Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261004T065028Z-behcet-c1q-k4000-corpus/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/logs/corpus_extract_try1_jsonerror.log

@@ -0,0 +1,49 @@
+001_A_collection_436154da-bcf1-4130-9c8b-120ff9a888_Perez_et {'shards_available': 6, 'shards_used': 6, 'cells': np.int64(6000)}
+005_A_collection_dde06e0f-ab3b-46be-96a2-a8082383c4_OneK1K_Y {'shards_available': 5, 'shards_used': 5, 'cells': np.int64(5000)}
+006_A_collection_ced320a1-29f3-47c1-a735-513c7084d5_AIDA_Asi {'shards_available': 6, 'shards_used': 6, 'cells': np.int64(6000)}
+007_A_collection_e1a9ca56-f2ee-435d-980a-4f49ab7a95_Miao_et_ {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+009_A_Human_Immune_Health_Atlas_Human_Immune_Health_Atlas_AI {'shards_available': 8, 'shards_used': 8, 'cells': np.int64(8000)}
+010_A_collection_4a9fd4d7-d870-4265-89a5-ad51ab811d_ScaleBio {'shards_available': 3, 'shards_used': 3, 'cells': np.int64(3000)}
+053_B_collection_b0cf0afa-ec40-4d65-b570-ed4ceacc68_Integrat {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+058_B_collection_eb735cc9-d0a7-48fa-b255-db726bf365_COVID_PB {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+061_A_GSE274680_Savage_Allen_RA_at-risk_longitudinal_progres {'shards_available': 239, 'shards_used': 8, 'cells': np.int64(8000)}
+065_A_GSE271896_GSE271896_Sound_Life_deep_longitudinal_immun {'shards_available': 59, 'shards_used': 8, 'cells': np.int64(8000)}
+071_C_JDM_CITE-seq_PBMC_CELLxGENE_JDM_CITE-seq_PBMC_CELLxGEN {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+074_A_COMBAT_CELLxGENE_collection_COMBAT_CELLxGENE_collectio {'shards_available': 4, 'shards_used': 4, 'cells': np.int64(4000)}
+081_B_Single-cell_atlas_of_peripheral_immune_respon_Single-c {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+093_C_Local_and_systemic_SARS-CoV-2_response_CELLxG_Local_an {'shards_available': 2, 'shards_used': 2, 'cells': np.int64(2000)}
+200_A_GSE275067_Immunobiology_of_Aging_Cohort_PBMC_Profiling {'shards_available': 16, 'shards_used': 8, 'cells': np.int64(8000)}
+202_B_GSE161918_Time-resolved_Systems_Immunology_Reveals_a_L {'shards_available': 2, 'shards_used': 2, 'cells': np.int64(2000)}
+203_B_CELLxGENE_665714af_Ancestral_and_environmental_diversi {'shards_available': 2, 'shards_used': 2, 'cells': np.int64(2000)}
+204_B_CELLxGENE_cHSPC_aging_MDS_Human_circulating_hematopoie {'shards_available': 5, 'shards_used': 5, 'cells': np.int64(5000)}
+300b_A_GSE132802_DRESS_DiHS_PBMC_only_scRNAseq {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+301_A_GSE163121_SLE_healthy_Bcell_PBMC_scRNAseq {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+302_A_GSE314010_SLE_IL36_stim_PBMC_scRNAseq {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+304_A_Parse_10M_PBMC_12donor_90cytokines {'shards_available': 39, 'shards_used': 8, 'cells': np.int64(8000)}
+Traceback (most recent call last):
+  File "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/tools/corpus_c1q.py", line 180, in <module>
+    sys.exit(extract() if sys.argv[1] == "extract" else analyze())
+             ^^^^^^^^^
+  File "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/tools/corpus_c1q.py", line 95, in extract
+    (WORK / "SAMPLE.json").write_text(json.dumps({"seed": SEED, "shards_per_dataset": SHARDS, "blocks_per_shard": BLOCKS,
+                                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/sj_server_1/miniforge3/envs/scanvi/lib/python3.12/json/__init__.py", line 238, in dumps
+    **kw).encode(obj)
+          ^^^^^^^^^^^
+  File "/home/sj_server_1/miniforge3/envs/scanvi/lib/python3.12/json/encoder.py", line 202, in encode
+    chunks = list(chunks)
+             ^^^^^^^^^^^^
+  File "/home/sj_server_1/miniforge3/envs/scanvi/lib/python3.12/json/encoder.py", line 432, in _iterencode
+    yield from _iterencode_dict(o, _current_indent_level)
+  File "/home/sj_server_1/miniforge3/envs/scanvi/lib/python3.12/json/encoder.py", line 406, in _iterencode_dict
+    yield from chunks
+  File "/home/sj_server_1/miniforge3/envs/scanvi/lib/python3.12/json/encoder.py", line 406, in _iterencode_dict
+    yield from chunks
+  File "/home/sj_server_1/miniforge3/envs/scanvi/lib/python3.12/json/encoder.py", line 406, in _iterencode_dict
+    yield from chunks
+  File "/home/sj_server_1/miniforge3/envs/scanvi/lib/python3.12/json/encoder.py", line 439, in _iterencode
+    o = _default(o)
+        ^^^^^^^^^^^
+  File "/home/sj_server_1/miniforge3/envs/scanvi/lib/python3.12/json/encoder.py", line 180, in default
+    raise TypeError(f'Object of type {o.__class__.__name__} '
+TypeError: Object of type int64 is not JSON serializable

