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/scsemi/ye2026_sepsis/disease/draw0/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/scsemi/ye2026_sepsis/disease/draw0/run_manifest.json +103 -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/status.json +11 -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/draw1/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/prepared.json
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{
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"run_signature": "80f20a8e0c04db617c23226c177240ff23552872f4f8f6d4cf775d436ef6b681",
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"seconds": 46.6,
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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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"hvset.npy": "cfaa2030fd9ecb492ab0449713053acc706c71d107e4f952ba9d7a5731757906",
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"hvmask.npy": "c9041ba160d58c351da2151f461fdb6171042966c1dbc72c32b71f39b03442a8",
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"status/init_representatives.txt": "5ff98883ae51376f534ea5c3419123e68bab7464330176bb97c6c0c881f837dc",
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"status/init_cluster_labels.txt": "7c28e969bb2bc06445f92102df7e2ac43d6200705f03b7c1cdf66fd6ef075509",
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"sample_sc/HC07.h5ad": "91b1b822bab799d5b568e58e8203b298824c082435775c1e9037035e11179042",
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"sample_sc/Abd-S66.h5ad": "611a106bcdf78fb387cc6bac7fa5740f9825d0c1403ab1afd397a3a53f70563e",
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| 14 |
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"sample_sc/Res-S150.h5ad": "5449096239add2bac5c7ed39d00606ebf31dee708e5cfe4ee627c9dbc48eb73e",
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"sample_sc/Skin-S74.h5ad": "c154427051db69b018de0b6c319997bfca29ce909a56ec1f8395e33884761fd3",
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| 16 |
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"sample_sc/Res-S77.h5ad": "5b6ef57ae4c80ebeadb0621a92f5202da9d9d3f7823b7e6de93729b235b98f53",
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| 17 |
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"geneset_scores/HC07.npy": "2cba207d44df1b51fdace0072f9c56fd456d953de2ea892d8cbdbc592e023f9d",
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| 18 |
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"geneset_scores/Abd-S66.npy": "535a14068075ea5c46fcefbc7fe5cb2e7d7ffd3995ff1e75afb3e72eef2db9b7",
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| 19 |
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"geneset_scores/Res-S150.npy": "6265f30900fdb69cb21ea331ce3228a4b0d507f375d9d2d3a5375d5331ab2f34",
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| 20 |
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"geneset_scores/Skin-S74.npy": "586b5a825d276fe3f99a7ff901660cf8ae3f1d4acaefba558a82b7acfa0ef499",
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| 21 |
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"geneset_scores/Res-S77.npy": "fe935dfb80325678ab54cdfbac29224964046d9c1af9fb042e213b66a1c78eca"
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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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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/run_manifest.json
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{
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"run_signature": "80f20a8e0c04db617c23226c177240ff23552872f4f8f6d4cf775d436ef6b681",
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| 3 |
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"protocol": {
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| 4 |
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"method": "scSemiProfiler",
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| 5 |
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"setting": "paired_fixed_representatives_realbulk_genesets",
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| 6 |
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"upstream_commit": "c2aea021188759e56ecf14578915c0237aaa75d2",
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"initsetup": {
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"logged": false,
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"normed": false,
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"geneselection": false,
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"batch": 1
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},
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"scprocess": {
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"logged": false,
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"normed": false,
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"cellfilter": false,
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"threshold": 0.001,
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"geneset": true,
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"weight": 0.5,
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"k": 15
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},
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"representatives": "fixed: every usable row of the split's training donors (no active learning)",
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"assignment": "upstream representative_selection.update_membership: nearest representative by Euclidean distance in processed_bulkdata.obsm['X_pca'] (initsetup PCA of log1p CP10K real bulk)",
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"pretrain1": {
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| 25 |
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"vaesteps": 100,
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| 26 |
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"gansteps": 100,
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| 27 |
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"lr": 0.001,
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"k": 15,
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"diagw": 1
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},
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| 31 |
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"pretrain2": {
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| 32 |
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"vaesteps": 50,
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| 33 |
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"gansteps": 50,
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| 34 |
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"lr": 0.0001,
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| 35 |
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"k": 15,
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| 36 |
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"diagw": 1.0
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| 37 |
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},
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| 38 |
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"infer": {
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| 39 |
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"bulktype": "real",
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| 40 |
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"pseudocount": 0.1,
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| 41 |
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"lr": 0.0002,
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| 42 |
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"epochs": 150,
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| 43 |
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"ministages": 5,
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| 44 |
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"k": 15,
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| 45 |
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"diagw": 1.0
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| 46 |
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},
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| 47 |
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"seeds": {
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| 48 |
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"base": 20260927,
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| 49 |
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"pretrain1": "base + 1000 + bulk row index",
