ribesstefano commited on
Commit
d8e9e07
·
verified ·
1 Parent(s): 74ed4c8

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 sha256:79808196a5a84d0cb2f05ba767a529b9d39d5218136e4c294d33e3e46c70ef18
3
  size 409608164
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:3ebcf628947539344ceabf7ebc899ef8df02dffe421cd545be0a587861b677d3
3
  size 409608164
last-checkpoint/optimizer.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:ff8812887e89c947496d8ab8cd71b420a24be6b82e488713e886e94f7913743f
3
  size 814647162
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:0dcbc0571930bcfbec38e9b3ad3f006283f8ce70e796ba399093f5d1028d150e
3
  size 814647162
last-checkpoint/rng_state.pth CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:74aad9d5b17d876be9e4d6b6f3353a4b59909eb061d599a7c44d6c2e03c798cf
3
  size 14244
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:67843930f7b36709f116e7aef57b5c4339f568f2de52a675685f06f1fd05ec66
3
  size 14244
last-checkpoint/scheduler.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:07d8f542b00c07a19198f5221b28a0ac02536cfb19e79fe9ff0a366dc086c68c
3
  size 1192
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f0e71261348e9b0dc59a24363376590c3d78e50ba5d84bd7d40a5576639924da
3
  size 1192
last-checkpoint/trainer_state.json CHANGED
@@ -1,278 +1,124 @@
1
  {
2
- "best_metric": 0.5381352187361909,
3
- "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25-rand-smiles/trial-number=17-learning_rate=2.8e-05-warmup_ratio=0.060-min_lr=0.000-factor=0.680/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": 0.829456627368927,
14
- "learning_rate": 2.8331451115475792e-05,
15
- "loss": 1.1848,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
- "grad_norm": 0.6500025391578674,
21
- "learning_rate": 2.8331451115475792e-05,
22
- "loss": 0.2962,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
- "grad_norm": 0.47073793411254883,
28
- "learning_rate": 2.8331451115475792e-05,
29
- "loss": 0.1468,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
- "grad_norm": 0.329457551240921,
35
- "learning_rate": 2.8331451115475792e-05,
36
- "loss": 0.0878,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
- "grad_norm": 0.3172358572483063,
42
- "learning_rate": 2.8331451115475792e-05,
43
- "loss": 0.0581,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
- "grad_norm": 0.2527906894683838,
49
- "learning_rate": 2.8331451115475792e-05,
50
- "loss": 0.0424,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
- "grad_norm": 0.20880313217639923,
56
- "learning_rate": 2.8331451115475792e-05,
57
- "loss": 0.0323,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
- "grad_norm": 0.22946058213710785,
63
- "learning_rate": 2.8331451115475792e-05,
64
- "loss": 0.0257,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
- "grad_norm": 0.22088561952114105,
70
- "learning_rate": 2.8331451115475792e-05,
71
- "loss": 0.0207,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
- "grad_norm": 0.22565944492816925,
77
- "learning_rate": 2.8331451115475792e-05,
78
- "loss": 0.0175,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
- "eval_all_ligands_equal": 0.4470172337604949,
84
- "eval_e3_equal": 0.7797613787008396,
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)": 0.9953159522757402,
88
- "eval_e3_heavy_atoms_difference": 0.2501988510826337,
89
- "eval_e3_heavy_atoms_difference_norm": 0.0008378467337176671,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
- "eval_e3_valid": 0.9953159522757402,
92
- "eval_has_all_attachment_points": 0.9885992045956694,
93
- "eval_has_three_substructures": 0.9992929739284137,
94
- "eval_heavy_atoms_difference": 5.620680512593902,
95
