Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/logs/build_dataset.log

@@ -0,0 +1,16 @@
+{
+ "paired_rows": [
+  "BDV4",
+  "BDV5",
+  "BDV6"
+ ],
+ "cells": 16635,
+ "cells_per_row": {
+  "BDV4": 6304,
+  "BDV5": 3508,
+  "BDV6": 6823
+ },
+ "sc_common_genes": 19293,
+ "sc_common_panel_genes": 5868,
+ "alpha_genes_estimated": 10961
+}

paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/logs/label-lora3_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_lora3_raw_s04",
+  "n_cells": 95000,
+  "n_genes": 1005,
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 63666,
+      "Monocyte": 13427,
+      "B cell": 9334,
+      "NK cell": 5768,
+      "DC": 1867,
+      "Other": 938
+    },
+    "aifi_l1": {
+      "T cell": 63666,
+      "Monocyte": 13427,
+      "B cell": 9334,
+      "NK cell": 5768,
+      "DC": 1867,
+      "Erythrocyte": 474,
+      "ILC": 238,
+      "Platelet": 173,
+      "Progenitor cell": 53
+    },
+    "aifi_l2": {
+      "Memory CD8 T cell": 15335,
+      "gdT": 13657,
+      "Memory CD4 T cell": 11344,
+      "Naive CD4 T cell": 9855,
+      "CD14 monocyte": 7606,
+      "Treg": 5044,
+      "Naive CD8 T cell": 4777,
+      "Naive B cell": 4198,
+      "CD56dim NK cell": 3982,
+      "Intermediate monocyte": 3868,
+      "Memory B cell": 3124,
+      "CD16 monocyte": 1953,
+      "cDC2": 1535,
+      "Effector B cell": 1375,
+      "MAIT": 1325,
+      "Proliferating NK cell": 1164,
+      "DN T cell": 1033,
+      "Proliferating T cell": 850,
+      "CD56bright NK cell": 622,
+      "Transitional B cell": 524,
+      "Erythrocyte": 474,
+      "CD8aa": 446,
+      "pDC": 264,
+      "ILC": 238,
+      "Platelet": 173,
+      "Plasma cell": 113,
+      "Progenitor cell": 53,
+      "cDC1": 49,
+      "ASDC": 19
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9171383768709083,
+    "mean_l1_mass": 0.9833546280860901,
+    "frac_l2_max_prob_ge_0.5": 0.9746526315789473
+  },
+  "timings_s": {
+    "predict": 0.4,
+    "total": 1.1
+  },
+  "subset": false
+}
+-> /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

paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/logs/label-lora3_raw_s13.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_lora3_raw_s13",
+  "n_cells": 95000,
+  "n_genes": 1005,
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 63684,
+      "Monocyte": 13378,
+      "B cell": 9319,
+      "NK cell": 5749,
+      "DC": 1903,
+      "Other": 967
+    },
+    "aifi_l1": {
+      "T cell": 63684,
+      "Monocyte": 13378,
+      "B cell": 9319,
+      "NK cell": 5749,
+      "DC": 1903,
+      "Erythrocyte": 486,
+      "ILC": 251,
+      "Platelet": 172,
+      "Progenitor cell": 58
+    },
+    "aifi_l2": {
+      "Memory CD8 T cell": 15246,
+      "gdT": 13568,
+      "Memory CD4 T cell": 11316,
+      "Naive CD4 T cell": 9944,
+      "CD14 monocyte": 7539,
+      "Treg": 4945,
+      "Naive CD8 T cell": 4801,
+      "Naive B cell": 4180,
+      "CD56dim NK cell": 3981,
+      "Intermediate monocyte": 3896,
+      "Memory B cell": 3111,
+      "CD16 monocyte": 1943,
+      "cDC2": 1558,
+      "Effector B cell": 1418,
+      "MAIT": 1393,
+      "Proliferating NK cell": 1164,
+      "DN T cell": 1098,
+      "Proliferating T cell": 916,
+      "CD56bright NK cell": 604,
+      "Transitional B cell": 501,
+      "Erythrocyte": 486,
+      "CD8aa": 457,
+      "pDC": 267,
+      "ILC": 251,
+      "Platelet": 172,
+      "Plasma cell": 109,
+      "Progenitor cell": 58,
+      "cDC1": 56,
+      "ASDC": 22
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9168813030446831,
+    "mean_l1_mass": 0.9833822250366211,
+    "frac_l2_max_prob_ge_0.5": 0.9744
+  },
+  "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_lora3_raw_s13_f01common/labels.parquet

paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/logs/label-zs_cal_s13.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_zs_cal_s13",
+  "n_cells": 95000,
+  "n_genes": 1005,
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 63817,
+      "Monocyte": 12362,
+      "B cell": 9860,
+      "NK cell": 6727,
+      "Other": 1418,
+      "DC": 816
+    },
+    "aifi_l1": {
+      "T cell": 63817,
+      "Monocyte": 12362,
+      "B cell": 9860,
+      "NK cell": 6727,
+      "Erythrocyte": 1066,
+      "DC": 816,
+      "Platelet": 131,
+      "Progenitor cell": 117,
+      "ILC": 104
+    },
+    "aifi_l2": {
+      "Memory CD8 T cell": 29611,
+      "Naive CD4 T cell": 10347,
+      "gdT": 10026,
+      "CD14 monocyte": 7679,
+      "Naive B cell": 5215,
+      "CD56dim NK cell": 4665,
+      "Memory CD4 T cell": 4580,
+      "Naive CD8 T cell": 3440,
+      "Memory B cell": 3436,
+      "Intermediate monocyte": 2888,
+      "Treg": 2249,
+      "DN T cell": 2248,
+      "CD16 monocyte": 1795,
+      "Proliferating NK cell": 1090,
+      "Erythrocyte": 1066,
+      "Effector B cell": 1019,
+      "CD56bright NK cell": 972,
+      "MAIT": 696,
+      "cDC2": 513,
+      "CD8aa": 317,
+      "Proliferating T cell": 303,
+      "pDC": 256,
+      "Platelet": 131,
+      "Progenitor cell": 117,
+      "ILC": 104,
+      "Plasma cell": 99,
+      "Transitional B cell": 91,
+      "cDC1": 36,
+      "ASDC": 11
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9291515276196756,
+    "mean_l1_mass": 0.9806368350982666,
+    "frac_l2_max_prob_ge_0.5": 0.9771052631578947
+  },
+  "timings_s": {
+    "predict": 1.0,
+    "total": 1.7
+  },
+  "subset": false
+}
+-> /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