junidude14 commited on
Commit
50b703e
·
verified ·
1 Parent(s): 90f631f

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 ADDED
The diff for this file is too large to render. See raw diff
 
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 ADDED
@@ -0,0 +1,24 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "run_signature": "8f40a903eb189eaeeb0becd8d8844d4831498b82d787a254a034bfbe611d0a9a",
3
+ "seconds": 40.1,
4
+ "files": {
5
+ "processed_bulkdata.h5ad": "338d1cbc197a436f1f6af194e0b954c6378b0db980547c6afdddcc2f144038a1",
6
+ "hvgenes.npy": "a7a9391c586345bd4b3256fa49f9306a83d0b0a67782f38d8e7cc45ac88bd904",
7
+ "sids.txt": "c588aba0674f666b60a23bc105e85757e794ad756a2e896aff8b448f32a70bab",
8
+ "hvset.npy": "0788938ab62fd0005871ae1790e1af7c146cc27e64174d71e65522ed556fe54f",
9
+ "hvmask.npy": "c9041ba160d58c351da2151f461fdb6171042966c1dbc72c32b71f39b03442a8",
10
+ "status/init_representatives.txt": "ea160f6608452bdde1eae18706e8907c15ebc2a0af78aee0e8b15e6ae7f3dffe",
11
+ "status/init_cluster_labels.txt": "58597b7f0dbff4780efd97559354c92fa0d08d438f5a3ed2bcad11d0a8b1f2f5",
12
+ "sample_sc/HC12.h5ad": "4e37260d6162cb5c06de8ae99e38ddd2a648d4c67232843be7ab0d14d4a5bf08",
13
+ "sample_sc/Res-S164.h5ad": "0c231a0bb3bfb5a261c500af6e0535846c971a73bfe4ed68e5edcb92d006dafb",
14
+ "sample_sc/Res-S166.h5ad": "65b92a41dea7185fb815ad05bc13f26526163952bd6912c2b976fcc6e38dea6e",
15
+ "sample_sc/Uri-S134.h5ad": "0ddda74bc9b558cb6565e1d7d44bcad7154d0bf4568197e6e3858da5d1c9adb0",
16
+ "sample_sc/Uri-S147.h5ad": "cf7986ee4e87453560711870f6fc8479f2cbd958141b4ca1295cf7edf39cfa22",
17
+ "geneset_scores/HC12.npy": "41e3b7bc44cd66e6b45453d6567894f7ef4722a1058f13a4e53f490e8e667505",
18
+ "geneset_scores/Res-S164.npy": "8749921fc466b3295be82584ff77b9cde39b727cd7d27d1cdaa8497e5fe62a7b",
19
+ "geneset_scores/Res-S166.npy": "a2b0241fd09a0cfaaba82fa6dff98b6ad56a3f06a8687a35db29863c7efa3ee6",
20
+ "geneset_scores/Uri-S134.npy": "85f7a32df9a9e24c5f126f32ab638953272a93d9bdc101823278aad4987e1c67",
21
+ "geneset_scores/Uri-S147.npy": "8ecfc9c72f5d01c597d7f0f33bfc325e81de9e826f474c16b92868c5016d2f76"
22
+ },
23
+ "genesets_gmt_sha256": "9c4386ac1ff666fc88301e126f1a1c6452122c6b63f311131a640bffe9c4d84b"
24
+ }
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 ADDED
@@ -0,0 +1,213 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "run_signature": "8f40a903eb189eaeeb0becd8d8844d4831498b82d787a254a034bfbe611d0a9a",
3
+ "protocol": {
4
+ "method": "scSemiProfiler",
5
+ "setting": "paired_fixed_representatives_realbulk_genesets",
6
+ "upstream_commit": "c2aea021188759e56ecf14578915c0237aaa75d2",
7
+ "initsetup": {
8
+ "logged": false,
9
+ "normed": false,
10
+ "geneselection": false,
11
+ "batch": 1
12
+ },
13
+ "scprocess": {
14
+ "logged": false,
15
+ "normed": false,
16
+ "cellfilter": false,
17
+ "threshold": 0.001,
18
+ "geneset": true,
19
+ "weight": 0.5,
20
+ "k": 15
21
+ },
22
+ "representatives": "fixed: every usable row of the split's training donors (no active learning)",
23
