Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_lora3_raw_s04_f01common/labels.manifest.json +168 -0
- paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_lora3_raw_s13_f01common/labels.manifest.json +168 -0
- paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_zs_cal_s13_f01common/labels.manifest.json +168 -0
- paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_zs_raw_s04_f01common/labels.manifest.json +168 -0
paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_lora3_raw_s04_f01common/labels.manifest.json
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| 1 |
+
{
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| 2 |
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"dataset_id": "GSE198533",
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| 3 |
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"split": "",
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| 4 |
+
"input_h5ad": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/lora3_raw_s04_poisson.h5ad",
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| 5 |
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"method": "generated_GSE198533_all19_lora3study_lora3_raw_s04",
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| 6 |
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"out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_lora3_raw_s04_f01common/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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| 10 |
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"labels": [
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| 11 |
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"T cell",
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| 12 |
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"B cell",
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| 13 |
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"Monocyte",
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| 14 |
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"NK cell",
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| 15 |
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"DC",
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| 16 |
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"Other"
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| 17 |
+
],
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| 18 |
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"l2_labels": [
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| 19 |
+
"ASDC",
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| 20 |
+
"CD14 monocyte",
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| 21 |
+
"CD16 monocyte",
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| 22 |
+
"CD56bright NK cell",
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| 23 |
+
"CD56dim NK cell",
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| 24 |
+
"CD8aa",
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| 25 |
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"DN T cell",
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| 26 |
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"Effector B cell",
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| 27 |
+
"Erythrocyte",
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| 28 |
+
"ILC",
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| 29 |
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"Intermediate monocyte",
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| 30 |
+
"MAIT",
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| 31 |
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"Memory B cell",
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| 32 |
+
"Memory CD4 T cell",
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| 33 |
+
"Memory CD8 T cell",
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| 34 |
+
"Naive B cell",
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| 35 |
+
"Naive CD4 T cell",
|
| 36 |
+
"Naive CD8 T cell",
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| 37 |
+
"Plasma cell",
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| 38 |
+
"Platelet",
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| 39 |
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"Progenitor cell",
|
| 40 |
+
"Proliferating NK cell",
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| 41 |
+
"Proliferating T cell",
|
| 42 |
+
"Transitional B cell",
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| 43 |
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"Treg",
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| 44 |
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"cDC1",
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| 45 |
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"cDC2",
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| 46 |
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"gdT",
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| 47 |
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"pDC"
|
| 48 |
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],
|
| 49 |
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"n_cells": 95000,
|
| 50 |
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"n_genes": 1005,
|
| 51 |
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"note": "Evaluation-only annotation with a frozen AIFI scANVI (zero query-training epochs); L1 outside PBMC5 -> Other, never dropped.",
|
| 52 |
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"label_source_column": "AIFI_L2 (reference) -> AIFI_L2_TO_L1 -> PBMC5 + Other",
|
| 53 |
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"query_train_epochs": 0,
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| 54 |
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"confidence_threshold": 0.0,
|
| 55 |
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"subset": false,
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| 56 |
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"evaluator_aligned": true,
|
| 57 |
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"gene_space": {
|
| 58 |
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"join_key": "ensembl_id",
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| 59 |
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"model_genes": 1005,
|
| 60 |
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"query_genes": 6000,
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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": 4995,
|
| 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 |
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},
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| 65 |
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"readout": {
|
| 66 |
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"batch_prefix": "",
|
| 67 |
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"input_matrix_key": "generated_counts",
|
| 68 |
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"input_n_cells": 95000,
|
| 69 |
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"input_nonzero_fraction": 0.047417291228070174,
|
| 70 |
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"input_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/generated/lora3_raw_s04.npz",
|
| 71 |
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"input_npz_sha256": "d09ec3161e726c1901b4d4b206109cf5cbb51f2781742cebc2a32878fdedd5a5",
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| 72 |
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"input_row_sum_median": 1671.44091796875,
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| 73 |
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"library_scale": 1.0,
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| 74 |
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"library_size_handling": "no rescaling (library_scale=1.0): E[library] = generated library",
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| 75 |
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"method_name": "generated_GSE198533_all19_lora3study_lora3_raw_s04",
|
| 76 |
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"n_cells": 95000,
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| 77 |
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"n_genes": 6000,
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| 78 |
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"output_nonzero_fraction": 0.03619651929824561,
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| 79 |
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"output_row_sum_median": 1671.0,
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| 80 |
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"rule": "counts ~ Poisson(generated_counts * library_scale), independent per entry, single draw",
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| 81 |
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"seed": 20260916,
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| 82 |
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"subset_rows": 95000,
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| 83 |
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"subset_seed": null,
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| 84 |
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"unlabeled_category": "Unknown"
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| 85 |
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},
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| 86 |