paper-releases/pbisc-diffusion/updates/20261004T065028Z-behcet-c1q-k4000-corpus/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/logs/corpus_extract_try2_fewblocks.log

@@ -0,0 +1,23 @@
+001_A_collection_436154da-bcf1-4130-9c8b-120ff9a888_Perez_et {'shards_available': 6, 'shards_used': 6, 'cells': np.int64(6000)}
+005_A_collection_dde06e0f-ab3b-46be-96a2-a8082383c4_OneK1K_Y {'shards_available': 5, 'shards_used': 5, 'cells': np.int64(5000)}
+006_A_collection_ced320a1-29f3-47c1-a735-513c7084d5_AIDA_Asi {'shards_available': 6, 'shards_used': 6, 'cells': np.int64(6000)}
+007_A_collection_e1a9ca56-f2ee-435d-980a-4f49ab7a95_Miao_et_ {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+009_A_Human_Immune_Health_Atlas_Human_Immune_Health_Atlas_AI {'shards_available': 8, 'shards_used': 8, 'cells': np.int64(8000)}
+010_A_collection_4a9fd4d7-d870-4265-89a5-ad51ab811d_ScaleBio {'shards_available': 3, 'shards_used': 3, 'cells': np.int64(3000)}
+053_B_collection_b0cf0afa-ec40-4d65-b570-ed4ceacc68_Integrat {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+058_B_collection_eb735cc9-d0a7-48fa-b255-db726bf365_COVID_PB {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+061_A_GSE274680_Savage_Allen_RA_at-risk_longitudinal_progres {'shards_available': 239, 'shards_used': 8, 'cells': np.int64(8000)}
+065_A_GSE271896_GSE271896_Sound_Life_deep_longitudinal_immun {'shards_available': 59, 'shards_used': 8, 'cells': np.int64(8000)}
+071_C_JDM_CITE-seq_PBMC_CELLxGENE_JDM_CITE-seq_PBMC_CELLxGEN {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+074_A_COMBAT_CELLxGENE_collection_COMBAT_CELLxGENE_collectio {'shards_available': 4, 'shards_used': 4, 'cells': np.int64(4000)}
+081_B_Single-cell_atlas_of_peripheral_immune_respon_Single-c {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+093_C_Local_and_systemic_SARS-CoV-2_response_CELLxG_Local_an {'shards_available': 2, 'shards_used': 2, 'cells': np.int64(2000)}
+200_A_GSE275067_Immunobiology_of_Aging_Cohort_PBMC_Profiling {'shards_available': 16, 'shards_used': 8, 'cells': np.int64(8000)}
+202_B_GSE161918_Time-resolved_Systems_Immunology_Reveals_a_L {'shards_available': 2, 'shards_used': 2, 'cells': np.int64(2000)}
+203_B_CELLxGENE_665714af_Ancestral_and_environmental_diversi {'shards_available': 2, 'shards_used': 2, 'cells': np.int64(2000)}
+204_B_CELLxGENE_cHSPC_aging_MDS_Human_circulating_hematopoie {'shards_available': 5, 'shards_used': 5, 'cells': np.int64(5000)}
+300b_A_GSE132802_DRESS_DiHS_PBMC_only_scRNAseq {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+301_A_GSE163121_SLE_healthy_Bcell_PBMC_scRNAseq {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+302_A_GSE314010_SLE_IL36_stim_PBMC_scRNAseq {'shards_available': 1, 'shards_used': 1, 'cells': np.int64(1000)}
+304_A_Parse_10M_PBMC_12donor_90cytokines {'shards_available': 39, 'shards_used': 8, 'cells': np.int64(8000)}
+cells (83000, 6000)

paper-releases/pbisc-diffusion/updates/20261004T065028Z-behcet-c1q-k4000-corpus/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/logs/corpus_label.log

