ribesstefano commited on
Commit
dd71322
·
verified ·
1 Parent(s): 5dfcca4

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 sha256:8c23742e474292a7c55d08fa35da5d386b6dc94e75b0758af539411b0a6300b0
3
  size 409608164
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:8c0489f4d8a0feab5d3e38c38764efb3065a72c0df1166c52788a4fb8b5db167
3
  size 409608164
last-checkpoint/optimizer.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:bcbac88bb42d64b5113d8b7784064778f08387dc103774db1d3e75a7d51df86b
3
  size 814647162
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:10a21a5a2f88c53aa60c7d7a14adc335d7340e642ca9d190920e4e42bed1705e
3
  size 814647162
last-checkpoint/rng_state.pth CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:551f4e1407f546402384ab496e542d88dbab87683febd9da9183e2d8deccce45
3
  size 14244
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:12f5435a54f71ddfe7351c79962b19289d71b582fb8054a3e03ea18859c1e069
3
  size 14244
last-checkpoint/scheduler.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:98a089bb4a69e00a7e8a8814929d1de493c84d2bd6273a6f081d3b7a9500a40d
3
  size 1064
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:a7c3ad366a455d36d790316ad7de46df5551299c0b50500acfaef90eebc7bbcf
3
  size 1064
last-checkpoint/trainer_state.json CHANGED
@@ -1,278 +1,124 @@
1
  {
2
- "best_metric": 0.0009721608484312859,
3
- "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_cosine-opt25/trial-number=20-learning_rate=4.8e-06-warmup_ratio=0.030-num_cycles=3.000/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": 2.0794825553894043,
14
- "learning_rate": 3.4057266290417822e-06,
15
- "loss": 4.898,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
- "grad_norm": 1.3309763669967651,
21
- "learning_rate": 4.331843781954863e-06,
22
- "loss": 1.2931,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
- "grad_norm": 1.2491517066955566,
28
- "learning_rate": 2.2556236723022006e-06,
29
- "loss": 0.8498,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
- "grad_norm": 1.1954443454742432,
35
- "learning_rate": 2.9711989198042844e-07,
36
- "loss": 0.7115,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
- "grad_norm": 1.1868677139282227,
42
- "learning_rate": 3.0102179436748257e-07,
43
- "loss": 0.6854,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
- "grad_norm": 1.359408974647522,
49
- "learning_rate": 2.263654228124041e-06,
50
- "loss": 0.6669,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
- "grad_norm": 1.3000223636627197,
56
- "learning_rate": 4.336439114656795e-06,
57
- "loss": 0.5823,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
- "grad_norm": 1.0815534591674805,
63
- "learning_rate": 4.567047206277767e-06,
64
- "loss": 0.4713,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
- "grad_norm": 0.9021003246307373,
70
- "learning_rate": 2.7382717272379126e-06,
71
- "loss": 0.385,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
- "grad_norm": 0.8889977335929871,
77
- "learning_rate": 5.726126235670513e-07,
78
- "loss": 0.3445,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
- "eval_all_ligands_equal": 0.00017675651789659743,
84
- "eval_e3_equal": 0.13239063190455147,
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)": 0.9877154220061864,
88
- "eval_e3_heavy_atoms_difference": -1.3631462660185594,
89
- "eval_e3_heavy_atoms_difference_norm": -0.07969778182157912,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
- "eval_e3_valid": 0.9877154220061864,
92
- "eval_has_all_attachment_points": 0.8787450287229341,
