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/fold1/arms/scsemi__raw/deg_top50_lists.csv +1 -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/fold1/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/fold1/arms/scsemi__raw/labels/labels.manifest.json +151 -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/fold1/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/fold1/arms/scsemi__raw/deg_top50_lists.csv
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
celltype,source,rank,gene_id
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold1/arms/scsemi__raw/generated_cells.parquet
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:3db2c97d96d9d77d637b9d457b546ccb34c7ea84a194f6bc36640779221d37f8
|
| 3 |
+
size 57486
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold1/arms/scsemi__raw/labels/labels.manifest.json
ADDED
|
@@ -0,0 +1,151 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 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/fold1/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/fold1/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": 7500,
|
| 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 |
+
"subset": false,
|
| 56 |
+
"evaluator_aligned": true,
|
| 57 |
+
"gene_space": {
|
| 58 |
+
"join_key": "ensembl_id",
|
| 59 |
+
"model_genes": 1005,
|
| 60 |
+
"query_genes": 1006,
|
| 61 |
+
"model_genes_missing_from_query_zero_padded": 0,
|
| 62 |
+
"query_genes_outside_model_dropped": 1,
|
| 63 |
+
"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/fold1/scsemi__raw.npz",
|
| 73 |
+
"source_sha256": "db8978f980ccc7c8d52ab1b428da340d9d09648cc4767a42b234a80a73f6a7df"
|
| 74 |
+
},
|
| 75 |
+
"model": {
|
| 76 |
+
"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 |
+
"model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
|
| 78 |
+
"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 |
+
"held_out_summary": {
|
| 80 |
+
"l2_accuracy": 0.8692869740488788,
|
| 81 |
+
"l2_macro_f1": 0.8500925599737216,
|
| 82 |
+
"l1_accuracy": 0.9918367346938776,
|
| 83 |
+
"l1_macro_f1": 0.9715232379009036,
|
| 84 |
+
"pbmc5_other_accuracy": 0.9920886873267826,
|
| 85 |
+
"pbmc5_other_macro_f1": 0.9812088972148597
|
| 86 |
+
}
|
| 87 |
+
},
|
| 88 |
+
"label_counts": {
|
| 89 |
+
"celltype_l1_pred": {
|
| 90 |
+
"T cell": 3877,
|
| 91 |
+
"Monocyte": 2136,
|
| 92 |
+
"NK cell": 761,
|
| 93 |
+
"B cell": 416,
|
| 94 |
+
"Other": 278,
|
| 95 |
+
"DC": 32
|
| 96 |
+
},
|
| 97 |
+
"aifi_l1": {
|
| 98 |
+
"T cell": 3877,
|
| 99 |
+
"Monocyte": 2136,
|
| 100 |
+
"NK cell": 761,
|
| 101 |
+
"B cell": 416,
|
| 102 |
+
"Platelet": 184,
|
| 103 |
+
"Erythrocyte": 85,
|
| 104 |
+
"DC": 32,
|
| 105 |
+
"ILC": 9
|
| 106 |
+
},
|
| 107 |
+
"aifi_l2": {
|
| 108 |
+
"Intermediate monocyte": 1404,
|
| 109 |
+
"CD8aa": 1350,
|
| 110 |
+
"Memory CD4 T cell": 793,
|
| 111 |
+
"Memory CD8 T cell": 630,
|
| 112 |
+
"MAIT": 462,
|
| 113 |
+
"CD14 monocyte": 390,
|
| 114 |
+
"CD56dim NK cell": 368,
|
| 115 |
+
"Proliferating NK cell": 366,
|
| 116 |
+
"CD16 monocyte": 342,
|
| 117 |
+
"gdT": 315,
|
| 118 |
+
"Naive B cell": 220,
|
| 119 |
+
"Platelet": 184,
|
| 120 |
+
"Proliferating T cell": 173,
|
| 121 |
+
"Transitional B cell": 165,
|
| 122 |
+
"Naive CD8 T cell": 106,
|
| 123 |
+
"Erythrocyte": 85,
|
| 124 |
+
"DN T cell": 38,
|
| 125 |
+
"Effector B cell": 31,
|
| 126 |
+
"CD56bright NK cell": 27,
|
| 127 |
+
"pDC": 17,
|
| 128 |
+
"cDC2": 13,
|
| 129 |
+
"ILC": 9,
|
| 130 |
+
"Naive CD4 T cell": 9,
|
| 131 |
+
"cDC1": 2,
|
| 132 |
+
"Treg": 1
|
| 133 |
+
}
|
| 134 |
+
},
|
| 135 |
+
"confidence": {
|
| 136 |
+
"mean_l2_max_prob": 0.8291328593512376,
|
| 137 |
+
"mean_l1_mass": 0.9566406011581421,
|
| 138 |
+
"frac_l2_max_prob_ge_0.5": 0.9213333333333333
|
| 139 |
+
},
|
| 140 |
+
"timings_s": {
|
| 141 |
+
"predict": 0.1,
|
| 142 |
+
"total": 0.2
|
| 143 |
+
},
|
| 144 |
+
"versions": {
|
| 145 |
+
"scvi-tools": "1.4.1",
|
| 146 |
+
"torch": "2.11.0+cu130",
|
| 147 |
+
"anndata": "0.12.19"
|
| 148 |
+
},
|
| 149 |
+
"device": "cpu",
|
| 150 |
+
"created_at_utc": "2026-10-08T01:55:56.265673+00:00"
|
| 151 |
+
}
|
paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/giroux2022/scsemi_cv_20261002/fold1/arms/scsemi__raw/labels/labels.parquet
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:a49db742783e5bffaced2f7caa2e04933b462d32bda2b5e0d88478c67ae30d87
|
| 3 |
+
size 205748
|