- "eval_heavy_atoms_difference_norm": 0.07341529464537826,
96
- "eval_linker_equal": 0.6448961555457358,
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)": 0.9975254087494476,
100
- "eval_linker_heavy_atoms_difference": 0.8009721608484313,
101
- "eval_linker_heavy_atoms_difference_norm": 0.02116394604640135,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
- "eval_linker_valid": 0.9975254087494476,
104
- "eval_loss": 0.2864011228084564,
105
- "eval_num_fragments": 3.0,
106
- "eval_poi_equal": 0.7278833406981883,
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)": 0.9450287229341582,
110
- "eval_poi_heavy_atoms_difference": 1.7335395492708794,
111
- "eval_poi_heavy_atoms_difference_norm": 0.051064183804263204,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
- "eval_poi_valid": 0.9450287229341582,
114
- "eval_reassembly": 0.45417587273530713,
115
- "eval_reassembly_nostereo": 0.4824569155987627,
116
- "eval_runtime": 1504.245,
117
- "eval_samples_per_second": 7.522,
118
- "eval_steps_per_second": 0.118,
119
- "eval_tanimoto_similarity": 0.0,
120
- "eval_valid": 0.9395492708793637,
121
- "step": 5000
122
- },
123
- {
124
- "epoch": 0.542513316235944,
125
- "grad_norm": 0.21528206765651703,
126
- "learning_rate": 2.8331451115475792e-05,
127
- "loss": 0.0151,
128
- "step": 5500
129
- },
130
- {
131
- "epoch": 0.5918327086210298,
132
- "grad_norm": 0.14188343286514282,
133
- "learning_rate": 2.8331451115475792e-05,
134
- "loss": 0.0133,
135
- "step": 6000
136
- },
137
- {
138
- "epoch": 0.6411521010061156,
139
- "grad_norm": 0.13938453793525696,
140
- "learning_rate": 2.8331451115475792e-05,
141
- "loss": 0.0116,
142
- "step": 6500
143
- },
144
- {
145
- "epoch": 0.6904714933912014,
146
- "grad_norm": 0.14794708788394928,
147
- "learning_rate": 2.8331451115475792e-05,
148
- "loss": 0.0102,
149
- "step": 7000
150
- },
151
- {
152
- "epoch": 0.7397908857762873,
153
- "grad_norm": 0.17807906866073608,
154
- "learning_rate": 2.8331451115475792e-05,
155
- "loss": 0.0092,
156
- "step": 7500
157
- },
158
- {
159
- "epoch": 0.7397908857762873,
160
- "eval_all_ligands_equal": 0.5155987627043748,
161
- "eval_e3_equal": 0.7997348652231551,
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)": 0.9950508174988952,
165
- "eval_e3_heavy_atoms_difference": 0.2891736632788334,
166
- "eval_e3_heavy_atoms_difference_norm": 0.0028955297689230454,
167
- "eval_e3_tanimoto_similarity": 0.0,
168
- "eval_e3_valid": 0.9950508174988952,
169
- "eval_has_all_attachment_points": 0.9878038002651348,
170
- "eval_has_three_substructures": 0.9990278391515687,
171
- "eval_heavy_atoms_difference": 5.2259832081308,
172
- "eval_heavy_atoms_difference_norm": 0.06936488082967972,
173
- "eval_linker_equal": 0.7362792752982766,
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)": 0.9962881131241714,
177
- "eval_linker_heavy_atoms_difference": 0.46539991162174105,
178
- "eval_linker_heavy_atoms_difference_norm": 0.007389768929469861,
179
- "eval_linker_tanimoto_similarity": 0.0,
180
- "eval_linker_valid": 0.9962881131241714,
181
- "eval_loss": 0.3027403950691223,
182
- "eval_num_fragments": 3.0004418912947415,
183
- "eval_poi_equal": 0.7507733097657976,
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)": 0.947326557666814,
187
- "eval_poi_heavy_atoms_difference": 1.571011931064958,
188
- "eval_poi_heavy_atoms_difference_norm": 0.04874062832136298,
189
- "eval_poi_tanimoto_similarity": 0.0,
190
- "eval_poi_valid": 0.947326557666814,
191
- "eval_reassembly": 0.5235528060097216,
192
- "eval_reassembly_nostereo": 0.5519222271321255,
193
- "eval_runtime": 1514.2596,
194
- "eval_samples_per_second": 7.472,
195
