ribesstefano commited on
Commit
57c7ce8
·
verified ·
1 Parent(s): 5f1061b

Training in progress, step 5000, checkpoint

Browse files
last-checkpoint/model.safetensors CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:a2d498b6989586a4df92f1e0058ec1bced211ce2db37118da1fd2cf0da27376c
3
  size 409608164
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f676607cd0397b1f5d8459ac2d3832aa6dc942f817980077bd2b7bdb170a2299
3
  size 409608164
last-checkpoint/optimizer.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:cb16037b50c4447d44ee30bff4ea3eeccfdf9c924946a1bbbb713c2c41e61c56
3
  size 814647162
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f7d11f3a46c7c00825c3eadc2dbdf53e3b820ad724200e9c0387872d22ba4248
3
  size 814647162
last-checkpoint/rng_state.pth CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:9b2d04eddfc7b6b071b8d646acad56be885bfe31cd3f719a42e4e188063e0e48
3
  size 14244
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:6de728555fabd8cf02c37f2038f990b0194c12700f952b8a8fbf3c13da0cdf9d
3
  size 14244
last-checkpoint/scheduler.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:415f69ad45e35e2c658f3eb70a29da7d1c48b1525f93317c1722ac741ba10d64
3
  size 1192
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:850c0f67bc5e910c481d6d749e2efd06031ffcdc3209d834462db0427281420d
3
  size 1192
last-checkpoint/trainer_state.json CHANGED
@@ -1,278 +1,124 @@
1
  {
2
- "best_metric": 0.5517454706142289,
3
- "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25/trial-number=18-learning_rate=4.6e-05-warmup_ratio=0.040-min_lr=0.000-factor=0.820/checkpoint-10000",
4
- "epoch": 0.9863878477017163,
5
  "eval_steps": 2500,
6
- "global_step": 10000,
7
  "is_hyper_param_search": true,
8
  "is_local_process_zero": true,
9
  "is_world_process_zero": true,
10
  "log_history": [
11
  {
12
  "epoch": 0.049319392385085814,
13
- "grad_norm": 0.6691174507141113,
14
- "learning_rate": 4.606381292021688e-05,
15
- "loss": 0.9843,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
- "grad_norm": 0.477989137172699,
21
- "learning_rate": 4.606381292021688e-05,
22
- "loss": 0.1813,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
- "grad_norm": 0.28420594334602356,
28
- "learning_rate": 4.606381292021688e-05,
29
- "loss": 0.0718,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
- "grad_norm": 0.27486521005630493,
35
- "learning_rate": 4.606381292021688e-05,
36
- "loss": 0.0395,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
- "grad_norm": 0.2175276130437851,
42
- "learning_rate": 4.606381292021688e-05,
43
- "loss": 0.0251,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
- "grad_norm": 0.1922473907470703,
49
- "learning_rate": 4.606381292021688e-05,
50
- "loss": 0.0177,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
- "grad_norm": 0.18892481923103333,
56
- "learning_rate": 4.606381292021688e-05,
57
- "loss": 0.0139,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
- "grad_norm": 0.1161535456776619,
63
- "learning_rate": 4.606381292021688e-05,
64
- "loss": 0.0111,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
- "grad_norm": 0.16154514253139496,
70
- "learning_rate": 4.606381292021688e-05,
71
- "loss": 0.0088,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
- "grad_norm": 0.16088169813156128,
77
- "learning_rate": 4.606381292021688e-05,
78
