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/label-lora3k4_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_lora3k4_raw_s13",
+  "n_cells": 95000,
+  "n_genes": 1005,
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 64397,
+      "Monocyte": 13196,
+      "B cell": 9174,
+      "NK cell": 5408,
+      "DC": 1953,
+      "Other": 872
+    },
+    "aifi_l1": {
+      "T cell": 64397,
+      "Monocyte": 13196,
+      "B cell": 9174,
+      "NK cell": 5408,
+      "DC": 1953,
+      "Erythrocyte": 426,
+      "ILC": 218,
+      "Platelet": 167,
+      "Progenitor cell": 61
+    },
+    "aifi_l2": {
+      "Memory CD8 T cell": 15566,
+      "gdT": 13517,
+      "Memory CD4 T cell": 11663,
+      "Naive CD4 T cell": 10244,
+      "CD14 monocyte": 7431,
+      "Treg": 4881,
+      "Naive CD8 T cell": 4854,
+      "Naive B cell": 4149,
+      "Intermediate monocyte": 3874,
+      "CD56dim NK cell": 3748,
+      "Memory B cell": 3115,
+      "CD16 monocyte": 1891,
+      "cDC2": 1621,
+      "MAIT": 1306,
+      "Effector B cell": 1278,
+      "Proliferating NK cell": 1084,
+      "DN T cell": 1026,
+      "Proliferating T cell": 928,
+      "CD56bright NK cell": 576,
+      "Transitional B cell": 509,
+      "Erythrocyte": 426,
+      "CD8aa": 412,
+      "pDC": 262,
+      "ILC": 218,
+      "Platelet": 167,
+      "Plasma cell": 123,
+      "Progenitor cell": 61,
+      "cDC1": 48,
+      "ASDC": 22
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9190728375607415,
+    "mean_l1_mass": 0.9843924045562744,
+    "frac_l2_max_prob_ge_0.5": 0.9755263157894737
+  },
+  "timings_s": {
+    "predict": 1.2,
+    "total": 1.9
+  },
+  "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_s13_f01common/labels.parquet

paper-releases/pbisc-diffusion/updates/20261004T065028Z-behcet-c1q-k4000-corpus/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/logs/label-zsk4_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_zsk4_raw_s13",
+  "n_cells": 95000,
+  "n_genes": 1005,
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 40909,
+      "Monocyte": 25253,
+      "NK cell": 13407,
+      "B cell": 12441,
+      "Other": 1853,
+      "DC": 1137
+    },
+    "aifi_l1": {
+      "T cell": 40909,
+      "Monocyte": 25253,
+      "NK cell": 13407,
+      "B cell": 12441,
+      "Erythrocyte": 1248,
+      "DC": 1137,
+      "Platelet": 418,
+      "ILC": 174,
+      "Progenitor cell": 13
+    },
+    "aifi_l2": {
+      "CD14 monocyte": 17398,
+      "Memory CD8 T cell": 14934,
+      "Naive B cell": 9055,
+      "Proliferating NK cell": 6868,
+      "gdT": 6199,
+      "CD56dim NK cell": 5766,
+      "Memory CD4 T cell": 5667,
+      "CD16 monocyte": 5498,
+      "Naive CD4 T cell": 4269,
+      "DN T cell": 3531,
+      "Intermediate monocyte": 2357,
+      "Naive CD8 T cell": 1965,
+      "Treg": 1736,
+      "Proliferating T cell": 1275,
+      "Erythrocyte": 1248,
+      "Memory B cell": 1221,
+      "MAIT": 1063,
+      "Transitional B cell": 1036,
+      "Effector B cell": 971,
+      "CD56bright NK cell": 773,
+      "cDC1": 499,
+      "Platelet": 418,
+      "cDC2": 407,
+      "CD8aa": 270,
+      "pDC": 221,
+      "ILC": 174,
+      "Plasma cell": 158,
+      "Progenitor cell": 13,
+      "ASDC": 10
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9145452904134989,
+    "mean_l1_mass": 0.9795705676078796,
+    "frac_l2_max_prob_ge_0.5": 0.9702421052631579
+  },
+  "timings_s": {
+    "predict": 0.7,
+    "total": 1.4
+  },
+  "subset": false
+}
+-> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/scanvi_labels_zsk4_raw_s13_f01common/labels.parquet

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

@@ -0,0 +1,22 @@
+{
+  "rule": "counts ~ Poisson(generated_counts * library_scale), independent per entry, single draw",
+  "seed": 20260916,
+  "library_scale": 1.0,
+  "library_size_handling": "no rescaling (library_scale=1.0): E[library] = generated library",
+  "unlabeled_category": "Unknown",
+  "n_cells": 95000,
+  "n_genes": 6000,
+  "input_row_sum_median": 1732.9273071289062,
+  "output_row_sum_median": 1733.0,
+  "input_nonzero_fraction": 0.048133843859649125,
+  "output_nonzero_fraction": 0.036612977192982454,
+  "method_name": "generated_GSE198533_all19_lora3study_lora3k4_raw_s04",
+  "batch_prefix": "",
+  "input_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/generated/lora3k4_raw_s04.npz",
+  "input_matrix_key": "generated_counts",
+  "input_n_cells": 95000,
+  "subset_rows": 95000,
+  "subset_seed": null,
+  "input_npz_sha256": "ac7c011f1707c1d47863f9db0e60a18d9986c66111772687471487022f33c94e",
+  "out": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/lora3k4_raw_s04_poisson.h5ad"
+}

paper-releases/pbisc-diffusion/updates/20261004T065028Z-behcet-c1q-k4000-corpus/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/logs/readout-lora3k4_raw_s13.log

@@ -0,0 +1,22 @@
+{
+  "rule": "counts ~ Poisson(generated_counts * library_scale), independent per entry, single draw",
+  "seed": 20260916,
+  "library_scale": 1.0,
+  "library_size_handling": "no rescaling (library_scale=1.0): E[library] = generated library",
+  "unlabeled_category": "Unknown",
+  "n_cells": 95000,
+  "n_genes": 6000,
+  "input_row_sum_median": 1733.4550170898438,
+  "output_row_sum_median": 1732.0,
+  "input_nonzero_fraction": 0.04813353859649123,
+  "output_nonzero_fraction": 0.036617963157894735,
+  "method_name": "generated_GSE198533_all19_lora3study_lora3k4_raw_s13",
+  "batch_prefix": "",
+  "input_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/generated/lora3k4_raw_s13.npz",
+  "input_matrix_key": "generated_counts",
+  "input_n_cells": 95000,
+  "subset_rows": 95000,
+  "subset_seed": null,
+  "input_npz_sha256": "92ed059037b4b45c583c7210046f4fe9c4cd513aabd6f2e442e58081126002d4",
+  "out": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/lora3k4_raw_s13_poisson.h5ad"
+}