+ "assignment": "upstream representative_selection.update_membership: nearest representative by Euclidean distance in processed_bulkdata.obsm['X_pca'] (initsetup PCA of log1p CP10K real bulk)",
24
+ "pretrain1": {
25
+ "vaesteps": 100,
26
+ "gansteps": 100,
27
+ "lr": 0.001,
28
+ "k": 15,
29
+ "diagw": 1
30
+ },
31
+ "pretrain2": {
32
+ "vaesteps": 50,
33
+ "gansteps": 50,
34
+ "lr": 0.0001,
35
+ "k": 15,
36
+ "diagw": 1.0
37
+ },
38
+ "infer": {
39
+ "bulktype": "real",
40
+ "pseudocount": 0.1,
41
+ "lr": 0.0002,
42
+ "epochs": 150,
43
+ "ministages": 5,
44
+ "k": 15,
45
+ "diagw": 1.0
46
+ },
47
+ "seeds": {
48
+ "base": 20260927,
49
+ "pretrain1": "base + 1000 + bulk row index",
50
+ "pretrain2": "base + 2000 + bulk row index",
51
+ "target": "base + bulk row index (frozen campaign rule)"
52
+ },
53
+ "output_unit": "normalized_expression (upstream fast_semi output: ZINB mean, rep-cell library, values <= 10 zeroed)",
54
+ "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)",
55
+ "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"
56
+ },
57
+ "inputs": {
58
+ "bulk.h5ad": "f534e3c2e8c9b656949a5f3ca5eb5f09f96958a3216d71343467f8c7f1594b1c",
59
+ "rep_sc.h5ad": "af8062499869e3bff21d12a5772982b86e9c37db8e4b9a7f43d73b32c0248655"
60
+ },
61
+ "source": {
62
+ "repository": "https://github.com/mcgilldinglab/scSemiProfiler",
63
+ "commit": "c2aea021188759e56ecf14578915c0237aaa75d2",
64
+ "compatibility_patch_sha256": "e9a97451cedfda3ed3da9a6dd6dfd48861bc9301316b259abea158367624c338",
65
+ "changes": [
66
+ "remove unused scvi.nn.one_hot import",
67
+ "translate legacy use_gpu to accelerator/devices",
68
+ "avoid empty slice when geneset_len is zero"
69
+ ],
70
+ "files": {
71
+ "scSemiProfiler/__init__.py": "4ee4e83fcd8456510c5cc44bb1eb2386894a51bcbab07a8308a804b07d85d856",
72
+ "scSemiProfiler/fast_generator.py": "1e384ec831461748c095b8c2fa2d57fee1a86758c4d832e6e0926f8f6c47ad8f",
73
+ "scSemiProfiler/get_eg_representatives.py": "f63ca0d6763546bbb3d7ec849254a6d4652d6c1a4063794b9c690be86f0a124c",
74
+ "scSemiProfiler/inference.py": "88997c6bf752d6c939ef527a0c9cfcf24065076faf204d84cf64cff5f0282d39",
75
+ "scSemiProfiler/initial_setup.py": "9f97b5cd0b7222bca234b4283f16147baf48b6a9baa3407a851301f1d6da6518",
76
+ "scSemiProfiler/oldinference.py": "61f026515f6307de4823b96abfdb0352f4c06f1b4ad08cfc1909f67b6db8aa00",
77
+ "scSemiProfiler/representative_selection.py": "9dae94b83ebbe3ffff6fe2daddaf480bff4d183ab6fcdc76c844d89c1de462cf",
78
+ "scSemiProfiler/singlecell_process.py": "512e0a2dd6f613175512dcecdcad2eb045bf9267b044020a7eff0d6d8393377a",
79
+ "scSemiProfiler/utils.py": "0a864ea2f202eda428c65c69400ebc93d981ce82a39cfe773db12ec5670d74af",
80
+ "scSemiProfiler/vaegan.py": "e847bf9d0739214940e136db5c1bb4c02a15af497136e2db087763124ae4193f"
81
+ }
82
+ },
83
+ "environment": {
84
+ "torch": "2.11.0+cu130",
85
+ "scvi-tools": "1.4.1",
86
+ "scanpy": "1.11.5",
87
+ "anndata": "0.12.19",
88
+ "lightning": "2.6.6",
89
+ "numpy": "2.5.3",
90
+ "scikit-learn": "1.9.1",
91
+ "faiss-cpu": "1.12.0",
92
+ "gseapy": "1.3.0"
93
+ },
94
+ "wrapper_sha256": "1962c774189adb7dd9442d70445c8dcf5f763dec4fe5a48076d4bcd78adf1b03",