- "eval_steps_per_second": 0.117,
196
- "eval_tanimoto_similarity": 0.0,
197
- "eval_valid": 0.9410517012814847,
198
- "step": 7500
199
- },
200
- {
201
- "epoch": 0.789110278161373,
202
- "grad_norm": 0.13021309673786163,
203
- "learning_rate": 2.8331451115475792e-05,
204
- "loss": 0.0083,
205
- "step": 8000
206
- },
207
- {
208
- "epoch": 0.8384296705464589,
209
- "grad_norm": 0.15480028092861176,
210
- "learning_rate": 2.8331451115475792e-05,
211
- "loss": 0.0078,
212
- "step": 8500
213
- },
214
- {
215
- "epoch": 0.8877490629315447,
216
- "grad_norm": 0.13444596529006958,
217
- "learning_rate": 2.8331451115475792e-05,
218
- "loss": 0.0069,
219
- "step": 9000
220
- },
221
- {
222
- "epoch": 0.9370684553166305,
223
- "grad_norm": 0.1448230892419815,
224
- "learning_rate": 2.8331451115475792e-05,
225
- "loss": 0.0065,
226
- "step": 9500
227
- },
228
- {
229
- "epoch": 0.9863878477017163,
230
- "grad_norm": 0.09779265522956848,
231
- "learning_rate": 2.8331451115475792e-05,
232
- "loss": 0.0061,
233
- "step": 10000
234
- },
235
- {
236
- "epoch": 0.9863878477017163,
237
- "eval_all_ligands_equal": 0.5381352187361909,
238
- "eval_e3_equal": 0.8015908086610694,
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)": 0.9930181175430844,
242
- "eval_e3_heavy_atoms_difference": 0.3586389748121962,
243
- "eval_e3_heavy_atoms_difference_norm": 0.004046618972503898,
244
- "eval_e3_tanimoto_similarity": 0.0,
245
- "eval_e3_valid": 0.9930181175430844,
246
- "eval_has_all_attachment_points": 0.9855943437914273,
247
- "eval_has_three_substructures": 0.9994697304463102,
248
- "eval_heavy_atoms_difference": 4.982677861246134,
249
- "eval_heavy_atoms_difference_norm": 0.06595580402806239,
250
- "eval_linker_equal": 0.7677419354838709,
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)": 0.9951391957578436,
254
- "eval_linker_heavy_atoms_difference": 0.29235528060097216,
255
- "eval_linker_heavy_atoms_difference_norm": -0.001514220633297117,
256
- "eval_linker_tanimoto_similarity": 0.0,
257
- "eval_linker_valid": 0.9951391957578436,
258
- "eval_loss": 0.3127844035625458,
259
- "eval_num_fragments": 2.9998232434821035,
260
- "eval_poi_equal": 0.7611135660627486,
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)": 0.9520106053910738,
264
- "eval_poi_heavy_atoms_difference": 1.4593901900132566,
265
- "eval_poi_heavy_atoms_difference_norm": 0.04606472460308478,
266
- "eval_poi_tanimoto_similarity": 0.0,
267
- "eval_poi_valid": 0.9520106053910738,
268
- "eval_reassembly": 0.5465311533362793,
269
- "eval_reassembly_nostereo": 0.5773751657092355,
270
- "eval_runtime": 1527.8773,
271
- "eval_samples_per_second": 7.406,
272
  "eval_steps_per_second": 0.116,
273
  "eval_tanimoto_similarity": 0.0,
274
- "eval_valid": 0.9422889969067609,
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": 8.729673191023411e+16,
296
  "train_batch_size": 128,
297
- "trial_name": "trial-number=17-learning_rate=2.8e-05-warmup_ratio=0.060-min_lr=0.000-factor=0.680",
298
  "trial_params": {
299
- "factor": 0.6799999999999999,
300
- "learning_rate": 2.8331451115475792e-05,
301
- "min_lr": 7.147010870778695e-11,
302
- "warmup_ratio": 0.060000000000000005
303
  }
304
  }
 
1
  {
2
+ "best_metric": 0.5203711886875828,
3
+ "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25-rand-smiles/trial-number=18-learning_rate=6.4e-05-warmup_ratio=0.050-min_lr=0.000-factor=0.240/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": 0.6651552319526672,
14
+ "learning_rate": 6.395962809058983e-05,
15
+ "loss": 0.8862,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
+ "grad_norm": 0.36618563532829285,
21
+ "learning_rate": 6.395962809058983e-05,
22
