ribesstefano commited on
Commit
26dc3f5
·
verified ·
1 Parent(s): a272783

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 sha256:7a61ea7637fda21b72fdbad601e1527d3ef6f2b0a62bbe17a590ef3a256223ab
3
  size 409608164
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:4facf2cd59bd07430325a7e95dc0f934639aab9c7a64d3e81ef63346734eb4a0
3
  size 409608164
last-checkpoint/optimizer.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:86a20c8dbafd6cda005fc73f9935dbaafa303b26467ff4119361b8b4f9a8987a
3
  size 814647162
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:33e882626ab2ec1176a85be8fbf00ddbe2963c220982b57cc77c6cbbd4537ecc
3
  size 814647162
last-checkpoint/rng_state.pth CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:7a82ee9ed7c6d88284a71c972a8c5b38503f8fe351bedb2aa6afa5ac28de3166
3
  size 14244
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:3107a8423b649a220f9ceee56b729bc016d33d9bae62e9f9acf02257a7f7e076
3
  size 14244
last-checkpoint/scheduler.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:71dc6d5dcb59b498bc7c266d177b67bc04670f5303f55431f1ef375618962c40
3
  size 1192
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:a5679015cfd19ea0d96ce6d5f4b084c997dfb24e64c9c229bd6b3335cb0bbf45
3
  size 1192
last-checkpoint/trainer_state.json CHANGED
@@ -1,278 +1,124 @@
1
  {
2
- "best_metric": 0.5429960229783474,
3
- "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25/trial-number=17-learning_rate=3.0e-05-warmup_ratio=0.040-min_lr=0.000-factor=0.920/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": 0.8111265301704407,
14
- "learning_rate": 2.9820202963061836e-05,
15
- "loss": 1.1535,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
- "grad_norm": 0.6221622228622437,
21
- "learning_rate": 2.9820202963061836e-05,
22
- "loss": 0.2655,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
- "grad_norm": 0.40338921546936035,
28
- "learning_rate": 2.9820202963061836e-05,
29
- "loss": 0.1215,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
- "grad_norm": 0.4261607527732849,
35
- "learning_rate": 2.9820202963061836e-05,
36
- "loss": 0.0693,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
- "grad_norm": 0.2943068742752075,
42
- "learning_rate": 2.9820202963061836e-05,
43
- "loss": 0.0448,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
- "grad_norm": 0.23645180463790894,
49
- "learning_rate": 2.9820202963061836e-05,
50
- "loss": 0.0315,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
- "grad_norm": 0.21555276215076447,
56
- "learning_rate": 2.9820202963061836e-05,
57
- "loss": 0.0234,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
- "grad_norm": 0.1779136061668396,
63
- "learning_rate": 2.9820202963061836e-05,
64
- "loss": 0.0185,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
- "grad_norm": 0.19552886486053467,
70
- "learning_rate": 2.9820202963061836e-05,
71
- "loss": 0.0148,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
- "grad_norm": 0.19583949446678162,
77
- "learning_rate": 2.9820202963061836e-05,
78
- "loss": 0.0125,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
- "eval_all_ligands_equal": 0.4684931506849315,
84
- "eval_e3_equal": 0.7917808219178082,
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)": 0.9860362350861688,
88
- "eval_e3_heavy_atoms_difference": 0.6702607158638975,
89
- "eval_e3_heavy_atoms_difference_norm": 0.016053258658166824,
90