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"query_build": null,
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| 87 |
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"model": {
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| 88 |
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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",
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| 89 |
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"model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
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| 90 |
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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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| 91 |
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"held_out_summary": {
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| 92 |
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"l2_accuracy": 0.8692869740488788,
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| 93 |
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"l2_macro_f1": 0.8500925599737216,
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| 94 |
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"l1_accuracy": 0.9918367346938776,
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| 95 |
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"l1_macro_f1": 0.9715232379009036,
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| 96 |
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"pbmc5_other_accuracy": 0.9920886873267826,
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| 97 |
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"pbmc5_other_macro_f1": 0.9812088972148597
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| 98 |
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}
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| 99 |
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},
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| 100 |
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"label_counts": {
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| 101 |
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"celltype_l1_pred": {
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| 102 |
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"T cell": 63666,
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| 103 |
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"Monocyte": 13427,
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| 104 |
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"B cell": 9334,
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| 105 |
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"NK cell": 5768,
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| 106 |
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"DC": 1867,
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| 107 |
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"Other": 938
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| 108 |
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},
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| 109 |
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"aifi_l1": {
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| 110 |
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"T cell": 63666,
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| 111 |
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"Monocyte": 13427,
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| 112 |
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"B cell": 9334,
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| 113 |
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"NK cell": 5768,
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| 114 |
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"DC": 1867,
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| 115 |
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"Erythrocyte": 474,
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| 116 |
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"ILC": 238,
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| 117 |
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"Platelet": 173,
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| 118 |
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"Progenitor cell": 53
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| 119 |
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},
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| 120 |
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"aifi_l2": {
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| 121 |
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"Memory CD8 T cell": 15335,
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| 122 |
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"gdT": 13657,
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| 123 |
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"Memory CD4 T cell": 11344,
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| 124 |
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"Naive CD4 T cell": 9855,
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| 125 |
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"CD14 monocyte": 7606,
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| 126 |
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"Treg": 5044,
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| 127 |
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"Naive CD8 T cell": 4777,
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| 128 |
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"Naive B cell": 4198,
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| 129 |
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"CD56dim NK cell": 3982,
|
| 130 |
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"Intermediate monocyte": 3868,
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| 131 |
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"Memory B cell": 3124,
|
| 132 |
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"CD16 monocyte": 1953,
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| 133 |
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"cDC2": 1535,
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| 134 |
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"Effector B cell": 1375,
|
| 135 |
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"MAIT": 1325,
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| 136 |
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"Proliferating NK cell": 1164,
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| 137 |
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"DN T cell": 1033,
|
| 138 |
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"Proliferating T cell": 850,
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| 139 |
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"CD56bright NK cell": 622,
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| 140 |
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"Transitional B cell": 524,
|
| 141 |
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"Erythrocyte": 474,
|
| 142 |
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"CD8aa": 446,
|
| 143 |
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"pDC": 264,
|
| 144 |
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"ILC": 238,
|
| 145 |
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"Platelet": 173,
|
| 146 |
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"Plasma cell": 113,
|
| 147 |
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"Progenitor cell": 53,
|
| 148 |
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"cDC1": 49,
|
| 149 |
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"ASDC": 19
|
| 150 |
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}
|
| 151 |
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},
|
| 152 |
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"confidence": {
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| 153 |
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"mean_l2_max_prob": 0.9171383768709083,
|
| 154 |
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"mean_l1_mass": 0.9833546280860901,
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| 155 |
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"frac_l2_max_prob_ge_0.5": 0.9746526315789473
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| 156 |
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},
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| 157 |
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"timings_s": {
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| 158 |
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"predict": 0.4,
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| 159 |
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"total": 1.1
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| 160 |
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},
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| 161 |
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"versions": {
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| 162 |
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"scvi-tools": "1.4.1",
|
| 163 |
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"torch": "2.11.0+cu130",
|
| 164 |
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"anndata": "0.12.19"
