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/draw1/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/draw1/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/scsemi/ye2026_sepsis/disease/draw1/adopted_legacy/run_manifest.json +213 -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/scsemi_project/models/fast_reconst1_HC12.receipt.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/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/draw1/adopted_legacy/prepared.json
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{
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"files": {
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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/run_manifest.json
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| 23 |
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| 131 |
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"k": 15
|
| 132 |
+
},
|
| 133 |
+
"representatives": "fixed: every usable row of the split's training donors (no active learning)",
|
| 134 |
+
"assignment": "upstream representative_selection.update_membership: nearest representative by Euclidean distance in processed_bulkdata.obsm['X_pca'] (initsetup PCA of log1p CP10K real bulk)",
|
| 135 |
+
"pretrain1": {
|
| 136 |
+
"vaesteps": 100,
|
| 137 |
+
"gansteps": 100,
|
| 138 |
+
"lr": 0.001,
|
| 139 |
+
"k": 15,
|
| 140 |
+
"diagw": 1
|
| 141 |
+
},
|
| 142 |
+
"pretrain2": {
|
| 143 |
+
"vaesteps": 50,
|
| 144 |
+
"gansteps": 50,
|
| 145 |
+
"lr": 0.0001,
|
| 146 |
+
"k": 15,
|
| 147 |
+
"diagw": 1.0
|
| 148 |
+
},
|
| 149 |
+
"infer": {
|
| 150 |
+
"bulktype": "real",
|
| 151 |
+
"pseudocount": 0.1,
|
| 152 |
+
"lr": 0.0002,
|
| 153 |
+
"epochs": 150,
|
| 154 |
+
"ministages": 5,
|
| 155 |
+
"k": 15,
|
| 156 |
+
"diagw": 1.0
|
| 157 |
+
},
|
| 158 |
+
"seeds": {
|
| 159 |
+
"base": 20260927,
|
| 160 |
+
"pretrain1": "base + 1000 + bulk row index",
|
| 161 |
+
"pretrain2": "base + 2000 + bulk row index",
|
| 162 |
+
"target": "base + bulk row index (frozen campaign rule)"
|
| 163 |
+
},
|
| 164 |
+
"output_unit": "normalized_expression (upstream fast_semi output: ZINB mean, rep-cell library, values <= 10 zeroed)",
|
| 165 |
+
"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)",
|
| 166 |
+
"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"
|
| 167 |
+
},
|
| 168 |
+
"inputs": {
|
| 169 |
+
"bulk.h5ad": "f534e3c2e8c9b656949a5f3ca5eb5f09f96958a3216d71343467f8c7f1594b1c",
|
| 170 |
+
"rep_sc.h5ad": "af8062499869e3bff21d12a5772982b86e9c37db8e4b9a7f43d73b32c0248655"
|
| 171 |
+
},
|
| 172 |
+
"source": {
|
| 173 |
+
"repository": "https://github.com/mcgilldinglab/scSemiProfiler",
|
| 174 |
+
"commit": "c2aea021188759e56ecf14578915c0237aaa75d2",
|
| 175 |
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"compatibility_patch_sha256": "314d353002ffb482b4ed4b61a32b280a50ff8b6a9933512ada9fdc74c17b1711",
|
| 176 |
+
"changes": [
|
| 177 |
+
"remove unused scvi.nn.one_hot import",
|
| 178 |
+
"translate legacy use_gpu to accelerator/devices",
|
| 179 |
+
"avoid empty slice when geneset_len is zero",
|
| 180 |
+
"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"
|
| 181 |
+
],
|
| 182 |
+
"files": {
|
| 183 |
+
"scSemiProfiler/__init__.py": "4ee4e83fcd8456510c5cc44bb1eb2386894a51bcbab07a8308a804b07d85d856",
|
| 184 |
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"scSemiProfiler/fast_generator.py": "1e384ec831461748c095b8c2fa2d57fee1a86758c4d832e6e0926f8f6c47ad8f",
|
| 185 |
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"scSemiProfiler/get_eg_representatives.py": "f63ca0d6763546bbb3d7ec849254a6d4652d6c1a4063794b9c690be86f0a124c",
|
| 186 |
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"scSemiProfiler/inference.py": "88997c6bf752d6c939ef527a0c9cfcf24065076faf204d84cf64cff5f0282d39",
|
| 187 |
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"scSemiProfiler/initial_setup.py": "9f97b5cd0b7222bca234b4283f16147baf48b6a9baa3407a851301f1d6da6518",
|
| 188 |
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"scSemiProfiler/oldinference.py": "61f026515f6307de4823b96abfdb0352f4c06f1b4ad08cfc1909f67b6db8aa00",
|
| 189 |
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"scSemiProfiler/representative_selection.py": "9dae94b83ebbe3ffff6fe2daddaf480bff4d183ab6fcdc76c844d89c1de462cf",
|
| 190 |
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"scSemiProfiler/singlecell_process.py": "512e0a2dd6f613175512dcecdcad2eb045bf9267b044020a7eff0d6d8393377a",
|
| 191 |
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"scSemiProfiler/utils.py": "0a864ea2f202eda428c65c69400ebc93d981ce82a39cfe773db12ec5670d74af",
|
| 192 |
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"scSemiProfiler/vaegan.py": "5d8d6638616ae29b443c5c95ed4664c3cf2b8f0f040d2e502f3c9d6157615e23"
|
| 193 |
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},
|
| 194 |
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"previous_manifest_sha256": "229f8a7070d49972a51430ed88a2ad604d85513cfda05c1d124a4e53a4aa0636"
|
| 195 |
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},
|
| 196 |
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"environment": {
|
| 197 |
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"torch": "2.11.0+cu130",
|
| 198 |
+
"scvi-tools": "1.4.1",
|
| 199 |
+
"scanpy": "1.11.5",
|
| 200 |
+
"anndata": "0.12.19",
|
| 201 |
+
"lightning": "2.6.6",
|
| 202 |
+
"numpy": "2.5.3",
|
| 203 |
+
"scikit-learn": "1.9.1",
|
| 204 |
+
"faiss-cpu": "1.12.0",
|
| 205 |
+
"gseapy": "1.3.0"
|
| 206 |
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},
|
| 207 |
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"wrapper_sha256": "330895e166241c2e0545178759a1fd340d1218890dbf99d4887bdd080ba08745",
|
| 208 |
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"lean_cellgraph_sha256": "0de823e4475786fcd86c0fb83302182ffebafe00a1dad44cdcccc99938430230",
|
| 209 |
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"geneset_mapped_gmt_sha256": "9c4386ac1ff666fc88301e126f1a1c6452122c6b63f311131a640bffe9c4d84b"
|
| 210 |
+
}
|
| 211 |
+
}
|
| 212 |
+
]
|
| 213 |
+
}
|
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/scsemi_project/models/fast_reconst1_HC12.receipt.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"run_signature": "8f40a903eb189eaeeb0becd8d8844d4831498b82d787a254a034bfbe611d0a9a",
|
| 3 |
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"sha256": "8a14e9060b42f71d17f0c310ed1ffbecb768e8edc0666500e1a24bb2a3a0a8bb",
|
| 4 |
+
"stage": 1,
|
| 5 |
+
"representative": "HC12",
|
| 6 |
+
"seed": 20261953,
|
| 7 |
+
"elapsed_seconds": 108.97139015400899,
|
| 8 |
+
"code_signature": "9d81fd0122fda71680d8bb75481dd3d4495f31eec7c316e6fed16dd28dcc220e",
|
| 9 |
+
"device": "cuda:0",
|
| 10 |
+
"complete": true
|
| 11 |
+
}
|