junidude14 commited on
Commit
ff7d36f
·
verified ·
1 Parent(s): 192147f

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 ADDED
@@ -0,0 +1,168 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "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_s04_poisson.h5ad",
5
+ "method": "generated_GSE198533_all19_lora3study_lora3_raw_s04",
6
+ "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",
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": 95000,
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": 6000,
61
+ "model_genes_missing_from_query_zero_padded": 0,
62
+ "query_genes_outside_model_dropped": 4995,
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": {
66
+ "batch_prefix": "",
67
+ "input_matrix_key": "generated_counts",
68
+ "input_n_cells": 95000,
69
+ "input_nonzero_fraction": 0.047417291228070174,
70
+ "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
+ "input_npz_sha256": "d09ec3161e726c1901b4d4b206109cf5cbb51f2781742cebc2a32878fdedd5a5",
72
+ "input_row_sum_median": 1671.44091796875,
73
+ "library_scale": 1.0,
74
+ "library_size_handling": "no rescaling (library_scale=1.0): E[library] = generated library",
75
+ "method_name": "generated_GSE198533_all19_lora3study_lora3_raw_s04",
76
+ "n_cells": 95000,
77
+ "n_genes": 6000,
78
+ "output_nonzero_fraction": 0.03619651929824561,
79
+ "output_row_sum_median": 1671.0,
80
+ "rule": "counts ~ Poisson(generated_counts * library_scale), independent per entry, single draw",
81
+ "seed": 20260916,
82
+ "subset_rows": 95000,
83
+ "subset_seed": null,
84
+ "unlabeled_category": "Unknown"
85
+ },
86
+ "query_build": null,
87
+ "model": {
88
+ "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",
89
+ "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
90
+ "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",
91
+ "held_out_summary": {
92
+ "l2_accuracy": 0.8692869740488788,
93
+ "l2_macro_f1": 0.8500925599737216,
94
+ "l1_accuracy": 0.9918367346938776,
95
+ "l1_macro_f1": 0.9715232379009036,
96
+ "pbmc5_other_accuracy": 0.9920886873267826,
97
+ "pbmc5_other_macro_f1": 0.9812088972148597
98
+ }
99
+ },
100
+ "label_counts": {
101
+ "celltype_l1_pred": {
102
+ "T cell": 63666,
103
+ "Monocyte": 13427,
104
+ "B cell": 9334,
105
+ "NK cell": 5768,
106
+ "DC": 1867,
107
+ "Other": 938
108
+ },
109
+ "aifi_l1": {
110
+ "T cell": 63666,
111
+ "Monocyte": 13427,
112
+ "B cell": 9334,
113
+ "NK cell": 5768,
114
+ "DC": 1867,
115
+ "Erythrocyte": 474,
116
+ "ILC": 238,
117
+ "Platelet": 173,
118
+ "Progenitor cell": 53
119
+ },
120
+ "aifi_l2": {
121
+ "Memory CD8 T cell": 15335,
122
+ "gdT": 13657,
123
+ "Memory CD4 T cell": 11344,
124
+ "Naive CD4 T cell": 9855,
125
+ "CD14 monocyte": 7606,
126
+ "Treg": 5044,
127
+ "Naive CD8 T cell": 4777,
128
+ "Naive B cell": 4198,
129
+ "CD56dim NK cell": 3982,
130
+ "Intermediate monocyte": 3868,
131
+ "Memory B cell": 3124,
132
+ "CD16 monocyte": 1953,
133
+ "cDC2": 1535,
134
+ "Effector B cell": 1375,
135
+ "MAIT": 1325,
136
+ "Proliferating NK cell": 1164,
137
+ "DN T cell": 1033,
138
+ "Proliferating T cell": 850,
139
+ "CD56bright NK cell": 622,
140
+ "Transitional B cell": 524,
141
+ "Erythrocyte": 474,
142
+ "CD8aa": 446,
143
+ "pDC": 264,
144
+ "ILC": 238,
145
+ "Platelet": 173,
146
+ "Plasma cell": 113,
147
+ "Progenitor cell": 53,
148
+ "cDC1": 49,
149
+ "ASDC": 19
150
+ }
151
+ },
152
+ "confidence": {
153
+ "mean_l2_max_prob": 0.9171383768709083,
154
+ "mean_l1_mass": 0.9833546280860901,
155
+ "frac_l2_max_prob_ge_0.5": 0.9746526315789473
156
+ },
157
+ "timings_s": {
158
+ "predict": 0.4,
159
+ "total": 1.1
160
+ },
161
+ "versions": {
162
+ "scvi-tools": "1.4.1",
163
+ "torch": "2.11.0+cu130",
164
+ "anndata": "0.12.19"
165
+ },
166
+ "device": "cpu",
167