- "eval_e3_tanimoto_similarity": 0.0,
91
- "eval_e3_valid": 0.9860362350861688,
92
- "eval_has_all_attachment_points": 0.9776403004860804,
93
- "eval_has_three_substructures": 0.9986743261157756,
94
- "eval_heavy_atoms_difference": 8.543172779496244,
95
- "eval_heavy_atoms_difference_norm": 0.11141826794923385,
96
- "eval_linker_equal": 0.6692001767565179,
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)": 0.9953159522757402,
100
- "eval_linker_heavy_atoms_difference": 0.6352629253203712,
101
- "eval_linker_heavy_atoms_difference_norm": 0.01089709976053881,
102
- "eval_linker_tanimoto_similarity": 0.0,
103
- "eval_linker_valid": 0.9953159522757402,
104
- "eval_loss": 0.2863834500312805,
105
- "eval_num_fragments": 2.999734865223155,
106
- "eval_poi_equal": 0.7314184710561202,
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)": 0.9161290322580645,
110
- "eval_poi_heavy_atoms_difference": 2.5583738400353515,
111
- "eval_poi_heavy_atoms_difference_norm": 0.08326207706377355,
112
- "eval_poi_tanimoto_similarity": 0.0,
113
- "eval_poi_valid": 0.9161290322580645,
114
- "eval_reassembly": 0.4752982766239505,
115
- "eval_reassembly_nostereo": 0.4969509500662837,
116
- "eval_runtime": 1575.0561,
117
- "eval_samples_per_second": 7.184,
118
- "eval_steps_per_second": 0.112,
119
- "eval_tanimoto_similarity": 0.0,
120
- "eval_valid": 0.9024304021210782,
121
- "step": 5000
122
- },
123
- {
124
- "epoch": 0.542513316235944,
125
- "grad_norm": 0.2314692586660385,
126
- "learning_rate": 2.9820202963061836e-05,
127
- "loss": 0.0111,
128
- "step": 5500
129
- },
130
- {
131
- "epoch": 0.5918327086210298,
132
- "grad_norm": 0.18242871761322021,
133
- "learning_rate": 2.9820202963061836e-05,
134
- "loss": 0.009,
135
- "step": 6000
136
- },
137
- {
138
- "epoch": 0.6411521010061156,
139
- "grad_norm": 0.10980498045682907,
140
- "learning_rate": 2.9820202963061836e-05,
141
- "loss": 0.0076,
142
- "step": 6500
143
- },
144
- {
145
- "epoch": 0.6904714933912014,
146
- "grad_norm": 0.16299337148666382,
147
- "learning_rate": 2.9820202963061836e-05,
148
- "loss": 0.0068,
149
- "step": 7000
150
- },
151
- {
152
- "epoch": 0.7397908857762873,
153
- "grad_norm": 0.12339688092470169,
154
- "learning_rate": 2.9820202963061836e-05,
155
- "loss": 0.006,
156
- "step": 7500
157
- },
158
- {
159
- "epoch": 0.7397908857762873,
160
- "eval_all_ligands_equal": 0.5241714538223597,
161
- "eval_e3_equal": 0.8060097216084843,
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)": 0.9925762262483429,
165
- "eval_e3_heavy_atoms_difference": 0.5046398585947857,
166
- "eval_e3_heavy_atoms_difference_norm": 0.012506766392800078,
167
  "eval_e3_tanimoto_similarity": 0.0,
168
- "eval_e3_valid": 0.9925762262483429,
169
- "eval_has_all_attachment_points": 0.98285461776403,
170
- "eval_has_three_substructures": 0.9989394608926204,
171
- "eval_heavy_atoms_difference": 7.9138311975254085,
172
- "eval_heavy_atoms_difference_norm": 0.10564871343022675,
173
- "eval_linker_equal": 0.745558992487848,
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)": 0.9953159522757402,
177
- "eval_linker_heavy_atoms_difference": 0.4954485196641626,
178
- "eval_linker_heavy_atoms_difference_norm": 0.010940469592472513,
179
- "eval_linker_tanimoto_similarity": 0.0,
180
- "eval_linker_valid": 0.9953159522757402,
181
- "eval_loss": 0.29941797256469727,
182
- "eval_num_fragments": 3.0001767565178965,
183
