ribesstefano commited on
Commit
73b5aff
·
verified ·
1 Parent(s): 0490efc

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:b5c048fadaf20fd7a08e650cba1230d4ca450bcea0914f7ac5ee473c2e969487
3
  size 409608164
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:cf6f03e925519677b02244996a0fa1b2beae473c87b1a65171a9f4835eeffa81
3
  size 409608164
last-checkpoint/optimizer.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:6e972b6c229380edc9a1874d6f6050ec4e8c9f61540dc012553a858ba139b946
3
  size 814647162
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:948039b37595fa392a314733c1753cdd541c636c84eb088d25804334742ce692
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:a3cc2cf51d792eb478c0268b254438e7c777f311f492edc1dc233e82f276b28f
3
  size 14244
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:5d449bd85854f756c0c33bb8aa144142f02345882498b7645423b0fa0bb3a022
3
  size 14244
last-checkpoint/scheduler.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:bae27f52aa5e4f7dfc11b827b12e1778787be379c764e4d29b5ce567fb552039
3
  size 1064
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:2f0948c3b28856d6d022fa77d1b89518ec9134e31d3deb6e7d14ce568f855a95
3
  size 1064
last-checkpoint/trainer_state.json CHANGED
@@ -1,278 +1,124 @@
1
  {
2
- "best_metric": 0.5648254529385771,
3
- "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_cosine_restarts-opt25/trial-number=22-learning_rate=7.8e-05-warmup_ratio=0.050-num_cycles=7/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": 0.6311352849006653,
14
- "learning_rate": 6.321657849706081e-05,
15
- "loss": 1.1975,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
- "grad_norm": 0.3875294029712677,
21
- "learning_rate": 2.266437844344336e-05,
22
- "loss": 0.1246,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
- "grad_norm": 0.31023937463760376,
28
- "learning_rate": 1.9519067734396335e-08,
29
- "loss": 0.0683,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
- "grad_norm": 0.28427359461784363,
35
- "learning_rate": 5.707999615476073e-05,
36
- "loss": 0.0528,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
- "grad_norm": 0.22120411694049835,
42
- "learning_rate": 1.6281206903827376e-05,
43
- "loss": 0.0246,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
- "grad_norm": 0.25376608967781067,
49
- "learning_rate": 7.705306860082544e-05,
50
- "loss": 0.0182,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
- "grad_norm": 0.1665523201227188,
56
- "learning_rate": 5.028164398882772e-05,
57
- "loss": 0.0197,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
- "grad_norm": 0.1313042938709259,
63
- "learning_rate": 1.0710840084315767e-05,
64
- "loss": 0.0104,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
- "grad_norm": 0.2163771092891693,
70
- "learning_rate": 7.52019442839167e-05,
71
- "loss": 0.0097,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
- "grad_norm": 0.12024851143360138,
77
- "learning_rate": 4.306723215947234e-05,
78
- "loss": 0.0118,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
- "eval_all_ligands_equal": 0.4987185152452497,
84
- "eval_e3_equal": 0.7911621741051701,
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)": 0.9909854175872735,
88
- "eval_e3_heavy_atoms_difference": 0.5697746354396819,
89
- "eval_e3_heavy_atoms_difference_norm": 0.013845663202264,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
- "eval_e3_valid": 0.9909854175872735,
92
- "eval_has_all_attachment_points": 0.9860362350861688,
93
- "eval_has_three_substructures": 0.9984091913389306,
