Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/runs/immicro/healthy/fold0/n5/lora/history.json +7 -0
- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/scsemi/ye2026_sepsis/disease/draw0/adopted_legacy/ADOPTION.json +308 -0
- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/scsemi/ye2026_sepsis/disease/draw0/adopted_legacy/inputs/inputs_manifest.json +0 -0
- paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/scsemi/ye2026_sepsis/disease/draw0/adopted_legacy/prepared.json +24 -0
paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/runs/immicro/healthy/fold0/n5/lora/history.json
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[
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{
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"step": 0,
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"inner_val_loss": NaN,
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"train_loss": null
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}
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]
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/scsemi/ye2026_sepsis/disease/draw0/adopted_legacy/ADOPTION.json
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| 1 |
+
{
|
| 2 |
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"schema": "pbisc.scsemi.legacy-adoption-proof.v1",
|
| 3 |
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"status": "verified_source_not_native_strict_run",
|
| 4 |
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"cohort": "ye2026_sepsis",
|
| 5 |
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"unit": "draw0_n5",
|
| 6 |
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"support_sha256": "ad30daaf76d46edb695df2ae02cb67f8d8b3ae709630e8ec7ae87056258f9bda",
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| 7 |
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"source_work": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scsemi/work/ye2026_sepsis/fewshot_n5/draw0",
|
| 8 |
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"strict_work": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scsemi/ye2026_sepsis/disease/draw0",
|
| 9 |
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"source_generated": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/ye2026_sepsis/fewshot_n5/draw0/scsemi5__raw.npz",
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"changes": [
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| 20 |
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"remove unused scvi.nn.one_hot import",
|
| 21 |
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| 22 |
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|
| 23 |
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| 24 |
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"files": {
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| 44 |
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"avoid empty slice when geneset_len is zero",
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| 45 |
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"drop a size-1 trailing training batch: scvi DataSplitter(drop_last=True) only when n_obs % batch_size == 1 (upstream's own commented-out remedy); all other cell counts unchanged"
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"approved_migration": {
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|
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|
| 94 |
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"representatives": "fixed: every usable row of the split's training donors (no active learning)",
|
| 95 |
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| 96 |
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| 119 |
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|
| 126 |
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"cellgraph_impl": "tools/lean_cellgraph.fast_cellgraph_lean replaces upstream singlecell_process.fast_cellgraph inside scprocess: same arithmetic, chunked (16 GiB CPU cap); bit-identical outputs verified (validation/lean_cellgraph_*.json)",
|
| 127 |
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"scprocess_orchestration": "cohort hvset first (upstream scprocess's own steps: sorted sample_ids, normalize_total 1e4, dense, X*(X>10), getGeneSetMatrix score formula, concatenate, log1p, highly_variable_genes) -> hvset.npy; then upstream scprocess once per representative (it skips hvset when hvset.npy exists). Bit-identical to one scprocess call over all representatives (validation/prepared_*.json); peak memory is one representative"
|
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"scientific_equivalence": "same exact five representatives and target samples, same raw bulk condition, modeled genes, depth, cell counts after identity alignment, n-only HVG and all pretraining assets, protocol/seed and verified source model/shard/output receipts",
|
| 305 |
+
"provenance_limit": "legacy work was run as fewshot, not as a native strict-support run; source signature and old metadata remain unchanged",
|
| 306 |
+
"adopted_evidence_dir": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scsemi/ye2026_sepsis/disease/draw0/adopted_legacy",
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| 307 |
+
"linked_files": 190
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| 308 |
+
}
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/scsemi/ye2026_sepsis/disease/draw0/adopted_legacy/inputs/inputs_manifest.json
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paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/scsemi/ye2026_sepsis/disease/draw0/adopted_legacy/prepared.json
ADDED
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{
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"run_signature": "d76aca33242c9d7cccbe1a6b2797b7d861d05e8c19660f9beeb566de73c41585",
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"seconds": 42.2,
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"files": {
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"processed_bulkdata.h5ad": "96e76475991997c2e06fa295c283d4581ca1c2b5a8354c7b6a77a584f08ad02c",
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"hvgenes.npy": "a7a9391c586345bd4b3256fa49f9306a83d0b0a67782f38d8e7cc45ac88bd904",
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"sids.txt": "c588aba0674f666b60a23bc105e85757e794ad756a2e896aff8b448f32a70bab",
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| 8 |
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"hvset.npy": "cfaa2030fd9ecb492ab0449713053acc706c71d107e4f952ba9d7a5731757906",
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"hvmask.npy": "c9041ba160d58c351da2151f461fdb6171042966c1dbc72c32b71f39b03442a8",
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| 10 |
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"status/init_representatives.txt": "70155d90263288472c3fe700825bf0b622114728039300f4e63ae84401c33942",
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"status/init_cluster_labels.txt": "1b16e2a9634588c26b101a68774ae0fa4fa34846c6d7e87e3a8d20d1351327f6",
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| 12 |
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"sample_sc/Abd-S66.h5ad": "611a106bcdf78fb387cc6bac7fa5740f9825d0c1403ab1afd397a3a53f70563e",
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"sample_sc/HC07.h5ad": "91b1b822bab799d5b568e58e8203b298824c082435775c1e9037035e11179042",
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"sample_sc/Res-S150.h5ad": "5449096239add2bac5c7ed39d00606ebf31dee708e5cfe4ee627c9dbc48eb73e",
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"sample_sc/Res-S77.h5ad": "5b6ef57ae4c80ebeadb0621a92f5202da9d9d3f7823b7e6de93729b235b98f53",
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"sample_sc/Skin-S74.h5ad": "c154427051db69b018de0b6c319997bfca29ce909a56ec1f8395e33884761fd3",
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"geneset_scores/Abd-S66.npy": "535a14068075ea5c46fcefbc7fe5cb2e7d7ffd3995ff1e75afb3e72eef2db9b7",
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"geneset_scores/HC07.npy": "2cba207d44df1b51fdace0072f9c56fd456d953de2ea892d8cbdbc592e023f9d",
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"geneset_scores/Res-S150.npy": "6265f30900fdb69cb21ea331ce3228a4b0d507f375d9d2d3a5375d5331ab2f34",
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"geneset_scores/Res-S77.npy": "fe935dfb80325678ab54cdfbac29224964046d9c1af9fb042e213b66a1c78eca",
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"geneset_scores/Skin-S74.npy": "586b5a825d276fe3f99a7ff901660cf8ae3f1d4acaefba558a82b7acfa0ef499"
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| 22 |
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},
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| 23 |
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"genesets_gmt_sha256": "9c4386ac1ff666fc88301e126f1a1c6452122c6b63f311131a640bffe9c4d84b"
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| 24 |
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}
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