- "loss": 0.0078,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
- "eval_all_ligands_equal": 0.5058771542200619,
84
- "eval_e3_equal": 0.7961113566062749,
85
  "eval_e3_graph_edit_distance": 9.999999999999999e+63,
86
  "eval_e3_graph_edit_distance_norm": 1.0,
87
- "eval_e3_has_attachment_point(s)": 0.9840919133893062,
88
- "eval_e3_heavy_atoms_difference": 0.6767123287671233,
89
- "eval_e3_heavy_atoms_difference_norm": 0.015499968999404092,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
- "eval_e3_valid": 0.9840919133893062,
92
- "eval_has_all_attachment_points": 0.9769332744144941,
93
- "eval_has_three_substructures": 0.9985859478568272,
94
- "eval_heavy_atoms_difference": 7.977021652673442,
95
- "eval_heavy_atoms_difference_norm": 0.105252234591077,
96
- "eval_linker_equal": 0.7311533362792753,
97
  "eval_linker_graph_edit_distance": 9.999999999999999e+63,
98
  "eval_linker_graph_edit_distance_norm": 1.0,
99
- "eval_linker_has_attachment_point(s)": 0.9948740609809986,
100
- "eval_linker_heavy_atoms_difference": 0.3779938135218736,
101
- "eval_linker_heavy_atoms_difference_norm": 0.0009991271739602798,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
- "eval_linker_valid": 0.9948740609809986,
104
- "eval_loss": 0.2940564453601837,
105
- "eval_num_fragments": 3.0001767565178965,
106
- "eval_poi_equal": 0.7464427750773309,
107
  "eval_poi_graph_edit_distance": 9.999999999999999e+63,
108
  "eval_poi_graph_edit_distance_norm": 1.0,
109
- "eval_poi_has_attachment_point(s)": 0.9214317277949624,
110
- "eval_poi_heavy_atoms_difference": 2.363411400795404,
111
- "eval_poi_heavy_atoms_difference_norm": 0.07635871742465364,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
- "eval_poi_valid": 0.9214317277949624,
114
- "eval_reassembly": 0.5125939019001325,
115
- "eval_reassembly_nostereo": 0.5362792752982766,
116
- "eval_runtime": 1595.0598,
117
- "eval_samples_per_second": 7.094,
118
- "eval_steps_per_second": 0.111,
119
  "eval_tanimoto_similarity": 0.0,
120
- "eval_valid": 0.9042863455589925,
121
  "step": 5000
122
- },
123
- {
124
- "epoch": 0.542513316235944,
125
- "grad_norm": 0.14987365901470184,
126
- "learning_rate": 4.606381292021688e-05,
127
- "loss": 0.0065,
128
- "step": 5500
129
- },
130
- {
131
- "epoch": 0.5918327086210298,
132
- "grad_norm": 0.09952245652675629,
133
- "learning_rate": 4.606381292021688e-05,
134
- "loss": 0.0059,
135
- "step": 6000
136
- },
137
- {
138
- "epoch": 0.6411521010061156,
139
- "grad_norm": 0.09798336774110794,
140
- "learning_rate": 4.606381292021688e-05,
141
- "loss": 0.0055,
142
- "step": 6500
143
- },
144
- {
145
- "epoch": 0.6904714933912014,
146
- "grad_norm": 0.09167756885290146,
147
- "learning_rate": 4.606381292021688e-05,
148
- "loss": 0.0048,
149
- "step": 7000
150
- },
151
- {
152
- "epoch": 0.7397908857762873,
153
- "grad_norm": 0.0671759694814682,
154
- "learning_rate": 4.606381292021688e-05,
155
- "loss": 0.0048,
156
- "step": 7500
157
- },
158
- {
159
- "epoch": 0.7397908857762873,
160
- "eval_all_ligands_equal": 0.5443216968625718,
161
- "eval_e3_equal": 0.8132567388422448,
162
- "eval_e3_graph_edit_distance": 9.999999999999999e+63,
163
- "eval_e3_graph_edit_distance_norm": 1.0,
164
- "eval_e3_has_attachment_point(s)": 0.9893946089262041,
165
- "eval_e3_heavy_atoms_difference": 0.5114449845338047,
166
- "eval_e3_heavy_atoms_difference_norm": 0.013358856534083323,