94
- "eval_heavy_atoms_difference": 6.771895713654441,
95
- "eval_heavy_atoms_difference_norm": 0.0888871888240822,
96
- "eval_linker_equal": 0.7210782147591692,
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)": 0.9970835174547061,
100
- "eval_linker_heavy_atoms_difference": 0.5161290322580645,
101
- "eval_linker_heavy_atoms_difference_norm": 0.006289913322434787,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
- "eval_linker_valid": 0.9970835174547061,
104
- "eval_loss": 0.2860860526561737,
105
- "eval_num_fragments": 3.0001767565178965,
106
- "eval_poi_equal": 0.7388422448077773,
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)": 0.9325673884224481,
110
- "eval_poi_heavy_atoms_difference": 2.120724701723376,
111
- "eval_poi_heavy_atoms_difference_norm": 0.06647977641739568,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
- "eval_poi_valid": 0.9325673884224481,
114
- "eval_reassembly": 0.5070260715863898,
115
- "eval_reassembly_nostereo": 0.5330976579761378,
116
- "eval_runtime": 1575.5066,
117
- "eval_samples_per_second": 7.182,
118
- "eval_steps_per_second": 0.112,
119
  "eval_tanimoto_similarity": 0.0,
120
- "eval_valid": 0.9245249668581529,
121
  "step": 5000
122
- },
123
- {
124
- "epoch": 0.542513316235944,
125
- "grad_norm": 0.09651552885770798,
126
- "learning_rate": 6.154605555214832e-06,
127
- "loss": 0.0057,
128
- "step": 5500
129
- },
130
- {
131
- "epoch": 0.5918327086210298,
132
- "grad_norm": 0.1872074007987976,
133
- "learning_rate": 7.2034075721712e-05,
134
- "loss": 0.0076,
135
- "step": 6000
136
- },
137
- {
138
- "epoch": 0.6411521010061156,
139
- "grad_norm": 0.08568382263183594,
140
- "learning_rate": 3.5697508307174225e-05,
141
- "loss": 0.008,
142
- "step": 6500
143
- },
144
- {
145
- "epoch": 0.6904714933912014,
146
- "grad_norm": 0.0762503519654274,
147
- "learning_rate": 2.777177503559546e-06,
148
- "loss": 0.0037,
149
- "step": 7000
150
- },
151
- {
152
- "epoch": 0.7397908857762873,
153
- "grad_norm": 0.128959521651268,
154
- "learning_rate": 6.766395793785041e-05,
155
- "loss": 0.006,
156
- "step": 7500
157
- },
158
- {
159
- "epoch": 0.7397908857762873,
160
- "eval_all_ligands_equal": 0.5049049933716305,
161
- "eval_e3_equal": 0.7996464869642068,
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)": 0.9888643393725144,
165
- "eval_e3_heavy_atoms_difference": 0.5322138753866549,
166
- "eval_e3_heavy_atoms_difference_norm": 0.011503559133904656,
167
- "eval_e3_tanimoto_similarity": 0.0,
168
- "eval_e3_valid": 0.9888643393725144,
169
- "eval_has_all_attachment_points": 0.9821475916924437,
170
- "eval_has_three_substructures": 0.9986743261157756,
171
- "eval_heavy_atoms_difference": 8.533451171011931,
172
- "eval_heavy_atoms_difference_norm": 0.11147858522514467,
173
- "eval_linker_equal": 0.7364560318161733,
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)": 0.994962439239947,
177
- "eval_linker_heavy_atoms_difference": 0.4474591250552364,
178
- "eval_linker_heavy_atoms_difference_norm": 0.0052732646233331305,
179
- "eval_linker_tanimoto_similarity": 0.0,
180
- "eval_linker_valid": 0.994962439239947,
181
- "eval_loss": 0.3063560128211975,
182
- "eval_num_fragments": 2.998851082633672,
183
- "eval_poi_equal": 0.7368095448519664,
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)": 0.9110030932390631,
187
- "eval_poi_heavy_atoms_difference": 2.787185152452497,
188
- "eval_poi_heavy_atoms_difference_norm": 0.0886750621661839,
189
- "eval_poi_tanimoto_similarity": 0.0,