93
- "eval_has_three_substructures": 0.9895713654441007,
94
- "eval_heavy_atoms_difference": 40.59840919133893,
95
- "eval_heavy_atoms_difference_norm": 0.5186137998425047,
96
- "eval_linker_equal": 0.0030048608042421566,
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)": 0.97870083959346,
100
- "eval_linker_heavy_atoms_difference": 6.881307998232435,
101
- "eval_linker_heavy_atoms_difference_norm": 0.3090588569977506,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
- "eval_linker_valid": 0.97870083959346,
104
- "eval_loss": 0.4682455062866211,
105
- "eval_num_fragments": 2.995581087052585,
106
- "eval_poi_equal": 0.053645603181617325,
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)": 0.5663278833406982,
110
- "eval_poi_heavy_atoms_difference": 16.751922227132127,
111
- "eval_poi_heavy_atoms_difference_norm": 0.4869952919604095,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
- "eval_poi_valid": 0.5663278833406982,
114
- "eval_reassembly": 0.00017675651789659743,
115
- "eval_reassembly_nostereo": 0.0002651347768448962,
116
- "eval_runtime": 1486.8909,
117
- "eval_samples_per_second": 7.61,
118
- "eval_steps_per_second": 0.119,
119
  "eval_tanimoto_similarity": 0.0,
120
- "eval_valid": 0.5612903225806452,
121
  "step": 5000
122
- },
123
- {
124
- "epoch": 0.542513316235944,
125
- "grad_norm": 0.7243369817733765,
126
- "learning_rate": 1.098761656065621e-07,
127
- "loss": 0.3332,
128
- "step": 5500
129
- },
130
- {
131
- "epoch": 0.5918327086210298,
132
- "grad_norm": 0.7796162962913513,
133
- "learning_rate": 1.785907831928506e-06,
134
- "loss": 0.3291,
135
- "step": 6000
136
- },
137
- {
138
- "epoch": 0.6411521010061156,
139
- "grad_norm": 0.794780433177948,
140
- "learning_rate": 4.02207509608434e-06,
141
- "loss": 0.3073,
142
- "step": 6500
143
- },
144
- {
145
- "epoch": 0.6904714933912014,
146
- "grad_norm": 0.8074055910110474,
147
- "learning_rate": 4.712160964261165e-06,
148
- "loss": 0.2687,
149
- "step": 7000
150
- },
151
- {
152
- "epoch": 0.7397908857762873,
153
- "grad_norm": 0.5401957035064697,
154
- "learning_rate": 3.206182491961818e-06,
155
- "loss": 0.2322,
156
- "step": 7500
157
- },
158
- {
159
- "epoch": 0.7397908857762873,
160
- "eval_all_ligands_equal": 0.000618647812638091,
161
- "eval_e3_equal": 0.2136986301369863,
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)": 0.993813521873619,
165
- "eval_e3_heavy_atoms_difference": -1.129562527618206,
166
- "eval_e3_heavy_atoms_difference_norm": -0.0636057389477739,
167
- "eval_e3_tanimoto_similarity": 0.0,
168
- "eval_e3_valid": 0.993813521873619,
169
- "eval_has_all_attachment_points": 0.9152452496685816,
170
- "eval_has_three_substructures": 0.9952275740167918,
171
- "eval_heavy_atoms_difference": 29.648608042421564,
172
- "eval_heavy_atoms_difference_norm": 0.3796774462658793,
173
- "eval_linker_equal": 0.0057445868316394165,
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)": 0.9870083959346001,
177
- "eval_linker_heavy_atoms_difference": 5.789659743703049,
178
- "eval_linker_heavy_atoms_difference_norm": 0.2506175164012725,
179
- "eval_linker_tanimoto_similarity": 0.0,
180
- "eval_linker_valid": 0.9870083959346001,
181
- "eval_loss": 0.3937079608440399,
182
- "eval_num_fragments": 2.9978789217852406,
183
- "eval_poi_equal": 0.16871409633230225,
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)": 0.691117984975696,
187
- "eval_poi_heavy_atoms_difference": 11.474149359257623,
188
- "eval_poi_heavy_atoms_difference_norm": 0.33367563586799615,
189
