ribesstefano commited on
Commit
f682094
·
verified ·
1 Parent(s): b69895f

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 sha256:36370843d1d338dddd594e733dae27f05afc004e2523c3386fdaf524aabe6609
3
  size 409608164
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:6cbe62c42a1be83e729dc373778371680f58d4107e72c90cb31439c48eadeb39
3
  size 409608164
last-checkpoint/optimizer.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:378fd576cfae3e233cce3eacb8db2b87c8b786da267ce70ad55847ef31647f54
3
  size 814647162
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:bff8b1080eb8f160dca1f0d5c11f901a4849ea6c60dbd72fe57b51ad7f40afbf
3
  size 814647162
last-checkpoint/rng_state.pth CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:79869b2e85a7837bbc4b2150e9097dcfdcaeff6d2060f8e854fab9dfebd663d8
3
  size 14244
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:25fa90a3c83a2c2adcc3c4f8bac69bbbc8b9b9fa9ac4c5229ce092b598a9c791
3
  size 14244
last-checkpoint/scheduler.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:8d92c5a2febec6a3debc54e07f631908af44ee341af8b138c2ac3072c6cfbde8
3
  size 1064
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f9622860b2ff3b52b1dc058cb630ef6381def4ff9274a76cbef21acbf286488a
3
  size 1064
last-checkpoint/trainer_state.json CHANGED
@@ -1,278 +1,124 @@
1
  {
2
- "best_metric": 8.837825894829872e-05,
3
- "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_cosine-opt25-rand-smiles/trial-number=21-learning_rate=1.6e-06-warmup_ratio=0.080-num_cycles=1.500/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": 4.175539493560791,
14
- "learning_rate": 1.1556051821104526e-06,
15
- "loss": 6.3946,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
- "grad_norm": 1.8938024044036865,
21
- "learning_rate": 1.5782537021726088e-06,
22
- "loss": 2.3689,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
- "grad_norm": 1.4588741064071655,
28
- "learning_rate": 1.3637510062898264e-06,
29
- "loss": 1.3991,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
- "grad_norm": 1.4487122297286987,
35
- "learning_rate": 1.0095554213221014e-06,
36
- "loss": 1.164,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
- "grad_norm": 1.3530123233795166,
42
- "learning_rate": 6.046599668215422e-07,
43
- "loss": 1.0414,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
- "grad_norm": 1.4081937074661255,
49
- "learning_rate": 2.5079620192718024e-07,
50
- "loss": 0.9813,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
- "grad_norm": 1.3146899938583374,
56
- "learning_rate": 3.687377510596774e-08,
57
- "loss": 0.9546,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
- "grad_norm": 1.405544638633728,
63
- "learning_rate": 1.664152886385891e-08,
64
- "loss": 0.9509,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
- "grad_norm": 1.4300780296325684,
70
- "learning_rate": 1.9518289383020806e-07,
71
- "loss": 0.9464,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
- "grad_norm": 1.3519362211227417,
77
- "learning_rate": 5.276386570231308e-07,
78
- "loss": 0.9309,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
- "eval_all_ligands_equal": 0.0,
84
- "eval_e3_equal": 0.023862129916040652,
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)": 0.8015024304021211,
88
- "eval_e3_heavy_atoms_difference": 6.527529827662395,
89
- "eval_e3_heavy_atoms_difference_norm": 0.17258164424657527,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
- "eval_e3_valid": 0.8015024304021211,
92
- "eval_has_all_attachment_points": 0.4949182501104728,
93
- "eval_has_three_substructures": 0.8086610693769333,
94
