Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/CHECKPOINT_ALIAS_PROOF.json

@@ -0,0 +1,8 @@
+{
+  "canonical": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/runs/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
+  "remote_resolved": "/home/sj_server_2/PBISC/paper-release-20260928/models/published_parents/f01_6k_1x_seed20260627/checkpoint_epoch_016.pt",
+  "sha256": "8c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633",
+  "source_host": "server_2",
+  "both_file_hashes_verified": true,
+  "original_validator_sha256": "bf6f264bfd377a6d9831ee42c553e58a6bcf44d5a926667eb75454b58dd34c42"
+}

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/REPORT.md

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+# Giroux paired disease: same-panel trunk ×1 vs ×4 LoRA
+
+2026-10-15. Existing generated cells reused; CPU evaluation only. No GPU training or generation.
+
+## Main result
+
+The ×4 model improves sample expression correlation, distribution coverage and mean composition error, but does not improve mean disease logFC correlation in these five support draws. This does not establish superior disease integrity.
+
+| Metric | ×1 LoRA | ×4 LoRA |
+|---|---:|---:|
+| composition_l1 | 0.2704 | 0.2606 |
+| coverage | 0.9552 | 0.9703 |
+| expression_r | 0.8617 | 0.9414 |
+| logfc_r | 0.2617 | 0.2506 |
+| partial_r | 0.1502 | 0.1513 |
+| deg_overlap | 0.0000 | 0.0000 |
+
+## Matched conditions
+
+Five exact support draws, rank16/alpha16, lr/warmup/batch/EMA, fixed3000 steps, training seed, held-out sample IDs, raw condition hash, DDIM steps/seed/EMA, exact6000 gene IDs/order, frozen annotator hash, reference hash, disease contrast (severe vs mild), sex-linked gene exclusion and DEG definition were checked. x4 existing scoring outputs were reused.
+
+Draws overlap in donors. These are descriptive means, not five independent cohort replications; no significance claim. The top50 DEG overlap metric is zero for both methods in all five draws; this is not a claim that every DEG analysis is equivalent.
+
+## Architecture
+
+Actual checkpoint model_config is checked in FIX_VERIFIED.json: trunk hidden dimensions1024/1024/512/256 become4096/4096/2048/1024. Context512, time128 and6000 genes stay fixed. Width×4 is not a claim of exactly4× total parameter count.
+
+## Checkpoint provenance repair
+
+Imperial draw4 pairedcal metadata records the server_2 archive target of a checkpoint symlink. Both real files have SHA2568c7cd0e83e2bc19fe03dfcbc084919a1e2f61be8cc8bc12f4caf543dfda91633. The old validator required exact canonical path text. The new wrapper accepts only this verified alias pair and exact SHA; unknown paths, different checkpoints and wrong hashes still fail. Frozen scorer source, checkpoints and generation metadata are unchanged.
+
+Original failed receipt is preserved in imperial_draw4_failed_score_receipt.json. The collection/scoring recovery service is pbisc-strict-priority-collect-fixed-20261015; it keeps x4 priority and waits before retrying CPU scoring. The direct Giroux comparison is complete independently.