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| 50 |
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"pretrain2": "base + 2000 + bulk row index",
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| 51 |
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"target": "base + bulk row index (frozen campaign rule)"
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| 52 |
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},
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| 53 |
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"output_unit": "normalized_expression (upstream fast_semi output: ZINB mean, rep-cell library, values <= 10 zeroed)",
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| 54 |
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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)",
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| 55 |
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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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| 56 |
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"hvset_impl": "tools/lean_hvset.cohort_hvset_lean: streamed, one representative in memory; output-identical to cohort_hvset (validation/hvset_dependence_20261002.json)"
|
| 57 |
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},
|
| 58 |
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"inputs": {
|
| 59 |
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"bulk.h5ad": "5ea6e4fefaa534d163127bc979c625ae053090947e4b51b80553d01b635c35ab",
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| 60 |
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"rep_sc.h5ad": "29d7b9354696f0e9e497427321e8fcea70fe49c7dbfcfd3fb343f7a63e25f749"
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| 61 |
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},
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| 62 |
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"source": {
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| 63 |
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"repository": "https://github.com/mcgilldinglab/scSemiProfiler",
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| 64 |
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"commit": "c2aea021188759e56ecf14578915c0237aaa75d2",
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| 65 |
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"compatibility_patch_sha256": "314d353002ffb482b4ed4b61a32b280a50ff8b6a9933512ada9fdc74c17b1711",
|
| 66 |
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"changes": [
|
| 67 |
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"remove unused scvi.nn.one_hot import",
|
| 68 |
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"translate legacy use_gpu to accelerator/devices",
|
| 69 |
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"avoid empty slice when geneset_len is zero",
|
| 70 |
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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"
|
| 71 |
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],
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| 72 |
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"files": {
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| 73 |
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"scSemiProfiler/__init__.py": "4ee4e83fcd8456510c5cc44bb1eb2386894a51bcbab07a8308a804b07d85d856",
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"scSemiProfiler/fast_generator.py": "1e384ec831461748c095b8c2fa2d57fee1a86758c4d832e6e0926f8f6c47ad8f",
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"scSemiProfiler/get_eg_representatives.py": "f63ca0d6763546bbb3d7ec849254a6d4652d6c1a4063794b9c690be86f0a124c",
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"scSemiProfiler/inference.py": "88997c6bf752d6c939ef527a0c9cfcf24065076faf204d84cf64cff5f0282d39",
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"scSemiProfiler/initial_setup.py": "9f97b5cd0b7222bca234b4283f16147baf48b6a9baa3407a851301f1d6da6518",
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"scSemiProfiler/oldinference.py": "61f026515f6307de4823b96abfdb0352f4c06f1b4ad08cfc1909f67b6db8aa00",
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| 83 |
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},
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| 84 |
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"previous_manifest_sha256": "229f8a7070d49972a51430ed88a2ad604d85513cfda05c1d124a4e53a4aa0636"
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| 85 |
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},
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| 86 |
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"environment": {
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| 87 |
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"torch": "2.11.0+cu130",
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| 88 |
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"scvi-tools": "1.4.1",
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| 89 |
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"scanpy": "1.11.5",
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| 90 |
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"anndata": "0.12.19",
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| 91 |
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"lightning": "2.6.6",
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| 92 |
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"numpy": "2.5.3",
|
| 93 |
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"scikit-learn": "1.9.1",
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| 94 |
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"faiss-cpu": "1.12.0",
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| 95 |
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"gseapy": "1.3.0"
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| 96 |
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| 97 |
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"wrapper_sha256": "24d36efb13500e9d555bcdf19976dea575f9710fd0a25c68fae836f51723fc7f",
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| 98 |
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"lean_cellgraph_sha256": "0de823e4475786fcd86c0fb83302182ffebafe00a1dad44cdcccc99938430230",
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"geneset_mapped_gmt_sha256": "9c4386ac1ff666fc88301e126f1a1c6452122c6b63f311131a640bffe9c4d84b",
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| 100 |
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"lean_hvset_sha256": "3783f6e9728c3ecdb41ec6068f15bc9bf44ff5fc25644ca0e8734c1981486e86",
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| 101 |
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"work": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paper_figures_strictpairs_20261012/scsemi/ye2026_sepsis/disease/draw0",
|
| 102 |
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"hostname": "spark-fa6b"
|
| 103 |
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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/status.json
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{
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"prepared": true,
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| 3 |
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"n_reps": 5,
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| 4 |
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"reps_pretrained": 0,
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| 5 |
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"n_targets": 77,
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| 6 |
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"targets_done": 0,
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| 7 |
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"pretrain_complete": false,
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| 8 |
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"infer_complete": false,
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| 9 |
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"run_signature": "80f20a8e0c04db617c23226c177240ff23552872f4f8f6d4cf775d436ef6b681",
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| 10 |
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"updated": "2026-10-12T12:32:10.479697+00:00"
|
| 11 |
+
}
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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/draw1/adopted_legacy/ADOPTION.json
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