ribesstefano commited on
Commit
8618ff2
·
verified ·
1 Parent(s): 6debcb3

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:df1101b9ef48c8a8e13a86f96d7c87c77002e5901c7124cedc5f1c4abb0269a3
3
  size 409608164
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:8db8efcad1aad20ea13d8d7d9984c578dc26107113f2497cf58241ecf64f4d31
3
  size 409608164
last-checkpoint/optimizer.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:0da88d6c1776a599023ee1ccfcd48faaa4e5554c05dc520a4e1ca8da964dadd1
3
  size 814647162
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:560f8225b4e422be5f485e5789c61967387596cfa41340c896b0266a600274ac
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:e83fecf83dbd00bd37cc0cf9fceb9e941a3938dfcac00cdc765aed3a0abd49a0
3
  size 14244
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:531dd6bbf77c44f3e63c47977249a318aeba5dfdb9fc88095e97b169b391cfae
3
  size 14244
last-checkpoint/scheduler.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:45c9aa4312086aa533a59b41f63cd1a73b3f25425cdd947baf7efebf9cc54e57
3
  size 1192
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:7cfc9e052be169b4866b608e61d6ced510b87df870008f31ab0cca1e2c28c1a8
3
  size 1192
last-checkpoint/trainer_state.json CHANGED
@@ -1,278 +1,124 @@
1
  {
2
- "best_metric": 0.014228899690676094,
3
- "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25-rand-smiles/trial-number=4-learning_rate=4.2e-06-warmup_ratio=0.030-min_lr=0.000-factor=0.800/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": 1.2561712265014648,
14
- "learning_rate": 4.170090767711237e-06,
15
- "loss": 2.4831,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
- "grad_norm": 1.2166751623153687,
21
- "learning_rate": 4.170090767711237e-06,
22
- "loss": 1.0063,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
- "grad_norm": 1.246788501739502,
28
- "learning_rate": 4.170090767711237e-06,
29
- "loss": 0.7292,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
- "grad_norm": 1.0463918447494507,
35
- "learning_rate": 4.170090767711237e-06,
36
- "loss": 0.5705,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
- "grad_norm": 1.0265284776687622,
42
- "learning_rate": 4.170090767711237e-06,
43
- "loss": 0.4664,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
- "grad_norm": 1.0784770250320435,
49
- "learning_rate": 4.170090767711237e-06,
50
- "loss": 0.3926,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
- "grad_norm": 0.7869899272918701,
56
- "learning_rate": 4.170090767711237e-06,
57
- "loss": 0.3353,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
- "grad_norm": 1.0476751327514648,
63
- "learning_rate": 4.170090767711237e-06,
64
- "loss": 0.2925,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
- "grad_norm": 0.7107057571411133,
70
- "learning_rate": 4.170090767711237e-06,
71
- "loss": 0.2574,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
- "grad_norm": 0.6933206915855408,
77
- "learning_rate": 4.170090767711237e-06,
78
- "loss": 0.2316,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
- "eval_all_ligands_equal": 8.837825894829872e-05,
84
- "eval_e3_equal": 0.19681838267786125,
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)": 0.9943437914273089,
88
- "eval_e3_heavy_atoms_difference": -1.1870967741935483,
89
- "eval_e3_heavy_atoms_difference_norm": -0.068259312401578,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
- "eval_e3_valid": 0.9943437914273089,
92
- "eval_has_all_attachment_points": 0.940521431727795,
93
- "eval_has_three_substructures": 0.9947856827220504,
94
- "eval_heavy_atoms_difference": 24.551922227132124,