- "eval_poi_tanimoto_similarity": 0.0,
190
- "eval_poi_valid": 0.691117984975696,
191
- "eval_reassembly": 0.000618647812638091,
192
- "eval_reassembly_nostereo": 0.0007954043305346885,
193
- "eval_runtime": 1476.2637,
194
- "eval_samples_per_second": 7.665,
195
- "eval_steps_per_second": 0.12,
196
- "eval_tanimoto_similarity": 0.0,
197
- "eval_valid": 0.6858152894387981,
198
- "step": 7500
199
- },
200
- {
201
- "epoch": 0.789110278161373,
202
- "grad_norm": 0.6613984704017639,
203
- "learning_rate": 9.226013039121686e-07,
204
- "loss": 0.2124,
205
- "step": 8000
206
- },
207
- {
208
- "epoch": 0.8384296705464589,
209
- "grad_norm": 0.6681215167045593,
210
- "learning_rate": 1.2292954959110304e-08,
211
- "loss": 0.2046,
212
- "step": 8500
213
- },
214
- {
215
- "epoch": 0.8877490629315447,
216
- "grad_norm": 0.6344013810157776,
217
- "learning_rate": 1.3326650929596504e-06,
218
- "loss": 0.2034,
219
- "step": 9000
220
- },
221
- {
222
- "epoch": 0.9370684553166305,
223
- "grad_norm": 0.8783854246139526,
224
- "learning_rate": 3.640076296365813e-06,
225
- "loss": 0.1964,
226
- "step": 9500
227
- },
228
- {
229
- "epoch": 0.9863878477017163,
230
- "grad_norm": 0.749924898147583,
231
- "learning_rate": 4.7612058274004114e-06,
232
- "loss": 0.1799,
233
- "step": 10000
234
- },
235
- {
236
- "epoch": 0.9863878477017163,
237
- "eval_all_ligands_equal": 0.0009721608484312859,
238
- "eval_e3_equal": 0.29155987627043745,
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)": 0.9963764913831198,
242
- "eval_e3_heavy_atoms_difference": -1.0244807777286788,
243
- "eval_e3_heavy_atoms_difference_norm": -0.05932507175480622,
244
- "eval_e3_tanimoto_similarity": 0.0,
245
- "eval_e3_valid": 0.9963764913831198,
246
- "eval_has_all_attachment_points": 0.9400795404330534,
247
- "eval_has_three_substructures": 0.9980556783031375,
248
- "eval_heavy_atoms_difference": 22.542465753424658,
249
- "eval_heavy_atoms_difference_norm": 0.288556240521232,
250
- "eval_linker_equal": 0.008749447635881574,
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)": 0.9902783915156872,
254
- "eval_linker_heavy_atoms_difference": 4.60362350861688,
255
- "eval_linker_heavy_atoms_difference_norm": 0.1790452881173788,
256
- "eval_linker_tanimoto_similarity": 0.0,
257
- "eval_linker_valid": 0.9902783915156872,
258
- "eval_loss": 0.36306923627853394,
259
- "eval_num_fragments": 2.99946973044631,
260
- "eval_poi_equal": 0.27370746796288115,
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)": 0.7658859920459566,
264
- "eval_poi_heavy_atoms_difference": 8.255148033583739,
265
- "eval_poi_heavy_atoms_difference_norm": 0.24317273637314274,
266
- "eval_poi_tanimoto_similarity": 0.0,
267
- "eval_poi_valid": 0.7658859920459566,
268
- "eval_reassembly": 0.0010605391073795847,
269
- "eval_reassembly_nostereo": 0.0019443216968625717,
270
- "eval_runtime": 1567.7756,
271
- "eval_samples_per_second": 7.217,
272
- "eval_steps_per_second": 0.113,
273
- "eval_tanimoto_similarity": 0.0,
274
- "eval_valid": 0.7593460008837826,
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=20-learning_rate=4.8e-06-warmup_ratio=0.030-num_cycles=3.000",
298
  "trial_params": {
299
- "learning_rate": 4.7612058274004114e-06,
300
- "num_cycles": 3.0,
301
- "warmup_ratio": 0.03
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-opt25/trial-number=21-learning_rate=1.6e-06-warmup_ratio=0.080-num_cycles=1.500/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": 4.178253650665283,
14
+ "learning_rate": 1.1556051821104526e-06,
15