167
- "eval_e3_tanimoto_similarity": 0.0,
168
- "eval_e3_valid": 0.9893946089262041,
169
- "eval_has_all_attachment_points": 0.982235969951392,
170
- "eval_has_three_substructures": 0.9985859478568272,
171
- "eval_heavy_atoms_difference": 8.227043747238179,
172
- "eval_heavy_atoms_difference_norm": 0.10852013342695678,
173
- "eval_linker_equal": 0.7702165267344233,
174
- "eval_linker_graph_edit_distance": 9.999999999999999e+63,
175
- "eval_linker_graph_edit_distance_norm": 1.0,
176
- "eval_linker_has_attachment_point(s)": 0.9939019001325674,
177
- "eval_linker_heavy_atoms_difference": 0.434025629695095,
178
- "eval_linker_heavy_atoms_difference_norm": 0.006870356807576514,
179
- "eval_linker_tanimoto_similarity": 0.0,
180
- "eval_linker_valid": 0.9939019001325674,
181
- "eval_loss": 0.30229106545448303,
182
- "eval_num_fragments": 3.0007070260715865,
183
- "eval_poi_equal": 0.7606716747680071,
184
- "eval_poi_graph_edit_distance": 9.999999999999999e+63,
185
- "eval_poi_graph_edit_distance_norm": 1.0,
186
- "eval_poi_has_attachment_point(s)": 0.9114449845338047,
187
- "eval_poi_heavy_atoms_difference": 2.584003535130358,
188
- "eval_poi_heavy_atoms_difference_norm": 0.08180244640712389,
189
- "eval_poi_tanimoto_similarity": 0.0,
190
- "eval_poi_valid": 0.9114449845338047,
191
- "eval_reassembly": 0.552364118426867,
192
- "eval_reassembly_nostereo": 0.5768448961555457,
193
- "eval_runtime": 1501.0589,
194
- "eval_samples_per_second": 7.538,
195
- "eval_steps_per_second": 0.118,
196
- "eval_tanimoto_similarity": 0.0,
197
- "eval_valid": 0.8990720282810428,
198
- "step": 7500
199
- },
200
- {
201
- "epoch": 0.789110278161373,
202
- "grad_norm": 0.10520212352275848,
203
- "learning_rate": 4.606381292021688e-05,
204
- "loss": 0.0036,
205
- "step": 8000
206
- },
207
- {
208
- "epoch": 0.8384296705464589,
209
- "grad_norm": 0.11396338790655136,
210
- "learning_rate": 4.606381292021688e-05,
211
- "loss": 0.0036,
212
- "step": 8500
213
- },
214
- {
215
- "epoch": 0.8877490629315447,
216
- "grad_norm": 0.09909546375274658,
217
- "learning_rate": 4.606381292021688e-05,
218
- "loss": 0.0034,
219
- "step": 9000
220
- },
221
- {
222
- "epoch": 0.9370684553166305,
223
- "grad_norm": 0.08407113701105118,
224
- "learning_rate": 4.606381292021688e-05,
225
- "loss": 0.0032,
226
- "step": 9500
227
- },
228
- {
229
- "epoch": 0.9863878477017163,
230
- "grad_norm": 0.0803075060248375,
231
- "learning_rate": 4.606381292021688e-05,
232
- "loss": 0.0033,
233
- "step": 10000
234
- },
235
- {
236
- "epoch": 0.9863878477017163,
237
- "eval_all_ligands_equal": 0.5517454706142289,
238
- "eval_e3_equal": 0.8123729562527618,
239
- "eval_e3_graph_edit_distance": 9.999999999999999e+63,
240
- "eval_e3_graph_edit_distance_norm": 1.0,
241
- "eval_e3_has_attachment_point(s)": 0.9821475916924437,
242
- "eval_e3_heavy_atoms_difference": 0.7959346000883782,
243
- "eval_e3_heavy_atoms_difference_norm": 0.0223010786971663,
244
- "eval_e3_tanimoto_similarity": 0.0,
245
- "eval_e3_valid": 0.9821475916924437,
246
- "eval_has_all_attachment_points": 0.9794962439239947,
247
- "eval_has_three_substructures": 0.9982324348210341,
248
- "eval_heavy_atoms_difference": 8.843128590366769,
249
- "eval_heavy_atoms_difference_norm": 0.1164947202784641,
250
- "eval_linker_equal": 0.7893062306672558,
251
- "eval_linker_graph_edit_distance": 9.999999999999999e+63,
