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/label-zs_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_zs_raw_s04",
+  "n_cells": 95000,
+  "n_genes": 1005,
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 41727,
+      "Monocyte": 24638,
+      "NK cell": 13657,
+      "B cell": 11923,
+      "Other": 2058,
+      "DC": 997
+    },
+    "aifi_l1": {
+      "T cell": 41727,
+      "Monocyte": 24638,
+      "NK cell": 13657,
+      "B cell": 11923,
+      "Erythrocyte": 1383,
+      "DC": 997,
+      "Platelet": 501,
+      "ILC": 161,
+      "Progenitor cell": 13
+    },
+    "aifi_l2": {
+      "Memory CD8 T cell": 17140,
+      "CD14 monocyte": 16913,
+      "Naive B cell": 8647,
+      "Proliferating NK cell": 6992,
+      "gdT": 6679,
+      "CD56dim NK cell": 5920,
+      "CD16 monocyte": 5242,
+      "Memory CD4 T cell": 5015,
+      "DN T cell": 3548,
+      "Naive CD4 T cell": 3418,
+      "Intermediate monocyte": 2483,
+      "Naive CD8 T cell": 1700,
+      "Treg": 1617,
+      "Erythrocyte": 1383,
+      "Proliferating T cell": 1375,
+      "Memory B cell": 1230,
+      "Effector B cell": 1032,
+      "MAIT": 973,
+      "Transitional B cell": 853,
+      "CD56bright NK cell": 745,
+      "Platelet": 501,
+      "cDC1": 384,
+      "cDC2": 382,
+      "CD8aa": 262,
+      "pDC": 224,
+      "Plasma cell": 161,
+      "ILC": 161,
+      "Progenitor cell": 13,
+      "ASDC": 7
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9142133311960258,
+    "mean_l1_mass": 0.9790278673171997,
+    "frac_l2_max_prob_ge_0.5": 0.9711157894736843
+  },
+  "timings_s": {
+    "predict": 0.5,
+    "total": 1.2
+  },
+  "subset": false
+}
+-> /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

paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/logs/label-zs_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_zs_raw_s13",
+  "n_cells": 95000,
+  "n_genes": 1005,
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 41687,
+      "Monocyte": 24653,
+      "NK cell": 13624,
+      "B cell": 11962,
+      "Other": 2059,
+      "DC": 1015
+    },
+    "aifi_l1": {
+      "T cell": 41687,
+      "Monocyte": 24653,
+      "NK cell": 13624,
+      "B cell": 11962,
+      "Erythrocyte": 1387,
+      "DC": 1015,
+      "Platelet": 502,
+      "ILC": 156,
+      "Progenitor cell": 14
+    },
+    "aifi_l2": {
+      "Memory CD8 T cell": 17097,
+      "CD14 monocyte": 16961,
+      "Naive B cell": 8675,
+      "Proliferating NK cell": 7020,
+      "gdT": 6644,
+      "CD56dim NK cell": 5855,
+      "CD16 monocyte": 5203,
+      "Memory CD4 T cell": 5036,
+      "DN T cell": 3567,
+      "Naive CD4 T cell": 3471,
+      "Intermediate monocyte": 2489,
+      "Naive CD8 T cell": 1693,
+      "Treg": 1605,
+      "Erythrocyte": 1387,
+      "Proliferating T cell": 1335,
+      "Memory B cell": 1228,
+      "Effector B cell": 1024,
+      "MAIT": 963,
+      "Transitional B cell": 869,
+      "CD56bright NK cell": 749,
+      "Platelet": 502,
+      "cDC1": 401,
+      "cDC2": 373,
+      "CD8aa": 276,
+      "pDC": 234,
+      "Plasma cell": 166,
+      "ILC": 156,
+      "Progenitor cell": 14,
+      "ASDC": 7
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9140965908416008,
+    "mean_l1_mass": 0.9791163802146912,
+    "frac_l2_max_prob_ge_0.5": 0.9708842105263158
+  },
+  "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_zs_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/readout-lora3_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": 1671.44091796875,
+  "output_row_sum_median": 1671.0,
+  "input_nonzero_fraction": 0.047417291228070174,
+  "output_nonzero_fraction": 0.03619651929824561,
+  "method_name": "generated_GSE198533_all19_lora3study_lora3_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/lora3_raw_s04.npz",
+  "input_matrix_key": "generated_counts",
+  "input_n_cells": 95000,
+  "subset_rows": 95000,
+  "subset_seed": null,
+  "input_npz_sha256": "d09ec3161e726c1901b4d4b206109cf5cbb51f2781742cebc2a32878fdedd5a5",
+  "out": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/lora3_raw_s04_poisson.h5ad"
+}

paper-releases/pbisc-diffusion/updates/20261004T051658Z-behcet-c1q-lora3/diffusion/dataset/server_1/model8/plans/behcet_c1q_lora3_20261004/logs/readout-lora3_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": 1671.5598754882812,
+  "output_row_sum_median": 1671.0,
+  "input_nonzero_fraction": 0.04741839824561404,
+  "output_nonzero_fraction": 0.03619416315789473,
+  "method_name": "generated_GSE198533_all19_lora3study_lora3_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/lora3_raw_s13.npz",
+  "input_matrix_key": "generated_counts",
+  "input_n_cells": 95000,
+  "subset_rows": 95000,
+  "subset_seed": null,
+  "input_npz_sha256": "5ed5f2f3efd5eef11418ec91c67bf45cd5bbc44851078fc722f19d17beb43228",
+  "out": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/behcet_c1q_lora3_20261004/work/lora3_raw_s13_poisson.h5ad"
+}