Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold3/summary.json +457 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold4/arms/scsemi__raw/generated_cells.parquet +3 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold4/arms/scsemi__raw/labels/labels.manifest.json +149 -0
- paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold4/arms/scsemi__raw/labels/labels.parquet +3 -0
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold3/summary.json
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|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_scores.v1",
|
| 3 |
+
"dataset": "giroux2022",
|
| 4 |
+
"written_utc": "2026-10-08T01:56:23.438844+00:00",
|
| 5 |
+
"command": [
|
| 6 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
|
| 7 |
+
"--dataset",
|
| 8 |
+
"giroux2022",
|
| 9 |
+
"--out",
|
| 10 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold3",
|
| 11 |
+
"--threads",
|
| 12 |
+
"8",
|
| 13 |
+
"--arm",
|
| 14 |
+
"scsemi__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/fold3/scsemi__raw.npz",
|
| 15 |
+
"--case-groups",
|
| 16 |
+
"severe",
|
| 17 |
+
"--control-groups",
|
| 18 |
+
"mild"
|
| 19 |
+
],
|
| 20 |
+
"arms": [
|
| 21 |
+
"scsemi__raw"
|
| 22 |
+
],
|
| 23 |
+
"donors": [
|
| 24 |
+
"82CCF5_d0",
|
| 25 |
+
"82CCF5_d7",
|
| 26 |
+
"82CCF5_d14",
|
| 27 |
+
"BAAF62_d0",
|
| 28 |
+
"BAAF62_d7",
|
| 29 |
+
"BAAF62_d14"
|
| 30 |
+
],
|
| 31 |
+
"n_donors": 6,
|
| 32 |
+
"reference": {
|
| 33 |
+
"cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022",
|
| 34 |
+
"reference_sha256": "dd0152f7bde41da80e1c71dabf54ee561982f36dc99a336b65fca419880a1593",
|
| 35 |
+
"features_sha256": "fb41b91617e3ff786d5153c4dc7869d66191ca5947ff28161d24215a24f819e5",
|
| 36 |
+
"n_r1_cells": 900,
|
| 37 |
+
"pca": {
|
| 38 |
+
"n_components": 50,
|
| 39 |
+
"explained_variance_ratio_sum": 0.2704233229160309,
|
| 40 |
+
"n_fit_cells": 900
|
| 41 |
+
},
|
| 42 |
+
"r2_control": {
|
| 43 |
+
"precision": 1.0,
|
| 44 |
+
"coverage": 1.0,
|
| 45 |
+
"density": 8.488333333333333,
|
| 46 |
+
"n_query": 900,
|
| 47 |
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"depth_matched": {
|
| 48 |
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"precision": 1.0,
|
| 49 |
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"coverage": 1.0,
|
| 50 |
+
"density": 8.209222222222222
|
| 51 |
+
}
|
| 52 |
+
},
|
| 53 |
+
"observed_l1_loo_null_mean": 0.2720088351480377
|
| 54 |
+
},
|
| 55 |
+
"contrast_definition": {
|
| 56 |
+
"enabled": true,
|
| 57 |
+
"rule": "explicit --case-groups / --control-groups",
|
| 58 |
+
"group_source": "features groups",
|
| 59 |
+
"case_groups": [
|
| 60 |
+
"severe"
|
| 61 |
+
],
|
| 62 |
+
"control_groups": [
|
| 63 |
+
"mild"
|
| 64 |
+
],
|
| 65 |
+
"n_case_donors": 3,
|
| 66 |
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"n_control_donors": 3,
|
| 67 |
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"n_donors_in_neither": 0,
|
| 68 |
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"case": [
|
| 69 |
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true,
|
| 70 |
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true,
|
| 71 |
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true,
|
| 72 |
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false,
|
| 73 |
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false,
|
| 74 |
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false
|
| 75 |
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],
|
| 76 |
+
"ctrl": [
|
| 77 |
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false,
|
| 78 |
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false,
|
| 79 |
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false,
|
| 80 |
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true,
|
| 81 |
+
true,
|
| 82 |
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true
|
| 83 |
+
],
|
| 84 |
+
"groups": [
|
| 85 |
+
"severe",
|
| 86 |
+
"severe",
|
| 87 |
+
"severe",
|
| 88 |
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"mild",
|
| 89 |
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"mild",
|
| 90 |
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"mild"
|
| 91 |
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]
|
| 92 |
+
},
|
| 93 |
+
"deg_definition": {
|
| 94 |
+
"enabled": true,
|
| 95 |
+
"score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
|
| 96 |
+