+ "created_at_utc": "2026-10-04T05:04:06.306847+00:00"
168
+ }
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 ADDED
@@ -0,0 +1,168 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "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
+ "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",
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": 95000,
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": 6000,
61
+ "model_genes_missing_from_query_zero_padded": 0,
62
+ "query_genes_outside_model_dropped": 4995,
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": {
66
+ "batch_prefix": "",
67
+ "input_matrix_key": "generated_counts",
68
+ "input_n_cells": 95000,
69
+ "input_nonzero_fraction": 0.04741839824561404,
70
+ "input_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/generated/lora3_raw_s13.npz",
71
+ "input_npz_sha256": "5ed5f2f3efd5eef11418ec91c67bf45cd5bbc44851078fc722f19d17beb43228",
72
+ "input_row_sum_median": 1671.5598754882812,
73
+ "library_scale": 1.0,
74
+ "library_size_handling": "no rescaling (library_scale=1.0): E[library] = generated library",
75
+ "method_name": "generated_GSE198533_all19_lora3study_lora3_raw_s13",
76
+ "n_cells": 95000,
77
+ "n_genes": 6000,
78
+ "output_nonzero_fraction": 0.03619416315789473,
79
+ "output_row_sum_median": 1671.0,
80
+ "rule": "counts ~ Poisson(generated_counts * library_scale), independent per entry, single draw",
81
+ "seed": 20260916,
82
+ "subset_rows": 95000,
83
+ "subset_seed": null,
84
+ "unlabeled_category": "Unknown"
85
+ },
86
+ "query_build": null,
87
+ "model": {
88
+ "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",
89
+ "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
90
+ "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",
91
+ "held_out_summary": {
92
+ "l2_accuracy": 0.8692869740488788,
93
+ "l2_macro_f1": 0.8500925599737216,
94
+ "l1_accuracy": 0.9918367346938776,
95
+ "l1_macro_f1": 0.9715232379009036,
96
+ "pbmc5_other_accuracy": 0.9920886873267826,
97
+ "pbmc5_other_macro_f1": 0.9812088972148597
98
+ }
99
+ },
100
+ "label_counts": {
101
+ "celltype_l1_pred": {
102
+ "T cell": 63684,
103
+ "Monocyte": 13378,
104
+ "B cell": 9319,
105
+ "NK cell": 5749,
106
+ "DC": 1903,
107
+ "Other": 967
108
+ },
109
+ "aifi_l1": {
110
+ "T cell": 63684,
111
+ "Monocyte": 13378,
112
+ "B cell": 9319,
113
+ "NK cell": 5749,
114
+ "DC": 1903,
115
+ "Erythrocyte": 486,
116
+ "ILC": 251,
117
+ "Platelet": 172,
118
+ "Progenitor cell": 58
119
+ },
120
+ "aifi_l2": {
121
+ "Memory CD8 T cell": 15246,
122
+ "gdT": 13568,
123
+ "Memory CD4 T cell": 11316,
124
+ "Naive CD4 T cell": 9944,
125
+ "CD14 monocyte": 7539,
126
+ "Treg": 4945,
127
+ "Naive CD8 T cell": 4801,
128
+ "Naive B cell": 4180,
129
+ "CD56dim NK cell": 3981,
130
+ "Intermediate monocyte": 3896,
131
+ "Memory B cell": 3111,
132
+ "CD16 monocyte": 1943,
133
+ "cDC2": 1558,
134
+ "Effector B cell": 1418,
135
+ "MAIT": 1393,
136
+ "Proliferating NK cell": 1164,
137
+ "DN T cell": 1098,
138
+ "Proliferating T cell": 916,
139
+ "CD56bright NK cell": 604,
140
+ "Transitional B cell": 501,
141
+ "Erythrocyte": 486,
142
+ "CD8aa": 457,
143
+ "pDC": 267,
144
+ "ILC": 251,
145
+ "Platelet": 172,
146
+ "Plasma cell": 109,
147
+ "Progenitor cell": 58,
148
+ "cDC1": 56,
149
+ "ASDC": 22
150
+ }
151
+ },
152
+ "confidence": {
153
+ "mean_l2_max_prob": 0.9168813030446831,
154
+ "mean_l1_mass": 0.9833822250366211,
155
+ "frac_l2_max_prob_ge_0.5": 0.9744
156
+ },
157
+ "timings_s": {
158
+ "predict": 0.8,
159
+ "total": 1.5
160
+ },
161
+ "versions": {
162
+ "scvi-tools": "1.4.1",
163
+ "torch": "2.11.0+cu130",
164
+ "anndata": "0.12.19"
165
+ },
166
+ "device": "cpu",
167
+ "created_at_utc": "2026-10-04T04:54:14.636695+00:00"
168
+ }