95
- "eval_heavy_atoms_difference_norm": 0.31476917674862775,
96
- "eval_linker_equal": 0.005125939019001326,
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)": 0.9897481219619974,
100
- "eval_linker_heavy_atoms_difference": 5.2481661511268225,
101
- "eval_linker_heavy_atoms_difference_norm": 0.21898110136881632,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
- "eval_linker_valid": 0.9897481219619974,
104
- "eval_loss": 0.386488139629364,
105
- "eval_num_fragments": 2.99531595227574,
106
- "eval_poi_equal": 0.1725143614670791,
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)": 0.748210340256297,
110
- "eval_poi_heavy_atoms_difference": 9.451701281484755,
111
- "eval_poi_heavy_atoms_difference_norm": 0.26897859855195805,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
- "eval_poi_valid": 0.748210340256297,
114
- "eval_reassembly": 0.00017675651789659743,
115
- "eval_reassembly_nostereo": 0.00035351303579319487,
116
- "eval_runtime": 1509.5004,
117
- "eval_samples_per_second": 7.496,
118
- "eval_steps_per_second": 0.117,
119
  "eval_tanimoto_similarity": 0.0,
120
- "eval_valid": 0.7445868316394167,
121
  "step": 5000
122
- },
123
- {
124
- "epoch": 0.542513316235944,
125
- "grad_norm": 0.5555406808853149,
126
- "learning_rate": 4.170090767711237e-06,
127
- "loss": 0.2088,
128
- "step": 5500
129
- },
130
- {
131
- "epoch": 0.5918327086210298,
132
- "grad_norm": 0.5531201958656311,
133
- "learning_rate": 4.170090767711237e-06,
134
- "loss": 0.1901,
135
- "step": 6000
136
- },
137
- {
138
- "epoch": 0.6411521010061156,
139
- "grad_norm": 0.46529698371887207,
140
- "learning_rate": 4.170090767711237e-06,
141
- "loss": 0.1745,
142
- "step": 6500
143
- },
144
- {
145
- "epoch": 0.6904714933912014,
146
- "grad_norm": 0.538395881652832,
147
- "learning_rate": 4.170090767711237e-06,
148
- "loss": 0.1613,
149
- "step": 7000
150
- },
151
- {
152
- "epoch": 0.7397908857762873,
153
- "grad_norm": 0.4872206449508667,
154
- "learning_rate": 4.170090767711237e-06,
155
- "loss": 0.1496,
156
- "step": 7500
157
- },
158
- {
159
- "epoch": 0.7397908857762873,
160
- "eval_all_ligands_equal": 0.003358373840035351,
161
- "eval_e3_equal": 0.34025629695095005,
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)": 0.9990278391515687,
165
- "eval_e3_heavy_atoms_difference": -0.9244365885992046,
166
- "eval_e3_heavy_atoms_difference_norm": -0.05036084634398262,
167
- "eval_e3_tanimoto_similarity": 0.0,
168
- "eval_e3_valid": 0.9990278391515687,
169
- "eval_has_all_attachment_points": 0.9679186920017676,
170
- "eval_has_three_substructures": 0.999116217410517,
171
- "eval_heavy_atoms_difference": 13.730181175430843,
172
- "eval_heavy_atoms_difference_norm": 0.17663834197618247,
173
- "eval_linker_equal": 0.015554573574900574,
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)": 0.9950508174988952,
177
- "eval_linker_heavy_atoms_difference": 3.765002209456474,
178
- "eval_linker_heavy_atoms_difference_norm": 0.1332725666526942,
179
- "eval_linker_tanimoto_similarity": 0.0,
180
- "eval_linker_valid": 0.9950508174988952,
181
- "eval_loss": 0.34545832872390747,
182
- "eval_num_fragments": 2.9998232434821035,
183
- "eval_poi_equal": 0.35704816615112683,
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)": 0.8675209898365002,
187
- "eval_poi_heavy_atoms_difference": 4.575430844012373,
188
- "eval_poi_heavy_atoms_difference_norm": 0.13147539573241804,
189
- "eval_poi_tanimoto_similarity": 0.0,
190
- "eval_poi_valid": 0.8675209898365002,
191
- "eval_reassembly": 0.00344675209898365,
192
- "eval_reassembly_nostereo": 0.004595669465311533,