"source": "/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/scripts/evaluate_generated_vs_truth.py",
|
| 97 |
+
"functions": [
|
| 98 |
+
"welch_bh_deg",
|
| 99 |
+
"top_deg_genes",
|
| 100 |
+
"jaccard"
|
| 101 |
+
],
|
| 102 |
+
"reproduces": "utility_studies_final6k_20260925/sle top-50 DEG 81 (1,006 genes) / 84 (2,279 genes) = sum over the six gated types of top50_overlap_count",
|
| 103 |
+
"top_n": 50,
|
| 104 |
+
"fdr": 0.05,
|
| 105 |
+
"n_genes": 5563,
|
| 106 |
+
"types": [
|
| 107 |
+
"T cell",
|
| 108 |
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"B cell",
|
| 109 |
+
"Monocyte",
|
| 110 |
+
"NK cell",
|
| 111 |
+
"DC"
|
| 112 |
+
],
|
| 113 |
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"aggregates_source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/giroux2022/deg_reference.npz",
|
| 114 |
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"aggregates_sha256": "412c44bba7481b0b851c3b12e695f1b7ff662163e1f7849d3a64359dfce6d50e",
|
| 115 |
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"aggregates_note": null,
|
| 116 |
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"types_not_scored_observed": [],
|
| 117 |
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"observed": {
|
| 118 |
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"T cell": {
|
| 119 |
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"n_significant": 2,
|
| 120 |
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"n_tested": 5189,
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| 121 |
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"n_case_donors": 3,
|
| 122 |
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"n_control_donors": 3,
|
| 123 |
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"n_cells": 38529,
|
| 124 |
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"top_list_size": 2
|
| 125 |
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},
|
| 126 |
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"B cell": {
|
| 127 |
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"n_significant": 18,
|
| 128 |
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"n_tested": 4796,
|
| 129 |
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"n_case_donors": 3,
|
| 130 |
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"n_control_donors": 3,
|
| 131 |
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"n_cells": 4493,
|
| 132 |
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"top_list_size": 18
|
| 133 |
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},
|
| 134 |
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"Monocyte": {
|
| 135 |
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"n_significant": 2,
|
| 136 |
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"n_tested": 5045,
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| 137 |
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"n_case_donors": 3,
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| 138 |
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"n_control_donors": 3,
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| 139 |
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"n_cells": 11454,
|
| 140 |
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"top_list_size": 2
|
| 141 |
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},
|
| 142 |
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"NK cell": {
|
| 143 |
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"n_significant": 0,
|
| 144 |
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"n_tested": 4824,
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| 145 |
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"n_case_donors": 3,
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| 146 |
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"n_control_donors": 3,
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| 147 |
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"n_cells": 7180,
|
| 148 |
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"top_list_size": 0
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| 149 |
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},
|
| 150 |
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"DC": {
|
| 151 |
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"n_significant": 0,
|
| 152 |
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"n_tested": 4564,