+ "loss": 6.3981,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
+ "grad_norm": 1.9749269485473633,
21
+ "learning_rate": 1.5782537021726088e-06,
22
+ "loss": 2.3749,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
+ "grad_norm": 1.4726980924606323,
28
+ "learning_rate": 1.3637510062898264e-06,
29
+ "loss": 1.4006,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
+ "grad_norm": 1.4031742811203003,
35
+ "learning_rate": 1.0095554213221014e-06,
36
+ "loss": 1.1642,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
+ "grad_norm": 1.421210527420044,
42
+ "learning_rate": 6.046599668215422e-07,
43
+ "loss": 1.0397,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
+ "grad_norm": 1.4061120748519897,
49
+ "learning_rate": 2.5079620192718024e-07,
50
+ "loss": 0.9784,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
+ "grad_norm": 1.4008420705795288,
56
+ "learning_rate": 3.687377510596774e-08,
57
+ "loss": 0.9519,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
+ "grad_norm": 1.39585280418396,
63
+ "learning_rate": 1.664152886385891e-08,
64
+ "loss": 0.9482,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
+ "grad_norm": 1.3957849740982056,
70
+ "learning_rate": 1.9518289383020806e-07,
71
+ "loss": 0.9436,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
+ "grad_norm": 1.4641075134277344,
77
+ "learning_rate": 5.276386570231308e-07,
78
+ "loss": 0.9277,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
+ "eval_all_ligands_equal": 0.0,
84
+ "eval_e3_equal": 0.023243482103402564,
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)": 0.7854175872735307,
88
+ "eval_e3_heavy_atoms_difference": 7.005744586831639,
89
+ "eval_e3_heavy_atoms_difference_norm": 0.19202268846027856,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
+ "eval_e3_valid": 0.7854175872735307,
92
+ "eval_has_all_attachment_points": 0.4845779938135219,
93
+ "eval_has_three_substructures": 0.7926646045072913,
94
+ "eval_heavy_atoms_difference": 71.70234202386213,
95
+ "eval_heavy_atoms_difference_norm": 0.9403941983073605,
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)": 0.7095006628369421,
100
+ "eval_linker_heavy_atoms_difference": 11.820945647370747,
101
+ "eval_linker_heavy_atoms_difference_norm": 0.6561966279132151,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
+ "eval_linker_valid": 0.7095006628369421,
104
+ "eval_loss": 0.9539049863815308,
105
+ "eval_num_fragments": 3.1619089703932834,
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)": 0.15510384445426426,
110
+ "eval_poi_heavy_atoms_difference": 29.169686257180732,
111
+ "eval_poi_heavy_atoms_difference_norm": 0.9225394246917481,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
+ "eval_poi_valid": 0.15510384445426426,
114
+ "eval_reassembly": 0.0,
115
+ "eval_reassembly_nostereo": 0.0,
116
+ "eval_runtime": 2245.7826,
117
+ "eval_samples_per_second": 5.038,
118
+ "eval_steps_per_second": 0.079,
119
  "eval_tanimoto_similarity": 0.0,
120
+ "eval_valid": 0.14653115333627928,
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=21-learning_rate=1.6e-06-warmup_ratio=0.080-num_cycles=1.500",
144
  "trial_params": {
145
+ "learning_rate": 1.6155360445904128e-06,
146
+ "num_cycles": 1.5,
147
+ "warmup_ratio": 0.08
148
  }
149
  }
last-checkpoint/training_args.bin CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:ecb78bd82e576fde3f68367b3825e6828ecaa9f0f56f0f0c7edba1aa4d63b16c
3
  size 7416
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:840779dc69cef9253cfbecd1665a91f7f3e4ecfabfa209711398b6be673cceed
3
  size 7416