193
- "eval_runtime": 1597.4791,
194
- "eval_samples_per_second": 7.083,
195
- "eval_steps_per_second": 0.111,
196
- "eval_tanimoto_similarity": 0.0,
197
- "eval_valid": 0.8638091029606717,
198
- "step": 7500
199
- },
200
- {
201
- "epoch": 0.789110278161373,
202
- "grad_norm": 0.5376918911933899,
203
- "learning_rate": 4.170090767711237e-06,
204
- "loss": 0.1402,
205
- "step": 8000
206
- },
207
- {
208
- "epoch": 0.8384296705464589,
209
- "grad_norm": 0.3944121301174164,
210
- "learning_rate": 4.170090767711237e-06,
211
- "loss": 0.1315,
212
- "step": 8500
213
- },
214
- {
215
- "epoch": 0.8877490629315447,
216
- "grad_norm": 0.48968130350112915,
217
- "learning_rate": 4.170090767711237e-06,
218
- "loss": 0.1237,
219
- "step": 9000
220
- },
221
- {
222
- "epoch": 0.9370684553166305,
223
- "grad_norm": 0.4314245879650116,
224
- "learning_rate": 4.170090767711237e-06,
225
- "loss": 0.117,
226
- "step": 9500
227
- },
228
- {
229
- "epoch": 0.9863878477017163,
230
- "grad_norm": 0.4241904616355896,
231
- "learning_rate": 4.170090767711237e-06,
232
- "loss": 0.111,
233
- "step": 10000
234
- },
235
- {
236
- "epoch": 0.9863878477017163,
237
- "eval_all_ligands_equal": 0.014228899690676094,
238
- "eval_e3_equal": 0.43243482103402564,
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)": 0.9985859478568272,
242
- "eval_e3_heavy_atoms_difference": -0.7708351745470614,
243
- "eval_e3_heavy_atoms_difference_norm": -0.046181472855197955,
244
- "eval_e3_tanimoto_similarity": 0.0,
245
- "eval_e3_valid": 0.9985859478568272,
246
- "eval_has_all_attachment_points": 0.9783473265576668,
247
- "eval_has_three_substructures": 0.9987627043747238,
248
- "eval_heavy_atoms_difference": 7.829960229783473,
249
- "eval_heavy_atoms_difference_norm": 0.09936110916411747,
250
- "eval_linker_equal": 0.040565620857269113,
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)": 0.9955810870525851,
254
- "eval_linker_heavy_atoms_difference": 1.6191780821917807,
255
- "eval_linker_heavy_atoms_difference_norm": 0.023629316247238026,
256
- "eval_linker_tanimoto_similarity": 0.0,
257
- "eval_linker_valid": 0.9955810870525851,
258
- "eval_loss": 0.32917484641075134,
259
- "eval_num_fragments": 2.9992929739284135,
260
- "eval_poi_equal": 0.4608926204153778,
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)": 0.9138311975254088,
264
- "eval_poi_heavy_atoms_difference": 2.668316394167035,
265
- "eval_poi_heavy_atoms_difference_norm": 0.06637303713815954,
266
- "eval_poi_tanimoto_similarity": 0.0,
267
- "eval_poi_valid": 0.9138311975254088,
268
- "eval_reassembly": 0.014670790985417587,
269
- "eval_reassembly_nostereo": 0.018912947414935925,
270
- "eval_runtime": 1533.4309,
271
- "eval_samples_per_second": 7.379,
272
- "eval_steps_per_second": 0.115,
273
- "eval_tanimoto_similarity": 0.0,
274
- "eval_valid": 0.9113566062748564,
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=4-learning_rate=4.2e-06-warmup_ratio=0.030-min_lr=0.000-factor=0.800",
298
  "trial_params": {
299
- "factor": 0.8,
300
- "learning_rate": 4.170090767711237e-06,
301
- "min_lr": 6.0724410942321634e-12,
302
- "warmup_ratio": 0.03
303
  }
304
  }
 
1
  {
2
+ "best_metric": 0.0,
3
+ "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25-rand-smiles/trial-number=5-learning_rate=1.1e-06-warmup_ratio=0.070-min_lr=0.000-factor=0.910/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": 3.6603024005889893,
14
+ "learning_rate": 1.1386440825931043e-06,
15
+ "loss": 4.2002,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
+ "grad_norm": 1.9637521505355835,
21
