PoorOtterBob commited on
Commit
69dad2c
·
verified ·
1 Parent(s): 854b447

Upload AutOmicScience foundation model repository metadata

Browse files
Files changed (2) hide show
  1. README.md +26 -0
  2. asset-manifest.json +296 -0
README.md ADDED
@@ -0,0 +1,26 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ---
2
+ license: other
3
+ library_name: automic-science
4
+ tags:
5
+ - biology
6
+ - bioinformatics
7
+ - single-cell
8
+ - omics
9
+ - foundation-model
10
+ ---
11
+
12
+ # AutOmicScience Foundation Models
13
+
14
+ Optional foundation-model checkpoints for AutOmicScience (AOS).
15
+
16
+ These assets are not required for the core CLI, UI, tests, or tiny Bio MAS smoke checks. Download them only for production Bio MAS workflows that need foundation-model adapters.
17
+
18
+ ## Install
19
+
20
+ ```bash
21
+ hf download PoorOtterBob/AutOmicScience-FoundationModels \
22
+ --repo-type model \
23
+ --local-dir src/bridge/runtime/checkpoints/foundation_models
24
+ ```
25
+
26
+ See `README.md` and `HUGGINGFACE_ASSETS.md` in the GitHub repository for environment variables and GPU safety notes.
asset-manifest.json ADDED
@@ -0,0 +1,296 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "repo_id": "PoorOtterBob/AutOmicScience-FoundationModels",
3
+ "repo_type": "model",
4
+ "generated_at": "2026-05-26T01:58:55.292Z",
5
+ "sha256_included": false,
6
+ "total_files": 57,
7
+ "total_bytes": 47644672174,
8
+ "missing_source_roots": [],
9
+ "files": [
10
+ {
11
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
12
+ "path_in_repo": "geneformer/Geneformer_code_only/config.json",
13
+ "bytes": 591
14
+ },
15
+ {
16
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
17
+ "path_in_repo": "geneformer/Geneformer_code_only/geneformer/gene_median_dictionary_gc104M.pkl",
18
+ "bytes": 1512661
19
+ },
20
+ {
21
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
22
+ "path_in_repo": "geneformer/Geneformer_code_only/geneformer/gene_name_id_dict_gc104M.pkl",
23
+ "bytes": 1660882
24
+ },
25
+ {
26
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
27
+ "path_in_repo": "geneformer/Geneformer_code_only/geneformer/token_dictionary_gc104M.pkl",
28
+ "bytes": 425590
29
+ },
30
+ {
31
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
32
+ "path_in_repo": "geneformer/model.safetensors",
33
+ "bytes": 1265455076
34
+ },
35
+ {
36
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
37
+ "path_in_repo": "kukanja_finetuned/Kukanja_EAE/checkpoints/uce_freeze_mouse_s3028/best_model.pth",
38
+ "bytes": 3456528659
39
+ },
40
+ {
41
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
42
+ "path_in_repo": "kukanja_finetuned/Kukanja_EAE/checkpoints/uce_freeze_mouse_s3028/test_features.npz",
43
+ "bytes": 257050497
44
+ },
45
+ {
46
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
47
+ "path_in_repo": "kukanja_finetuned/Kukanja_EAE/checkpoints/uce_full_mouse_s3028/best_model.pth",
48
+ "bytes": 3456528659
49
+ },
50
+ {
51
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
52
+ "path_in_repo": "kukanja_finetuned/Kukanja_EAE/checkpoints/uce_full_mouse_s3028/test_features.npz",
53
+ "bytes": 257118885
54
+ },
55
+ {
56
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
57
+ "path_in_repo": "kukanja_finetuned/Kukanja_MS/checkpoints/geneformer_freeze_s3028/best_model.pth",
58
+ "bytes": 1303103393
59
+ },
60
+ {
61
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
62
+ "path_in_repo": "kukanja_finetuned/Kukanja_MS/checkpoints/geneformer_freeze_s3028/test_features.npz",
63
+ "bytes": 1064481204
64
+ },
65
+ {
66
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
67
+ "path_in_repo": "kukanja_finetuned/Kukanja_MS/checkpoints/geneformer_full_s3028/best_model.pth",
68
+ "bytes": 1303103393
69
+ },
70
+ {
71
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
72