- "eval_heavy_atoms_difference": 71.589748121962,
95
- "eval_heavy_atoms_difference_norm": 0.9393652926517526,
96
- "eval_linker_equal": 0.0007954043305346885,
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)": 0.723376049491825,
100
- "eval_linker_heavy_atoms_difference": 11.69456473707468,
101
- "eval_linker_heavy_atoms_difference_norm": 0.6508096279718948,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
- "eval_linker_valid": 0.723376049491825,
104
- "eval_loss": 0.9551888108253479,
105
- "eval_num_fragments": 3.1498895271763145,
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)": 0.1647370746796288,
110
- "eval_poi_heavy_atoms_difference": 29.040653999116216,
111
- "eval_poi_heavy_atoms_difference_norm": 0.9184080533333931,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
- "eval_poi_valid": 0.1647370746796288,
114
- "eval_reassembly": 0.0,
115
- "eval_reassembly_nostereo": 0.0,
116
- "eval_runtime": 2290.4515,
117
- "eval_samples_per_second": 4.94,
118
- "eval_steps_per_second": 0.077,
119
  "eval_tanimoto_similarity": 0.0,
120
- "eval_valid": 0.1528060097216085,
121
  "step": 5000
122
- },
123
- {
124
- "epoch": 0.542513316235944,
125
- "grad_norm": 1.3835140466690063,
126
- "learning_rate": 9.304780137412219e-07,
127
- "loss": 0.8874,
128
- "step": 5500
129
- },
130
- {
131
- "epoch": 0.5918327086210298,
132
- "grad_norm": 1.3169989585876465,
133
- "learning_rate": 1.302486007417367e-06,
134
- "loss": 0.8215,
135
- "step": 6000
136
- },
137
- {
138
- "epoch": 0.6411521010061156,
139
- "grad_norm": 1.280273675918579,
140
- "learning_rate": 1.5501941814704978e-06,
141
- "loss": 0.7438,
142
- "step": 6500
143
- },
144
- {
145
- "epoch": 0.6904714933912014,
146
- "grad_norm": 1.4349747896194458,
147
- "learning_rate": 1.6113648928799203e-06,
148
- "loss": 0.669,
149
- "step": 7000
150
- },
151
- {
152
- "epoch": 0.7397908857762873,
153
- "grad_norm": 1.2315547466278076,
154
- "learning_rate": 1.4706287622758396e-06,
155
- "loss": 0.6043,
156
- "step": 7500
157
- },
158
- {
159
- "epoch": 0.7397908857762873,
160
- "eval_all_ligands_equal": 0.0,
161
- "eval_e3_equal": 0.05612019443216969,
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)": 0.9729562527618206,
165
- "eval_e3_heavy_atoms_difference": 0.5429960229783474,
166
- "eval_e3_heavy_atoms_difference_norm": -0.029541020730058737,
167
- "eval_e3_tanimoto_similarity": 0.0,
168
- "eval_e3_valid": 0.9729562527618206,
169
- "eval_has_all_attachment_points": 0.7827662395050817,
170
- "eval_has_three_substructures": 0.9756076005302695,
171
- "eval_heavy_atoms_difference": 61.464250994255416,
172
- "eval_heavy_atoms_difference_norm": 0.796061917426111,
173
- "eval_linker_equal": 0.0015024304021210783,
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)": 0.9462660185594344,
177
- "eval_linker_heavy_atoms_difference": 7.653822359699514,
178
- "eval_linker_heavy_atoms_difference_norm": 0.35586072765620425,
179
- "eval_linker_tanimoto_similarity": 0.0,
180
- "eval_linker_valid": 0.9462660185594344,
181
- "eval_loss": 0.6581697463989258,
182
- "eval_num_fragments": 3.012372956252762,
183
- "eval_poi_equal": 0.0015024304021210783,
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)": 0.3093239063190455,
187
- "eval_poi_heavy_atoms_difference": 25.47229341581971,
188
- "eval_poi_heavy_atoms_difference_norm": 0.778111477675356,
189
- "eval_poi_tanimoto_similarity": 0.0,
190
- "eval_poi_valid": 0.3093239063190455,
191
- "eval_reassembly": 0.0,
192
- "eval_reassembly_nostereo": 0.0,
193
- "eval_runtime": 1364.8374,
194
- "eval_samples_per_second": 8.29,
195
- "eval_steps_per_second": 0.13,
