Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/work/ablation_composition_v1/PREPARED.json +294 -0
- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/work/ablation_composition_v1/annotation/labels.manifest.json +153 -0
- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/work/ablation_composition_v1/annotation/labels.parquet +3 -0
- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/work/ablation_composition_v1/annotation/probabilities_l1.parquet +3 -0
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/work/ablation_composition_v1/PREPARED.json
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{
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|
| 278 |
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"query_rows.csv": {
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| 279 |
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|
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|
| 289 |
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|
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}
|
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/work/ablation_composition_v1/annotation/labels.manifest.json
ADDED
|
@@ -0,0 +1,153 @@
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|
| 1 |
+
{
|
| 2 |
+
"dataset_id": "004_A_GSE135779_SLE_PBMC",
|
| 3 |
+
"split": "primary_kmeans",
|
| 4 |
+
"input_h5ad": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/work/ablation_composition_v1/selected_readout.h5ad",
|
| 5 |
+
"method": "ablation_pc_selected_readout",
|
| 6 |
+
"out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/work/ablation_composition_v1/annotation/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": 42000,
|
| 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 |
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"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": "exact_pc_selected_readout",
|
| 68 |
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"pc_receipt_sha256": "d6b96cdc5303bdce7eee408a18e1bb21f7022b501df1884861904df245286ff3",
|
| 69 |
+
"poisson_seed": 20260916,
|
| 70 |
+
"real_cells_untouched": true
|
| 71 |
+
},
|
| 72 |
+
"model": {
|
| 73 |
+
"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",
|
| 74 |
+
"model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
|
| 75 |
+
"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",
|
| 76 |
+
"held_out_summary": {
|
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/work/ablation_composition_v1/annotation/labels.parquet
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