+ "learning_rate": 1.1386440825931043e-06,
22
+ "loss": 1.9187,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
+ "grad_norm": 1.449631929397583,
28
+ "learning_rate": 1.1386440825931043e-06,
29
+ "loss": 1.4159,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
+ "grad_norm": 1.434281826019287,
35
+ "learning_rate": 1.1386440825931043e-06,
36
+ "loss": 1.2066,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
+ "grad_norm": 1.311953067779541,
42
+ "learning_rate": 1.1386440825931043e-06,
43
+ "loss": 1.0605,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
+ "grad_norm": 1.3984962701797485,
49
+ "learning_rate": 1.1386440825931043e-06,
50
+ "loss": 0.9508,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
+ "grad_norm": 1.29249906539917,
56
+ "learning_rate": 1.1386440825931043e-06,
57
+ "loss": 0.8594,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
+ "grad_norm": 1.4493184089660645,
63
+ "learning_rate": 1.1386440825931043e-06,
64
+ "loss": 0.786,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
+ "grad_norm": 1.42921781539917,
70
+ "learning_rate": 1.1386440825931043e-06,
71
+ "loss": 0.7204,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
+ "grad_norm": 1.4308568239212036,
77
+ "learning_rate": 1.1386440825931043e-06,
78
+ "loss": 0.6681,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
+ "eval_all_ligands_equal": 0.0,
84
+ "eval_e3_equal": 0.04348210340256297,
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)": 0.9496243923994697,
88
+ "eval_e3_heavy_atoms_difference": 1.6608926204153778,
89
+ "eval_e3_heavy_atoms_difference_norm": 0.007137613196833208,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
+ "eval_e3_valid": 0.9496243923994697,
92
+ "eval_has_all_attachment_points": 0.6837825894829872,
93
+ "eval_has_three_substructures": 0.950596553247901,
94
+ "eval_heavy_atoms_difference": 64.6774193548387,
95
+ "eval_heavy_atoms_difference_norm": 0.8393433147141454,
96
+ "eval_linker_equal": 0.0013256738842244808,
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)": 0.9260273972602739,
100
+ "eval_linker_heavy_atoms_difference": 9.002651347768449,
101
+ "eval_linker_heavy_atoms_difference_norm": 0.45586405473119984,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
+ "eval_linker_valid": 0.9260273972602739,
104
+ "eval_loss": 0.7126381993293762,
105
+ "eval_num_fragments": 3.0372956252761822,
106
+ "eval_poi_equal": 0.00017675651789659743,
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)": 0.29854175872735306,
110
+ "eval_poi_heavy_atoms_difference": 25.908882015024304,
111
+ "eval_poi_heavy_atoms_difference_norm": 0.7922565446145508,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
+ "eval_poi_valid": 0.29854175872735306,
114
+ "eval_reassembly": 0.0,
115
+ "eval_reassembly_nostereo": 0.0,
116
+ "eval_runtime": 1368.1465,
117
+ "eval_samples_per_second": 8.27,
118
+ "eval_steps_per_second": 0.129,
119
  "eval_tanimoto_similarity": 0.0,
120
+ "eval_valid": 0.2896155545735749,
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=5-learning_rate=1.1e-06-warmup_ratio=0.070-min_lr=0.000-factor=0.910",
144
  "trial_params": {
145
+ "factor": 0.91,
146
+ "learning_rate": 1.1386440825931043e-06,
147
+ "min_lr": 1.1386082331680292e-12,
148
+ "warmup_ratio": 0.06999999999999999
149
  }
150
  }
last-checkpoint/training_args.bin CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:bb3a31938db14c7e84935e0b50cb36c1f4b49136a4342b4b9c8e65d937342068
3
  size 7544
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:a378ac23f30a31ba156b2d137739247698d58210a372732645c0744c38de224f
3
  size 7544