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/RESULT.json

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+{
+  "means": {
+    "x1_LoRA": {
+      "composition_l1": 0.27042738595627136,
+      "coverage": 0.9552141414141414,
+      "precision": 0.9996666666666667,
+      "expression_r": 0.8616924010624436,
+      "logfc_r": 0.26169989997221543,
+      "partial_r": 0.15019498658038383,
+      "deg_overlap": 0
+    },
+    "x4_LoRA": {
+      "composition_l1": 0.2606421644344827,
+      "coverage": 0.9703272727272727,
+      "precision": 0.9998888888888889,
+      "expression_r": 0.9413911182762126,
+      "logfc_r": 0.25062046255344994,
+      "partial_r": 0.1512554782186632,
+      "deg_overlap": 0
+    }
+  },
+  "draws": 5,
+  "proofs": [
+    {
+      "draw": 0,
+      "x1_binding": {
+        "arm": "lora",
+        "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw0/lora.npz",
+        "npz_sha256": "765845e9a73b40470b9d94fded33c190ccb8d73529f732ae5bc0fc2cea9cda6e",
+        "receipt": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw0/lora.log",
+        "receipt_sha256": "17a7b0046518b021f45c165b7417db8a99744c46965c216135cc7cea4da270d4",
+        "source_binding": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/giroux2022/disease/draw0/lora/RUN.json",
+        "source_binding_sha256": "7e86f51744c22136fc19fed11476d33043dc33347f50fa248d96fdbf58eea019",
+        "condition_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw0/test_raw.npz",
+        "condition_sha256": "f04c5725cf7d20ca4ca26d2ac43352d8c233b9d6c4d7ddc2116e3be4694623a9",
+        "checkpoint_sha256": "1da445cb2d3c86b2672e1b2dfa52e31b444b509108d125a7feb9b7ebf80dc0da",
+        "support_sha256": "074d1cf9ca3951ef1a032239eabb9d3a13f0f9a2030b030dcbe425ac71d46700"
+      },
+      "x4_summary_sha256": "09c23a58d1f074cd2513ff48a817f7194f91831b3f99afc9f8106c36af0fecf5",
+      "same_support_test_condition_seed_hyperparameters": true,
+      "same_reference_annotation_contrast_gene_exclusion": true
+    },
+    {
+      "draw": 1,
+      "x1_binding": {
+        "arm": "lora",
+        "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw1/lora.npz",
+        "npz_sha256": "23c22a3ecafc54d6a746016ef7c1c55ff6ec6fcb6df8f81d0cca50e86a2830c3",
+        "receipt": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw1/lora.log",
+        "receipt_sha256": "35725d61e154b7f1e2744efd3c7e2385aaab4ec3502beef0975ef89282397cfc",
+        "source_binding": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/giroux2022/disease/draw1/lora/RUN.json",
+        "source_binding_sha256": "3f2cf491d54065a30209321f8860fd7dccfa68352f0a0f31ef332db019c7a9cb",
+        "condition_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw1/test_raw.npz",
+        "condition_sha256": "935e890f67fc789b9ecf47b5c90157bfe0a1983d6ffdb1ea2d198b6de9767f47",
+        "checkpoint_sha256": "0492c0d21a4a15193013661d303b3ffa49f744c69d62330ee4eec3f6bf012a78",
+        "support_sha256": "1a20024ce53f3aeb268784fed7fed630ef326f8ffa89fa9bc150661c1506b7e2"
+      },
+      "x4_summary_sha256": "4509b41eb7579e7e90e9c3f8fe91c634f9ba9d2e2a3e64d41c57be58c3149aa4",
+      "same_support_test_condition_seed_hyperparameters": true,
+      "same_reference_annotation_contrast_gene_exclusion": true
+    },
+    {
+      "draw": 2,
+      "x1_binding": {
+        "arm": "lora",
+        "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw2/lora.npz",
+        "npz_sha256": "8d63ed804152bd4b19bf2a6910b247960df05da77474855cc76aeb87d0bf7bbc",
+        "receipt": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw2/lora.log",
+        "receipt_sha256": "da6139e5f555666d1df59db7460ab1d297d272cd390ad03850554a098329c2d5",
+        "source_binding": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/giroux2022/disease/draw2/lora/RUN.json",
+        "source_binding_sha256": "f0c51a5cb7a719af70376a5a6bc23af7ef57514698aec7fb6cfe22f49aeedc23",
+        "condition_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw2/test_raw.npz",
+        "condition_sha256": "fedb8e8039576499367bfec5479e15b4bac720126d8c5d7412d1d12f85531c28",
+        "checkpoint_sha256": "0a84ab6c8c78762ba3cca12894bd394d946d48b130e984793f0f01ad6ef6971d",
+        "support_sha256": "c9ac2355733aaf62165d452aaa3f2a4ee95874fc15e983c8c06cec01a9b0abb5"
+      },
+      "x4_summary_sha256": "0b94b69a178c5e8273ef302cb73d9d067c5640eac7e567587fa40e81e220b74d",
+      "same_support_test_condition_seed_hyperparameters": true,
+      "same_reference_annotation_contrast_gene_exclusion": true
+    },
+    {
+      "draw": 3,
+      "x1_binding": {
+        "arm": "lora",
+        "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw3/lora.npz",
+        "npz_sha256": "1f26bffd0b34659c337325923cf6d80184bf3778d601eea5ab6b3c72ee4bedba",
+        "receipt": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw3/lora.log",
+        "receipt_sha256": "85def6250b9f4e30574cdd7036a7a9ef4cee8a6884ceda01fcea7fffbdd4f976",
+        "source_binding": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/giroux2022/disease/draw3/lora/RUN.json",
+        "source_binding_sha256": "e6ab75be5e885ba03ff9e4f3289f2e4cbc488ce40fb430bcf6f57ce713ecbbf3",
+        "condition_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw3/test_raw.npz",
+        "condition_sha256": "4efbb07e4fe684710ed219d75c9a15685f617c761e2401541613e3e424146823",
+        "checkpoint_sha256": "33ea05fe24a8bcf81a13b09be5b354f60e63a8ef542d0db775dc8f0a8b665ae3",
+        "support_sha256": "6e7e31e9963228d5a291268fad234c49a14e285b7afa181e57d8d66d80195a15"
+      },
+      "x4_summary_sha256": "9344c11223adaf0ee3c86c7d18b505cb391bd454788166c39e16574d6e6e0325",
+      "same_support_test_condition_seed_hyperparameters": true,
+      "same_reference_annotation_contrast_gene_exclusion": true
+    },
+    {
+      "draw": 4,
+      "x1_binding": {
+        "arm": "lora",
+        "npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw4/lora.npz",
+        "npz_sha256": "7dc39e3963038c6e4c41d2681b5be1135bce425de1514732c4b91af899249afc",
+        "receipt": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/generated/giroux2022/disease/draw4/lora.log",
+        "receipt_sha256": "986e4876a6b229da8e23539f432e50c6dd5f6f3d69a45c7d52f13add9aa53149",
+        "source_binding": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/runs/giroux2022/disease/draw4/lora/RUN.json",
+        "source_binding_sha256": "237e2b577cc2fd6f634a0eb4681896c6b3fdcd4157e0406ed1818193a76f773b",
+        "condition_npz": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/data/giroux2022/disease/draw4/test_raw.npz",
+        "condition_sha256": "1339e7631cd54c77bef770b2248bdc2ca560a6dc70e244ed61cd4d38a835bf3f",
+        "checkpoint_sha256": "ccd39f782235579aae57cd576348a44f26f57e5c62d068b5d2554a6e87c68ea4",
+        "support_sha256": "df74fb20effc23b7784248bf76e32951803075e492251168f3d5f83dfdec81ea"
+      },
+      "x4_summary_sha256": "18ba680a703f5cb2bf65daa27d7877e88ed50d8508b2ef0593fd4af03f5f22b2",
+      "same_support_test_condition_seed_hyperparameters": true,
+      "same_reference_annotation_contrast_gene_exclusion": true
+    }
+  ],
+  "gpu_operations": 0,
+  "inference": "Overlapping support draws; descriptive means, not independent replicates or significance."
+}

