Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261004T141237Z-c1q-crossdisease/diffusion/dataset/server_1/model8/plans/c1q_crossdisease_20261004/logs/build_sle_try1_dtype.log

@@ -0,0 +1,16 @@
+/home/sj_server_1/miniforge3/envs/scanvi/lib/python3.12/site-packages/anndata/experimental/__init__.py:48: FutureWarning: Importing read_elem from `anndata.experimental` is deprecated. Import anndata.io.read_elem instead.
+  return module_get_attr_redirect(
+Traceback (most recent call last):
+  File "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/c1q_crossdisease_20261004/tools/build_inputs.py", line 170, in <module>
+    sys.exit(main())
+             ^^^^^^
+  File "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/c1q_crossdisease_20261004/tools/build_inputs.py", line 138, in main
+    X, measured, obs, info = load(ds, canon)
+                             ^^^^^^^^^^^^^^^
+  File "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/c1q_crossdisease_20261004/tools/build_inputs.py", line 103, in load
+    mito = np.char.startswith(sym, "MT-")
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/sj_server_1/miniforge3/envs/scanvi/lib/python3.12/site-packages/numpy/_core/strings.py", line 487, in startswith
+    return _startswith_ufunc(a, prefix, start, end)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+numpy._core._exceptions._UFuncNoLoopError: ufunc 'startswith' did not contain a loop with signature matching types (<class 'numpy.dtypes.ObjectDType'>, <class 'numpy.dtypes.StrDType'>, <class 'numpy.dtypes._PyLongDType'>, <class 'numpy.dtypes._PyLongDType'>) -> None

paper-releases/pbisc-diffusion/updates/20261004T141237Z-c1q-crossdisease/diffusion/dataset/server_1/model8/plans/c1q_crossdisease_20261004/logs/compare.log

@@ -0,0 +1,37 @@
+                                 0                1           2
+arm                   dress_zs_s13  kawasaki_zs_s13  sle_zs_s13
+dataset                      dress         kawasaki         sle
+samples                          7               15          56
+obs_monocytes                 4485            11050       70901
+gen_monocytes                 3793             7927       21833
+obs_median_mono_lib         3151.0           1821.0      1904.0
+gen_median_mono_lib         1913.0           2041.0      1822.0
+thin_factor                  0.607              1.0       0.957
+obs_c1q_ge1_pct             18.729            9.955       7.881
+obsthin_c1q_ge1_pct         17.324            9.955       7.735
+gen_c1q_ge1_pct             16.082            4.693       5.231
+ratio_c1q_ge1_pct            0.928            0.471       0.676
+spearman_c1q_ge1_pct         0.893            0.257       0.371
+obs_c1q_ge2_pct             13.066            5.457       2.571
+obsthin_c1q_ge2_pct         11.884            5.457       2.523
+gen_c1q_ge2_pct                2.9            0.542       0.499
+ratio_c1q_ge2_pct            0.244            0.099       0.198
+spearman_c1q_ge2_pct         0.964            0.173       0.417
+spearman_mono_pct            0.964            0.889       0.971
+obs_mono_pct_mean           11.779           11.824      20.865
+gen_mono_pct_mean           10.837           10.569      12.996
+            arm                      group  obs_mono_pct  gen_mono_pct  obsthin_c1q_ge1_pct  gen_c1q_ge1_pct  obsthin_c1q_ge2_pct  gen_c1q_ge2_pct
+   dress_zs_s13       DRESS|bacterial_stim         10.82         10.52                84.13            30.04                80.16             5.51
+   dress_zs_s13                 DRESS|none         18.28         14.10                 6.77             9.65                 3.75             2.13
+   dress_zs_s13          DRESS|tofacitinib          5.52          5.46                55.97            18.32                42.14             3.30
+   dress_zs_s13               healthy|none         22.69         22.96                 4.98             6.62                 1.69             0.96
+   dress_zs_s13 unspecified|bacterial_stim         15.27         16.22                73.18            26.88                59.60             4.56
+   dress_zs_s13        unspecified|control          5.33          4.02                55.13            17.41                33.84             3.48
+   dress_zs_s13           unspecified|none          4.53          2.58                 8.39             3.88                 3.69             1.55
+kawasaki_zs_s13                         HC          6.85          5.32                12.49             3.27                 4.11             0.13
+kawasaki_zs_s13                   KD_after          8.87          8.93                 7.16             5.55                 3.99             0.84
+kawasaki_zs_s13                  KD_before         17.27         14.83                11.66             4.85                 7.03             0.48
+     sle_zs_s13                        aHD         17.27         11.10                 4.85             5.82                 1.84             0.73
+     sle_zs_s13                       aSLE         27.58         16.14                 9.93             5.84                 3.34             0.62
+     sle_zs_s13                        cHD         10.48          5.55                 6.33             4.56                 1.67             0.43
+     sle_zs_s13                       cSLE         23.45         15.10                 6.62             5.26                 2.26             0.54