+ "path_in_repo": "kukanja_finetuned/Kukanja_MS/checkpoints/geneformer_full_s3028/test_features.npz",
73
+ "bytes": 1062018138
74
+ },
75
+ {
76
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
77
+ "path_in_repo": "kukanja_finetuned/Kukanja_MS/checkpoints/scgpt_freeze_human_s3028/best_model.pth",
78
+ "bytes": 214014819
79
+ },
80
+ {
81
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
82
+ "path_in_repo": "kukanja_finetuned/Kukanja_MS/checkpoints/scgpt_freeze_human_s3028/test_features.npz",
83
+ "bytes": 473874197
84
+ },
85
+ {
86
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
87
+ "path_in_repo": "kukanja_finetuned/Kukanja_MS/checkpoints/scgpt_full_human_s3028/best_model.pth",
88
+ "bytes": 214014819
89
+ },
90
+ {
91
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
92
+ "path_in_repo": "kukanja_finetuned/Kukanja_MS/checkpoints/scgpt_full_human_s3028/test_features.npz",
93
+ "bytes": 473893370
94
+ },
95
+ {
96
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
97
+ "path_in_repo": "kukanja_finetuned/Kukanja_MS/checkpoints/uce_freeze_human_s3028/best_model.pth",
98
+ "bytes": 3456483283
99
+ },
100
+ {
101
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
102
+ "path_in_repo": "kukanja_finetuned/Kukanja_MS/checkpoints/uce_freeze_human_s3028/test_features.npz",
103
+ "bytes": 1183205697
104
+ },
105
+ {
106
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
107
+ "path_in_repo": "kukanja_finetuned/Kukanja_MS/checkpoints/uce_full_human_s3028/best_model.pth",
108
+ "bytes": 3456483283
109
+ },
110
+ {
111
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
112
+ "path_in_repo": "kukanja_finetuned/Kukanja_MS/checkpoints/uce_full_human_s3028/test_features.npz",
113
+ "bytes": 1183526804
114
+ },
115
+ {
116
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
117
+ "path_in_repo": "kukanja_finetuned/main_nicheformer.py",
118
+ "bytes": 4092
119
+ },
120
+ {
121
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
122
+ "path_in_repo": "nicheformer/gene_name_id_dict_gc104M.pkl",
123
+ "bytes": 1660882
124
+ },
125
+ {
126
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
127
+ "path_in_repo": "nicheformer/merfish_mean_script.npy",
128
+ "bytes": 162608
129
+ },
130
+ {
131
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
132
+ "path_in_repo": "nicheformer/model.h5ad",
133
+ "bytes": 1066912
134
+ },
135
+ {
136
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
137
+ "path_in_repo": "nicheformer/nicheformer.ckpt",
138
+ "bytes": 572217913
139
+ },
140
+ {
141
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
142
+ "path_in_repo": "scANVI/SEA_AD_MTP_ST/checkpoints/s3028/scanvi_class/model.pt",
143
+ "bytes": 28855255
144
+ },
145
+ {
146
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
147
+ "path_in_repo": "scgpt/brain/args.json",
148
+ "bytes": 1043
149
+ },
150
+ {
151
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
152
+ "path_in_repo": "scgpt/brain/best_model.pt",
153
+ "bytes": 205385258
154
+ },
155
+ {
156
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
157
+ "path_in_repo": "scgpt/brain/vocab.json",
158
+ "bytes": 1317639
159
+ },
160
+ {
161
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
162
+ "path_in_repo": "scgpt/human/args.json",
163
+ "bytes": 1300
164
+ },
165
+ {
166
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
167
+ "path_in_repo": "scgpt/human/best_model.pt",
168
+ "bytes": 205385258
169
+ },
170
+ {
171
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
172
+ "path_in_repo": "scgpt/human/vocab.json",
173
+ "bytes": 1317639
174
+ },
175
+ {
176
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
177
+ "path_in_repo": "sklearn_baselines/lr/SEA_AD_MTP_ST/checkpoints/class_model.pkl",
178
+ "bytes": 4271
179
+ },
180
+ {
181
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