196
- "eval_tanimoto_similarity": 0.0,
197
- "eval_valid": 0.2988952717631463,
198
- "step": 7500
199
- },
200
- {
201
- "epoch": 0.789110278161373,
202
- "grad_norm": 1.26154363155365,
203
- "learning_rate": 1.1633462903366549e-06,
204
- "loss": 0.5573,
205
- "step": 8000
206
- },
207
- {
208
- "epoch": 0.8384296705464589,
209
- "grad_norm": 1.3200926780700684,
210
- "learning_rate": 7.667233943405157e-07,
211
- "loss": 0.5213,
212
- "step": 8500
213
- },
214
- {
215
- "epoch": 0.8877490629315447,
216
- "grad_norm": 1.1365368366241455,
217
- "learning_rate": 3.804131208984208e-07,
218
- "loss": 0.5012,
219
- "step": 9000
220
- },
221
- {
222
- "epoch": 0.9370684553166305,
223
- "grad_norm": 1.3047261238098145,
224
- "learning_rate": 1.014774300592085e-07,
225
- "loss": 0.4905,
226
- "step": 9500
227
- },
228
- {
229
- "epoch": 0.9863878477017163,
230
- "grad_norm": 1.003517985343933,
231
- "learning_rate": 0.0,
232
- "loss": 0.4875,
233
- "step": 10000
234
- },
235
- {
236
- "epoch": 0.9863878477017163,
237
- "eval_all_ligands_equal": 8.837825894829872e-05,
238
- "eval_e3_equal": 0.07397260273972603,
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)": 0.98285461776403,
242
- "eval_e3_heavy_atoms_difference": -0.7978789217852408,
243
- "eval_e3_heavy_atoms_difference_norm": -0.06986969786045168,
244
- "eval_e3_tanimoto_similarity": 0.0,
245
- "eval_e3_valid": 0.98285461776403,
246
- "eval_has_all_attachment_points": 0.8105170128148476,
247
- "eval_has_three_substructures": 0.9845338046840477,
248
- "eval_heavy_atoms_difference": 54.63950508174989,
249
- "eval_heavy_atoms_difference_norm": 0.7006005159368531,
250
- "eval_linker_equal": 0.0016791869200176756,
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)": 0.9719840919133893,
254
- "eval_linker_heavy_atoms_difference": 7.197967300044189,
255
- "eval_linker_heavy_atoms_difference_norm": 0.32378217560050643,
256
- "eval_linker_tanimoto_similarity": 0.0,
257
- "eval_linker_valid": 0.9719840919133893,
258
- "eval_loss": 0.5798121094703674,
259
- "eval_num_fragments": 3.00415377817057,
260
- "eval_poi_equal": 0.009721608484312859,
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)": 0.3849756959787892,
264
- "eval_poi_heavy_atoms_difference": 22.694829871851525,
265
- "eval_poi_heavy_atoms_difference_norm": 0.6749048721453627,
266
- "eval_poi_tanimoto_similarity": 0.0,
267
- "eval_poi_valid": 0.3849756959787892,
268
- "eval_reassembly": 8.837825894829872e-05,
269
- "eval_reassembly_nostereo": 8.837825894829872e-05,
270
- "eval_runtime": 1432.419,
271
- "eval_samples_per_second": 7.899,
272
- "eval_steps_per_second": 0.124,
273
- "eval_tanimoto_similarity": 0.0,
274
- "eval_valid": 0.38011489173663277,
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": 8.729673191023411e+16,
296
  "train_batch_size": 128,
297
- "trial_name": "trial-number=21-learning_rate=1.6e-06-warmup_ratio=0.080-num_cycles=1.500",
298
  "trial_params": {
299
- "learning_rate": 1.6155360445904128e-06,
300
- "num_cycles": 1.5,
301
- "warmup_ratio": 0.08
302
  }
303
  }
 
1
  {
2
+ "best_metric": 0.4762704374723818,
3
+ "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_cosine-opt25-rand-smiles/trial-number=22-learning_rate=7.8e-05-warmup_ratio=0.050-num_cycles=7.000/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": 1.0414072275161743,
14
+ "learning_rate": 5.546499519621046e-05,
15
+ "loss": 2.0468,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
+ "grad_norm": 0.5105423331260681,
21
+ "learning_rate": 4.446545588867061e-05,
22
+ "loss": 0.2323,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