paper-releases/pbisc-diffusion/updates/20261004T141237Z-c1q-crossdisease/diffusion/dataset/server_1/model8/plans/c1q_crossdisease_20261004/logs/label-dress_zs_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_c1qx_dress_zs_s13",
+  "n_cells": 35000,
+  "n_genes": 1005,
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 27578,
+      "Monocyte": 3793,
+      "B cell": 1938,
+      "NK cell": 1023,
+      "DC": 462,
+      "Other": 206
+    },
+    "aifi_l1": {
+      "T cell": 27578,
+      "Monocyte": 3793,
+      "B cell": 1938,
+      "NK cell": 1023,
+      "DC": 462,
+      "Erythrocyte": 119,
+      "ILC": 37,
+      "Platelet": 30,
+      "Progenitor cell": 20
+    },
+    "aifi_l2": {
+      "Naive CD4 T cell": 8602,
+      "Memory CD4 T cell": 7761,
+      "Naive CD8 T cell": 4372,
+      "Memory CD8 T cell": 2529,
+      "Intermediate monocyte": 2380,
+      "Treg": 1546,
+      "CD14 monocyte": 1090,
+      "Proliferating T cell": 1001,
+      "Naive B cell": 803,
+      "CD56dim NK cell": 730,
+      "Memory B cell": 682,
+      "DN T cell": 618,
+      "gdT": 602,
+      "MAIT": 397,
+      "Effector B cell": 349,
+      "CD16 monocyte": 323,
+      "cDC2": 306,
+      "CD56bright NK cell": 196,
+      "CD8aa": 150,
+      "cDC1": 135,
+      "Erythrocyte": 119,
+      "Proliferating NK cell": 97,
+      "Plasma cell": 76,
+      "ILC": 37,
+      "Platelet": 30,
+      "Transitional B cell": 28,
+      "Progenitor cell": 20,
+      "pDC": 11,
+      "ASDC": 10
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9361765263548919,
+    "mean_l1_mass": 0.9905846118927002,
+    "frac_l2_max_prob_ge_0.5": 0.9814571428571428
+  },
+  "timings_s": {
+    "predict": 0.3,
+    "total": 0.7
+  },
+  "subset": false
+}
+-> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/c1q_crossdisease_20261004/work/scanvi_labels_dress_zs_s13_f01common/labels.parquet

paper-releases/pbisc-diffusion/updates/20261004T141237Z-c1q-crossdisease/diffusion/dataset/server_1/model8/plans/c1q_crossdisease_20261004/logs/label-kawasaki_zs_s13.log

@@ -0,0 +1,81 @@
+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_c1qx_kawasaki_zs_s13",
+  "n_cells": 75000,
+  "n_genes": 1005,
+  "label_counts": {
+    "celltype_l1_pred": {
+      "T cell": 42408,
+      "B cell": 20998,
+      "Monocyte": 7927,
+      "NK cell": 3017,
+      "Other": 336,
+      "DC": 314
+    },
+    "aifi_l1": {
+      "T cell": 42408,
+      "B cell": 20998,
+      "Monocyte": 7927,
+      "NK cell": 3017,
+      "DC": 314,
+      "Erythrocyte": 131,
+      "Platelet": 73,
+      "Progenitor cell": 71,
+      "ILC": 61
+    },
+    "aifi_l2": {
+      "Naive CD4 T cell": 13979,
+      "Naive B cell": 11974,
+      "Memory CD4 T cell": 10148,
+      "Naive CD8 T cell": 7202,
+      "CD14 monocyte": 5771,
+      "Effector B cell": 4215,
+      "Memory CD8 T cell": 4168,
+      "Memory B cell": 2779,
+      "Treg": 2459,
+      "CD56dim NK cell": 2168,
+      "gdT": 1903,
+      "Transitional B cell": 1824,
+      "Intermediate monocyte": 1289,
+      "MAIT": 951,
+      "DN T cell": 892,
+      "CD16 monocyte": 867,
+      "CD56bright NK cell": 571,
+      "CD8aa": 376,
+      "Proliferating T cell": 330,
+      "cDC2": 282,
+      "Proliferating NK cell": 278,
+      "Plasma cell": 206,
+      "Erythrocyte": 131,
+      "Platelet": 73,
+      "Progenitor cell": 71,
+      "ILC": 61,
+      "pDC": 21,
+      "cDC1": 11
+    }
+  },
+  "confidence": {
+    "mean_l2_max_prob": 0.9433015090618531,
+    "mean_l1_mass": 0.9957360625267029,
+    "frac_l2_max_prob_ge_0.5": 0.9864533333333333
+  },
+  "timings_s": {
+    "predict": 0.4,
+    "total": 1.0
+  },
+  "subset": false
+}
+-> /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/c1q_crossdisease_20261004/work/scanvi_labels_kawasaki_zs_s13_f01common/labels.parquet