252
- "eval_linker_graph_edit_distance_norm": 1.0,
253
- "eval_linker_has_attachment_point(s)": 0.9941670349094123,
254
- "eval_linker_heavy_atoms_difference": 0.4202386212991604,
255
- "eval_linker_heavy_atoms_difference_norm": 0.007723105851183938,
256
- "eval_linker_tanimoto_similarity": 0.0,
257
- "eval_linker_valid": 0.9941670349094123,
258
- "eval_loss": 0.31081581115722656,
259
- "eval_num_fragments": 2.9998232434821035,
260
- "eval_poi_equal": 0.7584622182942996,
261
- "eval_poi_graph_edit_distance": 9.999999999999999e+63,
262
- "eval_poi_graph_edit_distance_norm": 1.0,
263
- "eval_poi_has_attachment_point(s)": 0.9136544410075121,
264
- "eval_poi_heavy_atoms_difference": 2.7370746796288112,
265
- "eval_poi_heavy_atoms_difference_norm": 0.08879554023759309,
266
- "eval_poi_tanimoto_similarity": 0.0,
267
- "eval_poi_valid": 0.9136544410075121,
268
- "eval_reassembly": 0.5607600530269554,
269
- "eval_reassembly_nostereo": 0.5870967741935483,
270
- "eval_runtime": 1541.0576,
271
- "eval_samples_per_second": 7.342,
272
- "eval_steps_per_second": 0.115,
273
- "eval_tanimoto_similarity": 0.0,
274
- "eval_valid": 0.8950950066283694,
275
- "step": 10000
276
  }
277
  ],
278
  "logging_steps": 500,
@@ -287,18 +133,18 @@
287
  "should_evaluate": false,
288
  "should_log": false,
289
  "should_save": true,
290
- "should_training_stop": true
291
  },
292
  "attributes": {}
293
  }
294
  },
295
- "total_flos": 8.663036348367667e+16,
296
  "train_batch_size": 128,
297
- "trial_name": "trial-number=18-learning_rate=4.6e-05-warmup_ratio=0.040-min_lr=0.000-factor=0.820",
298
  "trial_params": {
299
- "factor": 0.8200000000000001,
300
- "learning_rate": 4.606381292021688e-05,
301
- "min_lr": 9.570957186046748e-10,
302
- "warmup_ratio": 0.04
303
  }
304
  }
 
1
  {
2
+ "best_metric": 0.5199292973928413,
3
+ "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25/trial-number=19-learning_rate=8.0e-05-warmup_ratio=0.060-min_lr=0.000-factor=0.970/checkpoint-5000",
4
+ "epoch": 0.49319392385085814,
5
  "eval_steps": 2500,
6
+ "global_step": 5000,
7
  "is_hyper_param_search": true,
8
  "is_local_process_zero": true,
9
  "is_world_process_zero": true,
10
  "log_history": [
11
  {
12
  "epoch": 0.049319392385085814,
13
+ "grad_norm": 0.48272669315338135,
14
+ "learning_rate": 8.027431614642607e-05,
15
+ "loss": 0.8167,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
+ "grad_norm": 0.35677370429039,
21
+ "learning_rate": 8.027431614642607e-05,
22
+ "loss": 0.1099,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
+ "grad_norm": 0.28323549032211304,
28
+ "learning_rate": 8.027431614642607e-05,
29
+ "loss": 0.0399,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
+ "grad_norm": 0.18444126844406128,
35
+ "learning_rate": 8.027431614642607e-05,
36
+ "loss": 0.022,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
+ "grad_norm": 0.1738751381635666,
42
+ "learning_rate": 8.027431614642607e-05,
43
+ "loss": 0.0141,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
+ "grad_norm": 0.14796946942806244,
49
+ "learning_rate": 8.027431614642607e-05,
50
+ "loss": 0.0107,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
+ "grad_norm": 0.13383328914642334,
56
+ "learning_rate": 8.027431614642607e-05,
57
+ "loss": 0.0089,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
+ "grad_norm": 0.10535630583763123,
