Archive 4 checkpoints (1-4)

paper-releases/20260928/diffusion/data/inference_inputs/server_1/plans/behcet_c1q_repro_20260921/conditions/external_contract_validation.json

@@ -0,0 +1,36 @@
+{
+  "status": "PASS",
+  "loader": "pbisc_sdd.experiment.load_external_bulk_conditions",
+  "adapter": "SimpleNamespace streams adapter (tests/test_experiment.py::_external_streams pattern) carrying the real 20,097-gene canonical panel, the checkpoint's panel_positions and the real Model 7 conditioner replayed on CPU",
+  "checkpoint": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/s0_6k_allK_topup16_seed20260627_lossactive_v1/checkpoint_epoch_008.pt",
+  "checkpoint_sha256": "a5ec185b1dd070890115d02f5fdb897ab5a6c790b51daf66bb47932925be8a7e",
+  "checkpoint_schema": "pbisc_sdd.checkpoint.ladder.v1",
+  "base_conditions_shape": [
+    19,
+    6006
+  ],
+  "bulk_measurement_fraction_shape": [
+    19,
+    6000
+  ],
+  "output_availability_mask_shape": [
+    19,
+    6000
+  ],
+  "recipe_k_shape": [
+    19
+  ],
+  "cells_per_bulk_shape": [
+    19
+  ],
+  "sample_ids_shape": [
+    19
+  ],
+  "sample_ids_match_emitted_order": true,
+  "recipe_k_matches_emitted": true,
+  "cells_per_bulk_all_equal": 5000,
+  "base_conditions_finite": true,
+  "selected_panel_genes": 6000,
+  "selected_panel_genes_measured_in_bulk": 5972,
+  "input_sha256": "57c5a2dcd775c7888318bc4b202241a9629bedffd418e2336a793b76f5c1e312"
+}

paper-releases/20260928/diffusion/data/inference_inputs/server_1/plans/behcet_c1q_repro_20260921/conditions/samples.csv

@@ -0,0 +1,20 @@
+sample_id,gsm,raw_condition,age,sex,group,library_size_on_panel,library_size_in_source_matrix,panel_genes_detected,recipe_k,cells_per_bulk,implied_counts_per_cell
+BDU1,GSM5951808,BD patients,24,male,BD,19763015,20727638,15871,5000,5000,3952.603
+BDU2,GSM5951809,BD patients,30,male,BD,19605913,20603415,15621,5000,5000,3921.1826
+BDU3,GSM5951810,BD patients,25,male,BD,18121684,18994141,15673,5000,5000,3624.3368
+BDV1,GSM5951802,BD patients,46,male,BD,16828529,17613101,15630,5000,5000,3365.7058
+BDV2,GSM5951803,BD patients,24,male,BD,16226749,16965064,16522,5000,5000,3245.3498
+BDV3,GSM5951804,BD patients,42,male,BD,18107067,19186063,15742,5000,5000,3621.4134
+BDV4,GSM5951805,BD patients,31,male,BD,20248524,21237362,15827,5000,5000,4049.7048
+BDV5,GSM5951806,BD patients,58,male,BD,17631560,18462515,15530,5000,5000,3526.312
+BDV6,GSM5951807,BD patients,41,male,BD,18036208,18850500,16043,5000,5000,3607.2416
+HC1,GSM5951811,healthy control,18,male,HC,19817335,20894060,15863,5000,5000,3963.467
+HC10,GSM5951820,healthy control,48,male,HC,22979785,24116436,15851,5000,5000,4595.957
+HC2,GSM5951812,healthy control,47,male,HC,15801845,16600502,15640,5000,5000,3160.369
+HC3,GSM5951813,healthy control,18,male,HC,19033356,20012034,15744,5000,5000,3806.6712
+HC4,GSM5951814,healthy control,53,male,HC,17709796,18569195,15651,5000,5000,3541.9592
+HC5,GSM5951815,healthy control,58,male,HC,20354152,21333610,15695,5000,5000,4070.8304
+HC6,GSM5951816,healthy control,18,male,HC,18524453,19466951,15667,5000,5000,3704.8906
+HC7,GSM5951817,healthy control,41,male,HC,18598477,19667567,16012,5000,5000,3719.6954
+HC8,GSM5951818,healthy control,36,male,HC,20972151,21977378,15892,5000,5000,4194.4302
+HC9,GSM5951819,healthy control,36,male,HC,19489444,20540420,15864,5000,5000,3897.8888

paper-releases/20260928/diffusion/data/inference_inputs/server_1/plans/conditioning_use_20260921/conditions/MANIFEST.json

@@ -0,0 +1,135 @@
+{
+  "schema": "pbisc_sdd.conditioning_use.variants.v1",
+  "seed": 20260921,
+  "source_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/gse135779_scsemi_split_target42_20260913/donor_conditions.npz",
+  "source_sha256": "a5b2f51132f19e98917f9d53ee05e86dc22322e497d9701dec1ac1eec24df628",
+  "donors": 42,
+  "labels": {
+    "HC": 12,
+    "SLE": 30
+  },
+  "untouched_keys": [
+    "schema_version",
+    "output_availability_mask",
+    "recipe_k",
+    "cells_per_bulk",
+    "sample_ids",
+    "gene_ids",
+    "gene_symbols",
+    "donor_ids",
+    "raw_conditions",
+    "conditions",
+    "donor_n_cells"
+  ],
+  "variants": [
+    {
+      "variant": "condflip",
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/conditioning_use_20260921/conditions/donor_conditions_condflip.npz",
+      "sha256": "25985581cba0fe9526d81cd4a85081bd66d69a0ed2c6e7e47d3516af458cd4d6",
+      "source_donor_index": [
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+      ],
+      "donors_keeping_their_own_disease_label": 0,
+      "donors_with_own_bulk": 0
+    },
+    {
+      "variant": "condperm",
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/conditioning_use_20260921/conditions/donor_conditions_condperm.npz",
+      "sha256": "6ec7cecfcf2f4c39acb68a42a3d130666d2faf89dc9bbc2a42eaab0665f51d48",
+      "source_donor_index": [
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+      ],
+      "donors_keeping_their_own_disease_label": 28,
+      "donors_with_own_bulk": 0
+    },
+    {
+      "variant": "condmean",
+      "path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/conditioning_use_20260921/conditions/donor_conditions_condmean.npz",
+      "sha256": "488b755a0f3ef555ca26a53bbc5b1fb3c2a12a53f4d4c3b11c2ff9b2062e7990",
+      "source_donor_index": null,
+      "disease_label_of_source": "cohort mean"
+    }
+  ]
+}