190
- "eval_poi_valid": 0.9110030932390631,
191
- "eval_reassembly": 0.5122403888643394,
192
- "eval_reassembly_nostereo": 0.5371630578877596,
193
- "eval_runtime": 1510.5044,
194
- "eval_samples_per_second": 7.491,
195
- "eval_steps_per_second": 0.117,
196
- "eval_tanimoto_similarity": 0.0,
197
- "eval_valid": 0.8995139195757843,
198
- "step": 7500
199
- },
200
- {
201
- "epoch": 0.789110278161373,
202
- "grad_norm": 0.09418843686580658,
203
- "learning_rate": 2.8438833453583697e-05,
204
- "loss": 0.0047,
205
- "step": 8000
206
- },
207
- {
208
- "epoch": 0.8384296705464589,
209
- "grad_norm": 0.0902002677321434,
210
- "learning_rate": 7.006249789397529e-07,
211
- "loss": 0.0026,
212
- "step": 8500
213
- },
214
- {
215
- "epoch": 0.8877490629315447,
216
- "grad_norm": 0.12980258464813232,
217
- "learning_rate": 6.224953837527164e-05,
218
- "loss": 0.0066,
219
- "step": 9000
220
- },
221
- {
222
- "epoch": 0.9370684553166305,
223
- "grad_norm": 0.048701103776693344,
224
- "learning_rate": 2.155355502020242e-05,
225
- "loss": 0.0044,
226
- "step": 9500
227
- },
228
- {
229
- "epoch": 0.9863878477017163,
230
- "grad_norm": 0.06892744451761246,
231
- "learning_rate": 0.0,
232
- "loss": 0.002,
233
- "step": 10000
234
- },
235
- {
236
- "epoch": 0.9863878477017163,
237
- "eval_all_ligands_equal": 0.5648254529385771,
238
- "eval_e3_equal": 0.811842686699072,
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)": 0.9891294741493593,
242
- "eval_e3_heavy_atoms_difference": 0.5316836058329651,
243
- "eval_e3_heavy_atoms_difference_norm": 0.011111080767439089,
244
- "eval_e3_tanimoto_similarity": 0.0,
245
- "eval_e3_valid": 0.9891294741493593,
246
- "eval_has_all_attachment_points": 0.9803800265134777,
247
- "eval_has_three_substructures": 0.9994697304463102,
248
- "eval_heavy_atoms_difference": 6.5374281926646045,
249
- "eval_heavy_atoms_difference_norm": 0.08639325931869864,
250
- "eval_linker_equal": 0.8051259390190013,
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)": 0.9975254087494476,
254
- "eval_linker_heavy_atoms_difference": 0.28652231551038443,
255
- "eval_linker_heavy_atoms_difference_norm": 0.001050129570856685,
256
- "eval_linker_tanimoto_similarity": 0.0,
257
- "eval_linker_valid": 0.9975254087494476,
258
- "eval_loss": 0.29083964228630066,
259
- "eval_num_fragments": 2.99946973044631,
260
- "eval_poi_equal": 0.7801148917366328,
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)": 0.9341581970835174,
264
- "eval_poi_heavy_atoms_difference": 1.9076447193990278,
265
- "eval_poi_heavy_atoms_difference_norm": 0.06058139871085425,
266
- "eval_poi_tanimoto_similarity": 0.0,
267
- "eval_poi_valid": 0.9341581970835174,
268
- "eval_reassembly": 0.5731330092797172,
269
- "eval_reassembly_nostereo": 0.6010605391073796,
270
- "eval_runtime": 1507.1636,
271
- "eval_samples_per_second": 7.507,
272
- "eval_steps_per_second": 0.117,
273
- "eval_tanimoto_similarity": 0.0,
274
- "eval_valid": 0.9225806451612903,
275
- "step": 10000
276
  }
277
  ],
278
  "logging_steps": 500,
@@ -287,17 +133,17 @@
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=22-learning_rate=7.8e-05-warmup_ratio=0.050-num_cycles=7",
298
  "trial_params": {
299
- "learning_rate": 7.754006328430222e-05,
300
- "num_cycles": 7,
301
- "warmup_ratio": 0.05
302
  }
303
  }
 
1
  {
2
+ "best_metric": 0.0,
3
+ "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_cosine_restarts-opt25/trial-number=23-learning_rate=5.9e-04-warmup_ratio=0.070-num_cycles=5/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": 0.26378336548805237,