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| 153 |
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"n_case_donors": 3,
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| 154 |
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"n_control_donors": 3,
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| 155 |
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"n_cells": 1327,
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| 156 |
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"top_list_size": 0
|
| 157 |
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}
|
| 158 |
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|
| 1 |
+
{
|
| 2 |
+
"dataset_id": "Giroux2022",
|
| 3 |
+
"split": "generated",
|
| 4 |
+
"input_h5ad": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold4/arms/scsemi__raw/query.h5ad",
|
| 5 |
+
"method": "scsemi__raw",
|
| 6 |
+
"out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold4/arms/scsemi__raw/labels/labels.parquet",
|
| 7 |
+
"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",
|
| 8 |
+
"target_truth_used_for_fitting": false,
|
| 9 |
+
"classifier": "aifi_scanvi_rebuild_20260916_frozen_predict[aifi_scanvi_f01common_v1]",
|
| 10 |
+
"labels": [
|
| 11 |
+
"T cell",
|
| 12 |
+
"B cell",
|
| 13 |
+
"Monocyte",
|
| 14 |
+
"NK cell",
|
| 15 |
+
"DC",
|
| 16 |
+
"Other"
|
| 17 |
+
],
|
| 18 |
+
"l2_labels": [
|
| 19 |
+
"ASDC",
|
| 20 |
+
"CD14 monocyte",
|
| 21 |
+
"CD16 monocyte",
|
| 22 |
+
"CD56bright NK cell",
|
| 23 |
+
"CD56dim NK cell",
|
| 24 |
+
"CD8aa",
|
| 25 |
+
"DN T cell",
|
| 26 |
+
"Effector B cell",
|
| 27 |
+
"Erythrocyte",
|
| 28 |
+
"ILC",
|
| 29 |
+
"Intermediate monocyte",
|
| 30 |
+
"MAIT",
|
| 31 |
+
"Memory B cell",
|
| 32 |
+
"Memory CD4 T cell",
|
| 33 |
+
"Memory CD8 T cell",
|
| 34 |
+
"Naive B cell",
|
| 35 |
+
"Naive CD4 T cell",
|
| 36 |
+
"Naive CD8 T cell",
|
| 37 |
+
"Plasma cell",
|
| 38 |
+
"Platelet",
|
| 39 |
+
"Progenitor cell",
|
| 40 |
+
"Proliferating NK cell",
|
| 41 |
+
"Proliferating T cell",
|
| 42 |
+
"Transitional B cell",
|
| 43 |
+
"Treg",
|
| 44 |
+
"cDC1",
|
| 45 |
+
"cDC2",
|
| 46 |
+
"gdT",
|
| 47 |
+
"pDC"
|
| 48 |
+
],
|
| 49 |
+
"n_cells": 4500,
|
| 50 |
+
"n_genes": 1005,
|
| 51 |
+
"note": "Evaluation-only annotation with a frozen AIFI scANVI (zero query-training epochs); L1 outside PBMC5 -> Other, never dropped.",
|
| 52 |
+
"label_source_column": "AIFI_L2 (reference) -> AIFI_L2_TO_L1 -> PBMC5 + Other",
|
| 53 |
+
"query_train_epochs": 0,
|
| 54 |
+
"confidence_threshold": 0.0,
|
| 55 |
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"subset": false,
|
| 56 |
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"evaluator_aligned": true,
|
| 57 |
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"gene_space": {
|
| 58 |
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"join_key": "ensembl_id",
|
| 59 |
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"model_genes": 1005,
|
| 60 |
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"query_genes": 1006,
|
| 61 |
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"model_genes_missing_from_query_zero_padded": 0,
|
| 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"
|
| 64 |
+
},
|
| 65 |
+
"readout": null,
|
| 66 |
+
"query_build": {
|
| 67 |
+
"kind": "generated_npz",
|
| 68 |
+
"poisson_note": "one draw over the whole NPZ, then the scored donors' rows",
|
| 69 |
+
"readout": "poisson",
|
| 70 |
+
"seed": 20260916,
|
| 71 |
+
"set": "scsemi__raw",
|
| 72 |
+
"source_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/giroux2022/fold4/scsemi__raw.npz",
|
| 73 |
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"source_sha256": "af89697331ef1890ac9eb1a83e036b1c0073b883b1767c020c3707892911ef3f"
|
| 74 |
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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",
|
| 79 |
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"held_out_summary": {
|
| 80 |
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"l2_accuracy": 0.8692869740488788,
|
| 81 |
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"l2_macro_f1": 0.8500925599737216,
|
| 82 |
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"l1_accuracy": 0.9918367346938776,
|
| 83 |
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"l1_macro_f1": 0.9715232379009036,
|
| 84 |
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"pbmc5_other_accuracy": 0.9920886873267826,