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 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "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/zs_cal_s13_poisson.h5ad",
5
+ "method": "generated_GSE198533_all19_lora3study_zs_cal_s13",
6
+ "out_parquet": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_zs_cal_s13_f01common/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": 95000,
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": 6000,
61
+ "model_genes_missing_from_query_zero_padded": 0,
62
+ "query_genes_outside_model_dropped": 4995,
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": {
66
+ "batch_prefix": "",
67
+ "input_matrix_key": "generated_counts",
68
+ "input_n_cells": 95000,
69
+ "input_nonzero_fraction": 0.046742136842105264,
70
+ "input_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/generated/zs_cal_s13.npz",
71
+ "input_npz_sha256": "d50ff3ea5c5bb91fe9fc53a99cf89850459b7f3bccd892c596f9aa9814dc9a30",
72
+ "input_row_sum_median": 1107.2127075195312,
73
+ "library_scale": 1.0,
74
+ "library_size_handling": "no rescaling (library_scale=1.0): E[library] = generated library",
75
+ "method_name": "generated_GSE198533_all19_lora3study_zs_cal_s13",
76
+ "n_cells": 95000,
77
+ "n_genes": 6000,
78
+ "output_nonzero_fraction": 0.03527827894736842,
79
+ "output_row_sum_median": 1107.0,
80
+ "rule": "counts ~ Poisson(generated_counts * library_scale), independent per entry, single draw",
81
+ "seed": 20260916,
82
+ "subset_rows": 95000,
83
+ "subset_seed": null,
84
+ "unlabeled_category": "Unknown"
85
+ },
86
+ "query_build": null,
87
+ "model": {
88
+ "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",
89
+ "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
90
+ "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",
91
+ "held_out_summary": {
92
+ "l2_accuracy": 0.8692869740488788,
93
+ "l2_macro_f1": 0.8500925599737216,
94
+ "l1_accuracy": 0.9918367346938776,
95
+ "l1_macro_f1": 0.9715232379009036,
96
+ "pbmc5_other_accuracy": 0.9920886873267826,
97
+ "pbmc5_other_macro_f1": 0.9812088972148597
98
+ }
99
+ },
100
+ "label_counts": {
101
+ "celltype_l1_pred": {
102
+ "T cell": 63817,
103
+ "Monocyte": 12362,
104
+ "B cell": 9860,
105
+ "NK cell": 6727,
106
+ "Other": 1418,
107
+ "DC": 816
108
+ },
109
+ "aifi_l1": {
110
+ "T cell": 63817,
111
+ "Monocyte": 12362,
112
+ "B cell": 9860,
113
+ "NK cell": 6727,
114
+ "Erythrocyte": 1066,
115
+ "DC": 816,
116
+ "Platelet": 131,
117
+ "Progenitor cell": 117,
118
+ "ILC": 104
119
+ },
120
+ "aifi_l2": {
121
+ "Memory CD8 T cell": 29611,
122
+ "Naive CD4 T cell": 10347,
123
+ "gdT": 10026,
124
+ "CD14 monocyte": 7679,
125
+ "Naive B cell": 5215,
126
+ "CD56dim NK cell": 4665,
127
+ "Memory CD4 T cell": 4580,
128
+ "Naive CD8 T cell": 3440,
129
+ "Memory B cell": 3436,
130
+ "Intermediate monocyte": 2888,
131
+ "Treg": 2249,
132
+ "DN T cell": 2248,
133
+ "CD16 monocyte": 1795,
134
+ "Proliferating NK cell": 1090,
135
+ "Erythrocyte": 1066,
136
+ "Effector B cell": 1019,
137
+ "CD56bright NK cell": 972,
138
+ "MAIT": 696,
139
+ "cDC2": 513,
140
+ "CD8aa": 317,
141
+ "Proliferating T cell": 303,
142
+ "pDC": 256,
143
+ "Platelet": 131,
144
+ "Progenitor cell": 117,
145
+ "ILC": 104,
146
+ "Plasma cell": 99,
147
+ "Transitional B cell": 91,
148
+ "cDC1": 36,
149
+ "ASDC": 11
150
+ }
151
+ },
152
+ "confidence": {
153
+ "mean_l2_max_prob": 0.9291515276196756,
154
+ "mean_l1_mass": 0.9806368350982666,
155
+ "frac_l2_max_prob_ge_0.5": 0.9771052631578947
156
+ },
157
+ "timings_s": {
158
+ "predict": 1.0,
159
+ "total": 1.7
160
+ },
161
+ "versions": {
162
+ "scvi-tools": "1.4.1",
163
+ "torch": "2.11.0+cu130",
164
+ "anndata": "0.12.19"
165
+ },
166
+ "device": "cpu",
167
+ "created_at_utc": "2026-10-04T04:44:10.762895+00:00"
168
+ }