+ "grad_norm": 0.36100202798843384,
28
+ "learning_rate": 7.815797870732129e-06,
29
+ "loss": 0.0921,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
+ "grad_norm": 0.3516131043434143,
35
+ "learning_rate": 7.720759640693211e-05,
36
+ "loss": 0.0769,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
+ "grad_norm": 0.2069791704416275,
42
+ "learning_rate": 1.4921919604851097e-05,
43
+ "loss": 0.0424,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
+ "grad_norm": 0.20585626363754272,
49
+ "learning_rate": 3.433390507333742e-05,
50
+ "loss": 0.0277,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
+ "grad_norm": 0.18822892010211945,
56
+ "learning_rate": 6.894294973215218e-05,
57
+ "loss": 0.0291,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
+ "grad_norm": 0.13710656762123108,
63
+ "learning_rate": 1.8712978537945652e-07,
64
+ "loss": 0.0177,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
+ "grad_norm": 0.24122795462608337,
70
+ "learning_rate": 6.360667367381643e-05,
71
+ "loss": 0.0145,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
+ "grad_norm": 0.17789728939533234,
77
+ "learning_rate": 4.194209897608062e-05,
78
+ "loss": 0.0179,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
+ "eval_all_ligands_equal": 0.4762704374723818,
84
+ "eval_e3_equal": 0.7877154220061865,
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)": 0.9977021652673442,
88
+ "eval_e3_heavy_atoms_difference": 0.17472381794078656,
89
+ "eval_e3_heavy_atoms_difference_norm": -0.002642165439927071,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
+ "eval_e3_valid": 0.9977021652673442,
92
+ "eval_has_all_attachment_points": 0.9910737958462218,
93
+ "eval_has_three_substructures": 0.9992929739284137,
94
+ "eval_heavy_atoms_difference": 5.015112682280159,
95
+ "eval_heavy_atoms_difference_norm": 0.0645246406275191,
96
+ "eval_linker_equal": 0.6841361025187804,
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)": 0.9978789217852408,
100
+ "eval_linker_heavy_atoms_difference": 0.680777728678745,
101
+ "eval_linker_heavy_atoms_difference_norm": 0.014413720247737226,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
+ "eval_linker_valid": 0.9978789217852408,
104
+ "eval_loss": 0.29064735770225525,
105
+ "eval_num_fragments": 3.000353513035793,
106
+ "eval_poi_equal": 0.7382235969951392,
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)": 0.9501546619531596,
110
+ "eval_poi_heavy_atoms_difference": 1.6001767565178966,
111
+ "eval_poi_heavy_atoms_difference_norm": 0.044138871637433214,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
+ "eval_poi_valid": 0.9501546619531596,
114
+ "eval_reassembly": 0.4826336721166593,
115
+ "eval_reassembly_nostereo": 0.5145382235969952,
116
+ "eval_runtime": 1556.8958,
117
+ "eval_samples_per_second": 7.268,
118
+ "eval_steps_per_second": 0.114,
119
  "eval_tanimoto_similarity": 0.0,
120
+ "eval_valid": 0.9474149359257623,
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": 4.364959997072179e+16,
142
  "train_batch_size": 128,
143
+ "trial_name": "trial-number=22-learning_rate=7.8e-05-warmup_ratio=0.050-num_cycles=7.000",
144
  "trial_params": {
145
+ "learning_rate": 7.754006328430222e-05,
146
+ "num_cycles": 7.0,
147
+ "warmup_ratio": 0.05
148
  }
149
  }
last-checkpoint/training_args.bin CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:cbefcfb3ae3485c21410a4c0d3adfd89f163e7aa4441b2c14560931831d9b0ab
3
  size 7480
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:4004e7468a495317b64b5a5d18767c59da3cee7fc8ade7eb0f4a6f0bfe8fc240
3
  size 7480