95
+ "lean_cellgraph_sha256": "0de823e4475786fcd86c0fb83302182ffebafe00a1dad44cdcccc99938430230",
96
+ "geneset_mapped_gmt_sha256": "9c4386ac1ff666fc88301e126f1a1c6452122c6b63f311131a640bffe9c4d84b",
97
+ "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/draw1",
98
+ "hostname": "spark-fa6b",
99
+ "migrations": [
100
+ {
101
+ "at": "2026-09-28T21:24:19.585341+00:00",
102
+ "host": "spark-fa6b",
103
+ "from_code_signature": "8f40a903eb189eaeeb0becd8d8844d4831498b82d787a254a034bfbe611d0a9a",
104
+ "to_code_signature": "9d81fd0122fda71680d8bb75481dd3d4495f31eec7c316e6fed16dd28dcc220e",
105
+ "changed": [
106
+ "source",
107
+ "wrapper_sha256"
108
+ ],
109
+ "transitions": [
110
+ "trailing_size1_batch_20260928",
111
+ "wrapper_migration_support_20260928"
112
+ ],
113
+ "to_binding": {
114
+ "protocol": {
115
+ "method": "scSemiProfiler",
116
+ "setting": "paired_fixed_representatives_realbulk_genesets",
117
+ "upstream_commit": "c2aea021188759e56ecf14578915c0237aaa75d2",
118
+ "initsetup": {
119
+ "logged": false,
120
+ "normed": false,
121
+ "geneselection": false,
122
+ "batch": 1
123
+ },
124
+ "scprocess": {
125
+ "logged": false,
126
+ "normed": false,
127
+ "cellfilter": false,
128
+ "threshold": 0.001,
129
+ "geneset": true,
130
+ "weight": 0.5,
131
+ "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
+ "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
+ "scSemiProfiler/fast_generator.py": "1e384ec831461748c095b8c2fa2d57fee1a86758c4d832e6e0926f8f6c47ad8f",
185
+ "scSemiProfiler/get_eg_representatives.py": "f63ca0d6763546bbb3d7ec849254a6d4652d6c1a4063794b9c690be86f0a124c",
186
+ "scSemiProfiler/inference.py": "88997c6bf752d6c939ef527a0c9cfcf24065076faf204d84cf64cff5f0282d39",
187
+ "scSemiProfiler/initial_setup.py": "9f97b5cd0b7222bca234b4283f16147baf48b6a9baa3407a851301f1d6da6518",
188
+ "scSemiProfiler/oldinference.py": "61f026515f6307de4823b96abfdb0352f4c06f1b4ad08cfc1909f67b6db8aa00",
189
+ "scSemiProfiler/representative_selection.py": "9dae94b83ebbe3ffff6fe2daddaf480bff4d183ab6fcdc76c844d89c1de462cf",
190
+ "scSemiProfiler/singlecell_process.py": "512e0a2dd6f613175512dcecdcad2eb045bf9267b044020a7eff0d6d8393377a",
191
+ "scSemiProfiler/utils.py": "0a864ea2f202eda428c65c69400ebc93d981ce82a39cfe773db12ec5670d74af",
192
+ "scSemiProfiler/vaegan.py": "5d8d6638616ae29b443c5c95ed4664c3cf2b8f0f040d2e502f3c9d6157615e23"
193
+ },
194
+ "previous_manifest_sha256": "229f8a7070d49972a51430ed88a2ad604d85513cfda05c1d124a4e53a4aa0636"
195
+ },
196
+ "environment": {
197
+ "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
+ },
207
+ "wrapper_sha256": "330895e166241c2e0545178759a1fd340d1218890dbf99d4887bdd080ba08745",
208
+ "lean_cellgraph_sha256": "0de823e4475786fcd86c0fb83302182ffebafe00a1dad44cdcccc99938430230",
209
+ "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
@@ -0,0 +1,11 @@
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "run_signature": "8f40a903eb189eaeeb0becd8d8844d4831498b82d787a254a034bfbe611d0a9a",
3
+ "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
+ }