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 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "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/zs_raw_s04_poisson.h5ad",
5
+ "method": "generated_GSE198533_all19_lora3study_zs_raw_s04",
6
+ "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
+ "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": 95000,
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": 6000,
61
+ "model_genes_missing_from_query_zero_padded": 0,
62
+ "query_genes_outside_model_dropped": 4995,
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": {
66
+ "batch_prefix": "",
67
+ "input_matrix_key": "generated_counts",
68
+ "input_n_cells": 95000,
69
+ "input_nonzero_fraction": 0.06405771929824561,
70
+ "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",
71
+ "input_npz_sha256": "d119ee01021f8300035150cff230e8639e340b11b3bb347bbe0fdc529a0a60c8",
72
+ "input_row_sum_median": 521.0957641601562,
73
+ "library_scale": 1.0,
74
+ "library_size_handling": "no rescaling (library_scale=1.0): E[library] = generated library",
75
+ "method_name": "generated_GSE198533_all19_lora3study_zs_raw_s04",
76
+ "n_cells": 95000,
77
+ "n_genes": 6000,
78
+ "output_nonzero_fraction": 0.03972617192982456,
79
+ "output_row_sum_median": 522.0,
80
+ "rule": "counts ~ Poisson(generated_counts * library_scale), independent per entry, single draw",
81
+ "seed": 20260916,
82
+ "subset_rows": 95000,
83
+ "subset_seed": null,
84
+ "unlabeled_category": "Unknown"
85
+ },
86
+ "query_build": null,
87
+ "model": {
88
+ "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",
89
+ "model_pt_sha256": "bf3655899e5abee435340fc008656c4a17342da0f30b70cfd43de8e9223e1930",
90
+ "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",
91
+ "held_out_summary": {
92
+ "l2_accuracy": 0.8692869740488788,
93
+ "l2_macro_f1": 0.8500925599737216,
94
+ "l1_accuracy": 0.9918367346938776,
95
+ "l1_macro_f1": 0.9715232379009036,
96
+ "pbmc5_other_accuracy": 0.9920886873267826,
97
+ "pbmc5_other_macro_f1": 0.9812088972148597
98
+ }
99
+ },
100
+ "label_counts": {
101
+ "celltype_l1_pred": {
102
+ "T cell": 41727,
103
+ "Monocyte": 24638,
104
+ "NK cell": 13657,
105
+ "B cell": 11923,
106
+ "Other": 2058,
107
+ "DC": 997
108
+ },
109
+ "aifi_l1": {
110
+ "T cell": 41727,
111
+ "Monocyte": 24638,
112
+ "NK cell": 13657,
113
+ "B cell": 11923,
114
+ "Erythrocyte": 1383,
115
+ "DC": 997,
116
+ "Platelet": 501,
117
+ "ILC": 161,
118
+ "Progenitor cell": 13
119
+ },
120
+ "aifi_l2": {
121
+ "Memory CD8 T cell": 17140,
122
+ "CD14 monocyte": 16913,
123
+ "Naive B cell": 8647,
124
+ "Proliferating NK cell": 6992,
125
+ "gdT": 6679,
126
+ "CD56dim NK cell": 5920,
127
+ "CD16 monocyte": 5242,
128
+ "Memory CD4 T cell": 5015,
129
+ "DN T cell": 3548,
130
+ "Naive CD4 T cell": 3418,
131
+ "Intermediate monocyte": 2483,
132
+ "Naive CD8 T cell": 1700,
133
+ "Treg": 1617,
134
+ "Erythrocyte": 1383,
135
+ "Proliferating T cell": 1375,
136
+ "Memory B cell": 1230,
137
+ "Effector B cell": 1032,
138
+ "MAIT": 973,
139
+ "Transitional B cell": 853,
140
+ "CD56bright NK cell": 745,
141
+ "Platelet": 501,
142
+ "cDC1": 384,
143
+ "cDC2": 382,
144
+ "CD8aa": 262,
145
+ "pDC": 224,
146
+ "Plasma cell": 161,
147
+ "ILC": 161,
148
+ "Progenitor cell": 13,
149
+ "ASDC": 7
150
+ }
151
+ },
152
+ "confidence": {
153
+ "mean_l2_max_prob": 0.9142133311960258,
154
+ "mean_l1_mass": 0.9790278673171997,
155
+ "frac_l2_max_prob_ge_0.5": 0.9711157894736843
156
+ },
157
+ "timings_s": {
158
+ "predict": 0.5,
159
+ "total": 1.2
160
+ },
161
+ "versions": {
162
+ "scvi-tools": "1.4.1",
163
+ "torch": "2.11.0+cu130",
164
+ "anndata": "0.12.19"
165
+ },
166
+ "device": "cpu",
167
+ "created_at_utc": "2026-10-04T05:12:48.103250+00:00"
168
+ }