paper-releases/pbisc-diffusion/updates/20261015T065710Z-giroux-width-comparison/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/recoveries/giroux_width_comparison_20261015/validator_fix.py

@@ -0,0 +1,24 @@
+"""Exact, hash-bound checkpoint alias support. Frozen scorer is not modified."""
+from pathlib import Path
+import json,inspect,hashlib
+R=Path(__file__).resolve().parent
+
+def matches(receipt,meta,checkpoint,checkpoint_sha,proof):
+ if receipt.get('checkpoint_sha256')!=checkpoint_sha or meta.get('checkpoint_sha256')!=checkpoint_sha:return False
+ allowed={str(checkpoint)}
+ if str(checkpoint)==proof['canonical'] and checkpoint_sha==proof['sha256'] and proof['both_file_hashes_verified']:
+  allowed.add(proof['remote_resolved'])
+ return receipt.get('checkpoint') in allowed and meta.get('checkpoint') in allowed
+
+def install(module):
+ proof=json.loads((R/'CHECKPOINT_ALIAS_PROOF.json').read_text())
+ assert hashlib.sha256(Path(module.__file__).read_bytes()).hexdigest()==proof['original_validator_sha256']
+ with Path(proof['canonical']).open('rb') as f:assert hashlib.file_digest(f,'sha256').hexdigest()==proof['sha256']
+ old='''receipt.get("checkpoint") != str(checkpoint) or
+                              receipt.get("checkpoint_sha256") != checkpoint_sha or
+                              meta.get("checkpoint") != str(checkpoint) or
+                              meta.get("checkpoint_sha256") != checkpoint_sha'''
+ source=inspect.getsource(module.validate_generation_arm);assert source.count(old)==1
+ source=source.replace(old,'not _verified_checkpoint_match(receipt, meta, checkpoint, checkpoint_sha)')
+ module.__dict__['_verified_checkpoint_match']=lambda r,m,c,h:matches(r,m,c,h,proof)
+ exec(compile(source,str(R/'validator_fix.py'),'exec'),module.__dict__)