@@ -0,0 +1,81 @@
+INFO     File                                                                   
+         /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/pla
+         ns/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_mo
+         del/model.pt already downloaded                                        
+INFO     File                                                                   
+         /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/pla
+         ns/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_mo
+         del/model.pt already downloaded                                        
+INFO     Found 100.0% reference vars in query data.                             
+INFO     File                                                                   
+         /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/pla
+         ns/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_mo
+         del/model.pt already downloaded                                        
+{
+  "method": "corpus_sample_c1q",
+  "n_cells": 179750,
+  "n_genes": 1005,
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 93391,
+      "Monocyte": 32766,
+      "B cell": 24494,
+      "NK cell": 15068,
+      "Other": 12071,
+      "DC": 1960
+    },
+    "aifi_l1": {
+      "T cell": 93391,
+      "Monocyte": 32766,
+      "B cell": 24494,
+      "NK cell": 15068,
+      "Progenitor cell": 5896,
+      "Erythrocyte": 4248,
+      "DC": 1960,
+      "Platelet": 1459,
+      "ILC": 468
+    },
+    "aifi_l2": {
+      "CD14 monocyte": 24203,
+      "Naive CD4 T cell": 23887,
+      "Memory CD4 T cell": 18323,
+      "Memory CD8 T cell": 14283,
+      "Naive CD8 T cell": 11392,
+      "Naive B cell": 9377,
+      "CD56dim NK cell": 8796,
+      "Memory B cell": 8285,
+      "gdT": 6225,
+      "DN T cell": 6153,
+      "Progenitor cell": 5896,
+      "Treg": 5180,
+      "Proliferating NK cell": 4813,
+      "Intermediate monocyte": 4646,
+      "Erythrocyte": 4248,
+      "CD16 monocyte": 3917,
+      "Effector B cell": 3444,
+      "MAIT": 3340,
+      "Transitional B cell": 2551,
+      "CD8aa": 2363,
+      "Proliferating T cell": 2245,
+      "CD56bright NK cell": 1459,
+      "Platelet": 1459,
+      "cDC2": 1247,
+      "Plasma cell": 837,
+      "ILC": 468,
+      "pDC": 406,
+      "cDC1": 251,
+      "ASDC": 56
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9274980575783031,
+    "mean_l1_mass": 0.979417622089386,
+    "frac_l2_max_prob_ge_0.5": 0.9749541029207233
+  },
+  "timings_s": {
+    "predict": 2.5,
+    "total": 4.8
+  },
+  "subset": false
+}
+-> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/corpus_c1q/scanvi_labels/labels.parquet

paper-releases/pbisc-diffusion/updates/20261004T065028Z-behcet-c1q-k4000-corpus/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/logs/label-lora3k4_raw_s04.log

@@ -0,0 +1,82 @@
+Seed set to 20260916
+INFO     File                                                                   
+         /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/pla
+         ns/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_mo
+         del/model.pt already downloaded                                        
+INFO     File                                                                   
+         /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/pla
+         ns/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_mo
+         del/model.pt already downloaded                                        
+INFO     Found 100.0% reference vars in query data.                             
+INFO     File                                                                   
+         /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/pla
+         ns/aifi_scanvi_rebuild_20260916/runs/aifi_scanvi_f01common_v1/scanvi_mo
+         del/model.pt already downloaded                                        
+{
+  "method": "generated_GSE198533_all19_lora3study_lora3k4_raw_s04",
+  "n_cells": 95000,
+  "n_genes": 1005,
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 64403,
+      "Monocyte": 13233,
+      "B cell": 9135,
+      "NK cell": 5433,
+      "DC": 1926,
+      "Other": 870
+    },
+    "aifi_l1": {
+      "T cell": 64403,
+      "Monocyte": 13233,
+      "B cell": 9135,
+      "NK cell": 5433,
+      "DC": 1926,
+      "Erythrocyte": 423,
+      "ILC": 223,
+      "Platelet": 168,
+      "Progenitor cell": 56
+    },
+    "aifi_l2": {
+      "Memory CD8 T cell": 15539,
+      "gdT": 13526,
+      "Memory CD4 T cell": 11638,
+      "Naive CD4 T cell": 10282,
+      "CD14 monocyte": 7464,
+      "Naive CD8 T cell": 4898,
+      "Treg": 4866,
+      "Naive B cell": 4124,
+      "Intermediate monocyte": 3881,
+      "CD56dim NK cell": 3735,
+      "Memory B cell": 3030,
+      "CD16 monocyte": 1888,
+      "cDC2": 1600,
+      "Effector B cell": 1318,
+      "MAIT": 1267,
+      "Proliferating NK cell": 1136,
+      "DN T cell": 1072,
+      "Proliferating T cell": 879,
+      "CD56bright NK cell": 562,
+      "Transitional B cell": 544,
+      "CD8aa": 436,
+      "Erythrocyte": 423,
+      "pDC": 261,
+      "ILC": 223,
+      "Platelet": 168,
+      "Plasma cell": 119,
+      "Progenitor cell": 56,
+      "cDC1": 48,
+      "ASDC": 17
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9178780015918769,
+    "mean_l1_mass": 0.983802318572998,
+    "frac_l2_max_prob_ge_0.5": 0.975
+  },
+  "timings_s": {
+    "predict": 0.8,
+    "total": 1.5
+  },
+  "subset": false
+}
+-> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_lora3k4_raw_s04_f01common/labels.parquet