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| 136 |
+
"Transitional B cell": 8,
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| 137 |
+
"ASDC": 5
|
| 138 |
+
}
|
| 139 |
+
},
|
| 140 |
+
"confidence": {
|
| 141 |
+
"mean_l2_max_prob": 0.8848754408982668,
|
| 142 |
+
"mean_l1_mass": 0.9699332118034363,
|
| 143 |
+
"frac_l2_max_prob_ge_0.5": 0.948
|
| 144 |
+
},
|
| 145 |
+
"timings_s": {
|
| 146 |
+
"predict": 0.1,
|
| 147 |
+
"total": 0.3
|
| 148 |
+
},
|
| 149 |
+
"versions": {
|
| 150 |
+
"scvi-tools": "1.4.1",
|
| 151 |
+
"torch": "2.11.0+cu130",
|
| 152 |
+
"anndata": "0.12.19"
|
| 153 |
+
},
|
| 154 |
+
"device": "cpu",
|
| 155 |
+
"created_at_utc": "2026-10-15T06:52:24.178044+00:00"
|
| 156 |
+
}
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paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/metadata/NOTE.md
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# PBISC-diffusion update 20261015T065710Z-giroux-width-comparison
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| 2 |
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| 3 |
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CPU-only matched Giroux x1/x4 LoRA comparison across5 existing support draws; exact checkpoint alias repair for Imperial scoring; actual trunk×4 checkpoint structure verified. Disease logFC superiority not established.
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| 4 |
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| 5 |
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Payload states are recorded as supplied. Inference locations are pointers, not archived generated outputs.
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paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/metadata/inference_locations.json
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| 1 |
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{
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| 2 |
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"locations": [
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| 3 |
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{
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| 4 |
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"host": "server_1",
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| 5 |
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"observed_output": {
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| 6 |
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"kind": "file",
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| 7 |
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"presence": "observed",
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| 8 |
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"stat": {
|
| 9 |
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"dev": 66306,
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| 10 |
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"ino": 36968916,
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| 11 |
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"mtime_ns": 1791993004763249914,
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| 12 |
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"size": 431411237
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| 13 |
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}
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| 14 |
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},
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| 15 |
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"observed_receipt": {
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| 16 |
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"kind": "file",
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| 17 |
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"presence": "observed",
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| 18 |
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"stat": {
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| 19 |
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"dev": 66306,
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| 20 |
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"ino": 36968915,
|
| 21 |
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"mtime_ns": 1791993004954261282,
|
| 22 |
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"size": 1502
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| 23 |
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}
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| 24 |
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},
|
| 25 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw0/lora.npz",
|
| 26 |
+
"reason": "Existing server_2 x1 output imported and hash-verified for CPU-only matched trunk-width comparison; no regeneration.",
|
| 27 |
+
"receipt": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw0/lora.log",
|
| 28 |
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"sha256": "765845e9a73b40470b9d94fded33c190ccb8d73529f732ae5bc0fc2cea9cda6e",
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| 29 |
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"sha256_basis": "existing_receipt",
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| 30 |
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"sha_basis": "existing_receipt",
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| 31 |
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"state": "completed"
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| 32 |
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},
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| 33 |
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{
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| 34 |
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"host": "server_1",
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paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/metadata/request.json
ADDED
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@@ -0,0 +1,318 @@
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