14
+ "learning_rate": 0.0005319819238555916,
15
+ "loss": 0.8781,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
+ "grad_norm": 0.26860642433166504,
21
+ "learning_rate": 0.0003369078003427231,
22
+ "loss": 0.1831,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
+ "grad_norm": 0.3114512264728546,
28
+ "learning_rate": 0.00011653163666206531,
29
+ "loss": 0.1642,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
+ "grad_norm": 0.4044862985610962,
35
+ "learning_rate": 2.429070832855221e-06,
36
+ "loss": 0.1558,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
+ "grad_norm": 0.5458288788795471,
42
+ "learning_rate": 0.0005271959652135703,
43
+ "loss": 2.7241,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
+ "grad_norm": 0.7785220146179199,
49
+ "learning_rate": 0.0003290315839343549,
50
+ "loss": 3.5665,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
+ "grad_norm": 1.143982172012329,
56
+ "learning_rate": 0.00011026765926286528,
57
+ "loss": 3.5575,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
+ "grad_norm": 1.1621668338775635,
63
+ "learning_rate": 1.5172415558257588e-06,
64
+ "loss": 3.5531,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
+ "grad_norm": 0.5300591588020325,
70
+ "learning_rate": 0.0005213489853416686,
71
+ "loss": 3.5607,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
+ "grad_norm": 0.8344257473945618,
77
+ "learning_rate": 0.000319733743673733,
78
+ "loss": 3.5623,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
+ "eval_all_ligands_equal": 0.0,
84
+ "eval_e3_equal": 0.0,
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)": 0.0,
88
+ "eval_e3_heavy_atoms_difference": 28.086433937251435,
89
+ "eval_e3_heavy_atoms_difference_norm": 1.0,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
+ "eval_e3_valid": 0.0,
92
+ "eval_has_all_attachment_points": 0.0,
93
+ "eval_has_three_substructures": 0.0,
94
+ "eval_heavy_atoms_difference": 75.67370746796288,
95
+ "eval_heavy_atoms_difference_norm": 1.0,
96
+ "eval_linker_equal": 0.0,
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)": 0.0,
100
+ "eval_linker_heavy_atoms_difference": 16.430402121078213,
101
+ "eval_linker_heavy_atoms_difference_norm": 1.0,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
+ "eval_linker_valid": 0.0,
104
+ "eval_loss": 3.5808053016662598,
105
+ "eval_num_fragments": 1.0018559434379142,
106
+ "eval_poi_equal": 0.0,
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)": 0.0,
110
+ "eval_poi_heavy_atoms_difference": 31.15687140963323,
111
+ "eval_poi_heavy_atoms_difference_norm": 1.0,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
+ "eval_poi_valid": 0.0,
114
+ "eval_reassembly": 0.0,
115
+ "eval_reassembly_nostereo": 0.0,
116
+ "eval_runtime": 5643.0408,
117
+ "eval_samples_per_second": 2.005,
118
+ "eval_steps_per_second": 0.031,
119
  "eval_tanimoto_similarity": 0.0,
120
+ "eval_valid": 0.0,
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=23-learning_rate=5.9e-04-warmup_ratio=0.070-num_cycles=5",
144
  "trial_params": {
145
+ "learning_rate": 0.0005890587774708618,
146
+ "num_cycles": 5,
147
+ "warmup_ratio": 0.06999999999999999
148
  }
149
  }
last-checkpoint/training_args.bin CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:ba024ca1598855de20b7dedcadbcfc630c71b61849b062104d468853b275667a
3
  size 7480
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:ffc23a2ea6db09dedd83ecaab57dfa5dc9d9036df116c7da8ed463ecb098ff40
3
  size 7480