|
| 165 |
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},
|
| 166 |
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"device": "cpu",
|
| 167 |
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"created_at_utc": "2026-10-04T05:04:06.306847+00:00"
|
| 168 |
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}
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paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_lora3_raw_s13_f01common/labels.manifest.json
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| 1 |
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{
|
| 2 |
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"dataset_id": "GSE198533",
|
| 3 |
+
"split": "",
|
| 4 |
+
"input_h5ad": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/lora3_raw_s13_poisson.h5ad",
|
| 5 |
+
"method": "generated_GSE198533_all19_lora3study_lora3_raw_s13",
|
| 6 |
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"out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_lora3_raw_s13_f01common/labels.parquet",
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| 7 |
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| 11 |
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| 12 |
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| 13 |
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| 14 |
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| 15 |
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| 16 |
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|
| 17 |
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|
| 18 |
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"l2_labels": [
|
| 19 |
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|
| 20 |
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|
| 21 |
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| 22 |
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| 23 |
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| 24 |
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|
| 25 |
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| 26 |
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| 27 |
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| 28 |
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| 29 |
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| 30 |
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| 31 |
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| 32 |
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| 33 |
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| 34 |
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| 36 |
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| 37 |
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|
| 38 |
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| 39 |
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| 40 |
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|
paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_zs_cal_s13_f01common/labels.manifest.json
ADDED
|
@@ -0,0 +1,168 @@
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| 97 |
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"pbmc5_other_macro_f1": 0.9812088972148597
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| 98 |
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|
| 99 |
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| 100 |
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"label_counts": {
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| 101 |
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"celltype_l1_pred": {
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| 102 |
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"T cell": 63817,
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| 103 |
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"Monocyte": 12362,
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| 104 |
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"B cell": 9860,
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| 105 |
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"NK cell": 6727,
|
| 106 |
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"Other": 1418,
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| 107 |
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"DC": 816
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| 108 |
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| 109 |
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| 110 |
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| 111 |
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"Monocyte": 12362,
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| 112 |
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"B cell": 9860,
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| 113 |
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| 114 |
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| 115 |
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"DC": 816,
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| 116 |
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| 117 |
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| 118 |
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"ILC": 104
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| 119 |
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| 120 |
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"aifi_l2": {
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| 121 |
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| 122 |
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| 123 |
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| 124 |
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"CD14 monocyte": 7679,
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| 125 |
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| 126 |
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| 127 |
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|
| 128 |
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"Naive CD8 T cell": 3440,
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| 129 |
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"Memory B cell": 3436,
|
| 130 |
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"Intermediate monocyte": 2888,
|
| 131 |
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"Treg": 2249,
|
| 132 |
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"DN T cell": 2248,
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| 133 |
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"CD16 monocyte": 1795,
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| 134 |
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|
| 135 |
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"Erythrocyte": 1066,
|
| 136 |
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"Effector B cell": 1019,
|
| 137 |
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"CD56bright NK cell": 972,
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| 138 |
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"MAIT": 696,
|
| 139 |
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"cDC2": 513,
|
| 140 |
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"CD8aa": 317,
|
| 141 |
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"Proliferating T cell": 303,
|
| 142 |
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"pDC": 256,
|
| 143 |
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|
| 144 |
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"Progenitor cell": 117,
|
| 145 |
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"ILC": 104,
|
| 146 |
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"Plasma cell": 99,
|
| 147 |
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"Transitional B cell": 91,
|
| 148 |
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"cDC1": 36,
|
| 149 |
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"ASDC": 11
|
| 150 |
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}
|
| 151 |
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},
|
| 152 |
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"confidence": {
|
| 153 |
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"mean_l2_max_prob": 0.9291515276196756,
|
| 154 |
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"mean_l1_mass": 0.9806368350982666,
|
| 155 |
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"frac_l2_max_prob_ge_0.5": 0.9771052631578947
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| 156 |
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},
|
| 157 |
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"timings_s": {
|
| 158 |
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"predict": 1.0,
|
| 159 |
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"total": 1.7
|
| 160 |
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},
|
| 161 |
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"versions": {
|
| 162 |
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"scvi-tools": "1.4.1",
|
| 163 |
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"torch": "2.11.0+cu130",
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| 164 |
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"anndata": "0.12.19"
|
| 165 |
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},
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| 166 |
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"device": "cpu",
|
| 167 |
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"created_at_utc": "2026-10-04T04:44:10.762895+00:00"