+ "loss": 0.1584,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
+ "grad_norm": 0.24036307632923126,
28
+ "learning_rate": 6.395962809058983e-05,
29
+ "loss": 0.0632,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
+ "grad_norm": 0.20140977203845978,
35
+ "learning_rate": 6.395962809058983e-05,
36
+ "loss": 0.036,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
+ "grad_norm": 0.20425930619239807,
42
+ "learning_rate": 6.395962809058983e-05,
43
+ "loss": 0.0238,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
+ "grad_norm": 0.17172357439994812,
49
+ "learning_rate": 6.395962809058983e-05,
50
+ "loss": 0.0176,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
+ "grad_norm": 0.1477121263742447,
56
+ "learning_rate": 6.395962809058983e-05,
57
+ "loss": 0.0136,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
+ "grad_norm": 0.14009247720241547,
63
+ "learning_rate": 6.395962809058983e-05,
64
+ "loss": 0.0117,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
+ "grad_norm": 0.15225987136363983,
70
+ "learning_rate": 6.395962809058983e-05,
71
+ "loss": 0.0101,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
+ "grad_norm": 0.10719581693410873,
77
+ "learning_rate": 6.395962809058983e-05,
78
+ "loss": 0.0091,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
+ "eval_all_ligands_equal": 0.5203711886875828,
84
+ "eval_e3_equal": 0.7986743261157755,
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)": 0.9968183826778613,
88
+ "eval_e3_heavy_atoms_difference": 0.2883782589482987,
89
+ "eval_e3_heavy_atoms_difference_norm": 0.0026646216057636496,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
+ "eval_e3_valid": 0.9968183826778613,
92
+ "eval_has_all_attachment_points": 0.9934600088378259,
93
+ "eval_has_three_substructures": 0.9997348652231551,
94
+ "eval_heavy_atoms_difference": 3.5762262483429077,
95
+ "eval_heavy_atoms_difference_norm": 0.04541662513362855,
96
+ "eval_linker_equal": 0.7444984533804684,
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)": 0.9977905435262925,
100
+ "eval_linker_heavy_atoms_difference": 0.5421122403888643,
101
+ "eval_linker_heavy_atoms_difference_norm": 0.011771790126169518,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
+ "eval_linker_valid": 0.9977905435262925,
104
+ "eval_loss": 0.30581870675086975,
105
+ "eval_num_fragments": 3.0000883782589485,
106
+ "eval_poi_equal": 0.7498895271763146,
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)": 0.9690676093680954,
110
+ "eval_poi_heavy_atoms_difference": 0.9461776403004861,
111
+ "eval_poi_heavy_atoms_difference_norm": 0.020891734527612723,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
+ "eval_poi_valid": 0.9690676093680954,
114
+ "eval_reassembly": 0.5271763146266019,
115
+ "eval_reassembly_nostereo": 0.5572249226690235,
116
+ "eval_runtime": 1528.5096,
117
+ "eval_samples_per_second": 7.403,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
118
  "eval_steps_per_second": 0.116,
119
  "eval_tanimoto_similarity": 0.0,
120
+ "eval_valid": 0.9646486964206805,
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=18-learning_rate=6.4e-05-warmup_ratio=0.050-min_lr=0.000-factor=0.240",
144
  "trial_params": {
145
+ "factor": 0.24000000000000002,
146
+ "learning_rate": 6.395962809058983e-05,
147
+ "min_lr": 2.960963543629417e-11,
148
+ "warmup_ratio": 0.05
149
  }
150
  }
last-checkpoint/training_args.bin CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:1fcc15b3e8d0f3d92cb620d02832c5928bcf97a45dce5fd03bf77c673c58eafa
3
  size 7544
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:a4caf8b92e41afe1413a9109a3dd0d39d9313ce66cb8219e2d7a9d77a7c66cd7
3
  size 7544