182
+ "path_in_repo": "sklearn_baselines/lr/SEA_AD_MTP_ST/checkpoints/subclass_model.pkl",
183
+ "bytes": 28119
184
+ },
185
+ {
186
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
187
+ "path_in_repo": "sklearn_baselines/lr/SEA_AD_MTP_ST/checkpoints/supertype_model.pkl",
188
+ "bytes": 156495
189
+ },
190
+ {
191
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
192
+ "path_in_repo": "sklearn_baselines/svm/SEA_AD_MTP_ST/checkpoints/class_model.pkl",
193
+ "bytes": 13243
194
+ },
195
+ {
196
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
197
+ "path_in_repo": "sklearn_baselines/svm/SEA_AD_MTP_ST/checkpoints/subclass_model.pkl",
198
+ "bytes": 88995
199
+ },
200
+ {
201
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
202
+ "path_in_repo": "sklearn_baselines/svm/SEA_AD_MTP_ST/checkpoints/supertype_model.pkl",
203
+ "bytes": 496715
204
+ },
205
+ {
206
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
207
+ "path_in_repo": "sklearn_baselines/xgboost/SEA_AD_MTP_ST/checkpoints/class_model.pkl",
208
+ "bytes": 4414218
209
+ },
210
+ {
211
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
212
+ "path_in_repo": "sklearn_baselines/xgboost/SEA_AD_MTP_ST/checkpoints/subclass_model.pkl",
213
+ "bytes": 33810521
214
+ },
215
+ {
216
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
217
+ "path_in_repo": "sklearn_baselines/xgboost/SEA_AD_MTP_ST/checkpoints/supertype_model.pkl",
218
+ "bytes": 160796181
219
+ },
220
+ {
221
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
222
+ "path_in_repo": "spatial_gnn/SEA_AD_MTP_ST/checkpoints/k15_gcn2_h256_z128_s3028/best_model.pth",
223
+ "bytes": 1378101
224
+ },
225
+ {
226
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
227
+ "path_in_repo": "spatial_gnn/SEA_AD_MTP_ST/checkpoints/k15_gcn2_h256_z128_s3028/test_features.npz",
228
+ "bytes": 196098571
229
+ },
230
+ {
231
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
232
+ "path_in_repo": "uce_33l/33l_8ep_1024t_1280.torch",
233
+ "bytes": 2985072640
234
+ },
235
+ {
236
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
237
+ "path_in_repo": "uce_33l/4layer_model.torch",
238
+ "bytes": 3403514339
239
+ },
240
+ {
241
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
242
+ "path_in_repo": "uce_33l/all_tokens.torch",
243
+ "bytes": 2979205876
244
+ },
245
+ {
246
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
247
+ "path_in_repo": "uce_33l/species_chrom.csv",
248
+ "bytes": 4097781
249
+ },
250
+ {
251
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
252
+ "path_in_repo": "uce_33l/species_offsets.pkl",
253
+ "bytes": 139
254
+ },
255
+ {
256
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
257
+ "path_in_repo": "uce_4l/4layer_model.torch",
258
+ "bytes": 3403514339
259
+ },
260
+ {
261
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
262
+ "path_in_repo": "uce_4l/all_tokens.torch",
263
+ "bytes": 2979205876
264
+ },
265
+ {
266
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
267
+ "path_in_repo": "uce_4l/species_chrom.csv",
268
+ "bytes": 4097781
269
+ },
270
+ {
271
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
272
+ "path_in_repo": "uce_4l/species_offsets.pkl",
273
+ "bytes": 139
274
+ },
275
+ {
276
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
277
+ "path_in_repo": "uce/4layer_model.torch",
278
+ "bytes": 3403514339
279
+ },
280
+ {
281
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
282
+ "path_in_repo": "uce/all_tokens.torch",
283
+ "bytes": 2979205876
284
+ },
285
+ {
286
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
287
+ "path_in_repo": "uce/species_chrom.csv",
288
+ "bytes": 4097781
289
+ },
290
+ {
291
+ "source_root": "src/bridge/runtime/checkpoints/foundation_models",
292
+ "path_in_repo": "uce/species_offsets.pkl",
293
+ "bytes": 139
294
+ }
295
+ ]
296
+ }