63
+ "learning_rate": 8.027431614642607e-05,
64
+ "loss": 0.0073,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
+ "grad_norm": 0.11387604475021362,
70
+ "learning_rate": 8.027431614642607e-05,
71
+ "loss": 0.0062,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
+ "grad_norm": 0.11770522594451904,
77
+ "learning_rate": 8.027431614642607e-05,
78
+ "loss": 0.0059,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
+ "eval_all_ligands_equal": 0.5199292973928413,
84
+ "eval_e3_equal": 0.7980556783031374,
85
  "eval_e3_graph_edit_distance": 9.999999999999999e+63,
86
  "eval_e3_graph_edit_distance_norm": 1.0,
87
+ "eval_e3_has_attachment_point(s)": 0.976049491825011,
88
+ "eval_e3_heavy_atoms_difference": 0.9379584622182943,
89
+ "eval_e3_heavy_atoms_difference_norm": 0.02296914272883557,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
+ "eval_e3_valid": 0.976049491825011,
92
+ "eval_has_all_attachment_points": 0.9775519222271322,
93
+ "eval_has_three_substructures": 0.9992045956694653,
94
+ "eval_heavy_atoms_difference": 8.915245249668581,
95
+ "eval_heavy_atoms_difference_norm": 0.11359321330061124,
96
+ "eval_linker_equal": 0.7530711444984534,
97
  "eval_linker_graph_edit_distance": 9.999999999999999e+63,
98
  "eval_linker_graph_edit_distance_norm": 1.0,
99
+ "eval_linker_has_attachment_point(s)": 0.9946973044631021,
100
+ "eval_linker_heavy_atoms_difference": 0.3158638974812196,
101
+ "eval_linker_heavy_atoms_difference_norm": -0.005294061039033342,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
+ "eval_linker_valid": 0.9946973044631021,
104
+ "eval_loss": 0.29772570729255676,
105
+ "eval_num_fragments": 2.9995581087052585,
106
+ "eval_poi_equal": 0.7513919575784357,
107
  "eval_poi_graph_edit_distance": 9.999999999999999e+63,
108
  "eval_poi_graph_edit_distance_norm": 1.0,
109
+ "eval_poi_has_attachment_point(s)": 0.9204595669465312,
110
+ "eval_poi_heavy_atoms_difference": 2.561201944321697,
111
+ "eval_poi_heavy_atoms_difference_norm": 0.07901894293442624,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
+ "eval_poi_valid": 0.9204595669465312,
114
+ "eval_reassembly": 0.5268228015908086,
115
+ "eval_reassembly_nostereo": 0.5501546619531595,
116
+ "eval_runtime": 1487.2402,
117
+ "eval_samples_per_second": 7.608,
118
+ "eval_steps_per_second": 0.119,
119
  "eval_tanimoto_similarity": 0.0,
120
+ "eval_valid": 0.8945647370746797,
121
  "step": 5000
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
122
  }
123
  ],
124
  "logging_steps": 500,
 
133
  "should_evaluate": false,
134
  "should_log": false,
135
  "should_save": true,
136
+ "should_training_stop": false
137
  },
138
  "attributes": {}
139
  }
140
  },
141
+ "total_flos": 4.33139477262336e+16,
142
  "train_batch_size": 128,
143
+ "trial_name": "trial-number=19-learning_rate=8.0e-05-warmup_ratio=0.060-min_lr=0.000-factor=0.970",
144
  "trial_params": {
145
+ "factor": 0.9700000000000001,
146
+ "learning_rate": 8.027431614642607e-05,
147
+ "min_lr": 7.655589150964243e-09,
148
+ "warmup_ratio": 0.06
149
  }
150
  }
last-checkpoint/training_args.bin CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:2e04b41249f2af71631a96b3a173f413442176c6aa411f0cd997e7794a68d4b4
3
  size 7480
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:8fd9e4a725db2ab30f7bf911ea9e6be239c00d1942a0bc3faad39f344c30b894
3
  size 7480