|
| 168 |
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}
|
paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_zs_raw_s04_f01common/labels.manifest.json
ADDED
|
@@ -0,0 +1,168 @@
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|
| 1 |
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{
|
| 2 |
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"dataset_id": "GSE198533",
|
| 3 |
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"split": "",
|
| 4 |
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"input_h5ad": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/zs_raw_s04_poisson.h5ad",
|
| 5 |
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"method": "generated_GSE198533_all19_lora3study_zs_raw_s04",
|
| 6 |
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"out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_zs_raw_s04_f01common/labels.parquet",
|
| 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",
|
| 8 |
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"target_truth_used_for_fitting": false,
|
| 9 |
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"classifier": "aifi_scanvi_rebuild_20260916_frozen_predict[aifi_scanvi_f01common_v1]",
|
| 10 |
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"labels": [
|
| 11 |
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"T cell",
|
| 12 |
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"B cell",
|
| 13 |
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"Monocyte",
|
| 14 |
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"NK cell",
|
| 15 |
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"DC",
|
| 16 |
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"Other"
|
| 17 |
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],
|
| 18 |
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"l2_labels": [
|
| 19 |
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"ASDC",
|
| 20 |
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"CD14 monocyte",
|
| 21 |
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"CD16 monocyte",
|
| 22 |
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"CD56bright NK cell",
|
| 23 |
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"CD56dim NK cell",
|
| 24 |
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"CD8aa",
|
| 25 |
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"DN T cell",
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| 26 |
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"Effector B cell",
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| 27 |
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"Erythrocyte",
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| 28 |
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"ILC",
|
| 29 |
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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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|
| 33 |
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"Memory CD8 T cell",
|
| 34 |
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"Naive B cell",
|
| 35 |
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"Naive CD4 T cell",
|
| 36 |
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"Naive CD8 T cell",
|
| 37 |
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"Plasma cell",
|
| 38 |
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"Platelet",
|
| 39 |
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"Progenitor cell",
|
| 40 |
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"Proliferating NK cell",
|
| 41 |
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"Proliferating T cell",
|
| 42 |
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"Transitional B cell",
|
| 43 |
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"Treg",
|
| 44 |
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"cDC1",
|
| 45 |
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"cDC2",
|
| 46 |
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"gdT",
|
| 47 |
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"pDC"
|
| 48 |
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],
|
| 49 |
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"n_cells": 95000,
|
| 50 |
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"n_genes": 1005,
|
| 51 |
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"note": "Evaluation-only annotation with a frozen AIFI scANVI (zero query-training epochs); L1 outside PBMC5 -> Other, never dropped.",
|
| 52 |
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"label_source_column": "AIFI_L2 (reference) -> AIFI_L2_TO_L1 -> PBMC5 + Other",
|
| 53 |
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"query_train_epochs": 0,
|
| 54 |
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| 55 |
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| 56 |
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| 57 |
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"gene_space": {
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| 58 |
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| 59 |
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| 60 |
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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": 4995,
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| 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 |
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},
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| 65 |
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"readout": {
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| 66 |
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"batch_prefix": "",
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| 67 |
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"input_matrix_key": "generated_counts",
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| 68 |
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"input_n_cells": 95000,
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| 69 |
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"input_nonzero_fraction": 0.06405771929824561,
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| 70 |
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"input_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/generated/zs_raw_s04.npz",
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| 71 |
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"input_npz_sha256": "d119ee01021f8300035150cff230e8639e340b11b3bb347bbe0fdc529a0a60c8",
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| 72 |
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"input_row_sum_median": 521.0957641601562,
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| 73 |
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"library_scale": 1.0,
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| 74 |
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"library_size_handling": "no rescaling (library_scale=1.0): E[library] = generated library",
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| 75 |
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"method_name": "generated_GSE198533_all19_lora3study_zs_raw_s04",
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| 76 |
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"n_cells": 95000,
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"n_genes": 6000,
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"output_nonzero_fraction": 0.03972617192982456,
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"output_row_sum_median": 522.0,
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| 80 |
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"rule": "counts ~ Poisson(generated_counts * library_scale), independent per entry, single draw",
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| 81 |
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"seed": 20260916,
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| 82 |
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"subset_rows": 95000,
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| 83 |
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"subset_seed": null,
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| 84 |
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"unlabeled_category": "Unknown"
|
| 85 |
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},
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| 86 |
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"query_build": null,
|
| 87 |
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"model": {
|
| 88 |
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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",
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| 89 |
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"model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
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| 90 |
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| 91 |
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"held_out_summary": {
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| 92 |
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"l2_accuracy": 0.8692869740488788,
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"label_counts": {
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"Other": 2058,
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| 109 |
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| 111 |
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