|
| 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": {
|
| 89 |
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"celltype_l1_pred": {
|
| 90 |
+
"T cell": 1927,
|
| 91 |
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"Monocyte": 1538,
|
| 92 |
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"NK cell": 793,
|
| 93 |
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"B cell": 130,
|
| 94 |
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"Other": 85,
|
| 95 |
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"DC": 27
|
| 96 |
+
},
|
| 97 |
+
"aifi_l1": {
|
| 98 |
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"T cell": 1927,
|
| 99 |
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"Monocyte": 1538,
|
| 100 |
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"NK cell": 793,
|
| 101 |
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"B cell": 130,
|
| 102 |
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"Platelet": 77,
|
| 103 |
+
"DC": 27,
|
| 104 |
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"Erythrocyte": 5,
|
| 105 |
+
"ILC": 3
|
| 106 |
+
},
|
| 107 |
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"aifi_l2": {
|
| 108 |
+
"Intermediate monocyte": 1091,
|
| 109 |
+
"CD56dim NK cell": 694,
|
| 110 |
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"CD8aa": 604,
|
| 111 |
+
"Memory CD8 T cell": 369,
|
| 112 |
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"MAIT": 270,
|
| 113 |
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"Memory CD4 T cell": 260,
|
| 114 |
+
"gdT": 254,
|
| 115 |
+
"CD14 monocyte": 236,
|
| 116 |
+
"CD16 monocyte": 211,
|
| 117 |
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"Proliferating T cell": 116,
|
| 118 |
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"Proliferating NK cell": 84,
|
| 119 |
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"Naive B cell": 78,
|
| 120 |
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"Platelet": 77,
|
| 121 |
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"Transitional B cell": 50,
|
| 122 |
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"DN T cell": 36,
|
| 123 |
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"Naive CD8 T cell": 18,
|
| 124 |
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"CD56bright NK cell": 15,
|
| 125 |
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"cDC2": 14,
|
| 126 |
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"pDC": 12,
|
| 127 |
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"Erythrocyte": 5,
|
| 128 |
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"ILC": 3,
|
| 129 |
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"Plasma cell": 2,
|
| 130 |
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"cDC1": 1
|
| 131 |
+
}
|
| 132 |
+
},
|
| 133 |
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"confidence": {
|
| 134 |
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"mean_l2_max_prob": 0.8601398419108656,
|
| 135 |
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"mean_l1_mass": 0.9736760258674622,
|
| 136 |
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"frac_l2_max_prob_ge_0.5": 0.9426666666666667
|
| 137 |
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},
|
| 138 |
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"timings_s": {
|
| 139 |
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"predict": 0.0,
|
| 140 |
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"total": 0.2
|
| 141 |
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},
|
| 142 |
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"versions": {
|
| 143 |
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"scvi-tools": "1.4.1",
|
| 144 |
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"torch": "2.11.0+cu130",
|
| 145 |
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"anndata": "0.12.19"
|
| 146 |
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},
|
| 147 |
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"device": "cpu",
|
| 148 |
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"created_at_utc": "2026-10-08T01:56:35.108925+00:00"
|
| 149 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold4/arms/scsemi__raw/labels/labels.parquet
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:fb653a5591dc3318ffd7ffdb2a1f56261a9344495666eac056a4e71db191c8cc
|
| 3 |
+
size 121903
|