- "eval_poi_equal": 0.7492708793636765,
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)": 0.9146266018559435,
187
- "eval_poi_heavy_atoms_difference": 2.3985859478568274,
188
- "eval_poi_heavy_atoms_difference_norm": 0.07887315198549666,
189
- "eval_poi_tanimoto_similarity": 0.0,
190
- "eval_poi_valid": 0.9146266018559435,
191
- "eval_reassembly": 0.5321254971277066,
192
- "eval_reassembly_nostereo": 0.5574900574458683,
193
- "eval_runtime": 1485.9806,
194
- "eval_samples_per_second": 7.615,
195
- "eval_steps_per_second": 0.119,
196
- "eval_tanimoto_similarity": 0.0,
197
- "eval_valid": 0.9061422889969067,
198
- "step": 7500
199
- },
200
- {
201
- "epoch": 0.789110278161373,
202
- "grad_norm": 0.12520654499530792,
203
- "learning_rate": 2.9820202963061836e-05,
204
- "loss": 0.0055,
205
- "step": 8000
206
- },
207
- {
208
- "epoch": 0.8384296705464589,
209
- "grad_norm": 0.1034364253282547,
210
- "learning_rate": 2.9820202963061836e-05,
211
- "loss": 0.005,
212
- "step": 8500
213
- },
214
- {
215
- "epoch": 0.8877490629315447,
216
- "grad_norm": 0.10550062358379364,
217
- "learning_rate": 2.9820202963061836e-05,
218
- "loss": 0.0048,
219
- "step": 9000
220
- },
221
- {
222
- "epoch": 0.9370684553166305,
223
- "grad_norm": 0.13824567198753357,
224
- "learning_rate": 2.9820202963061836e-05,
225
- "loss": 0.0043,
226
- "step": 9500
227
- },
228
- {
229
- "epoch": 0.9863878477017163,
230
- "grad_norm": 0.15833278000354767,
231
- "learning_rate": 2.9820202963061836e-05,
232
- "loss": 0.0038,
233
- "step": 10000
234
- },
235
- {
236
- "epoch": 0.9863878477017163,
237
- "eval_all_ligands_equal": 0.5429960229783474,
238
- "eval_e3_equal": 0.8071586389748122,
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)": 0.984887317719841,
242
- "eval_e3_heavy_atoms_difference": 0.8034467520989836,
243
- "eval_e3_heavy_atoms_difference_norm": 0.02125446432315408,
244
- "eval_e3_tanimoto_similarity": 0.0,
245
- "eval_e3_valid": 0.984887317719841,
246
  "eval_has_all_attachment_points": 0.9769332744144941,
247
- "eval_has_three_substructures": 0.999116217410517,
248
- "eval_heavy_atoms_difference": 8.502253645603181,
249
- "eval_heavy_atoms_difference_norm": 0.11227440088334313,
250
- "eval_linker_equal": 0.7692443658859921,
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)": 0.994962439239947,
254
- "eval_linker_heavy_atoms_difference": 0.4276623950508175,
255
- "eval_linker_heavy_atoms_difference_norm": 0.005157246912280847,
256
  "eval_linker_tanimoto_similarity": 0.0,
257
- "eval_linker_valid": 0.994962439239947,
258
- "eval_loss": 0.3057071268558502,
259
- "eval_num_fragments": 2.99946973044631,
260
- "eval_poi_equal": 0.765090587715422,
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)": 0.9160406539991163,
264
- "eval_poi_heavy_atoms_difference": 2.5110030932390632,
265
- "eval_poi_heavy_atoms_difference_norm": 0.08489418307327841,
266
  "eval_poi_tanimoto_similarity": 0.0,
267
- "eval_poi_valid": 0.9160406539991163,
268
- "eval_reassembly": 0.5519222271321255,
269
- "eval_reassembly_nostereo": 0.5775519222271321,
270
- "eval_runtime": 1479.3283,
271
- "eval_samples_per_second": 7.649,
272
- "eval_steps_per_second": 0.12,
273
  "eval_tanimoto_similarity": 0.0,
274
- "eval_valid": 0.8999558108705259,
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": 8.663036348367667e+16,
296
  "train_batch_size": 128,
297
- "trial_name": "trial-number=17-learning_rate=3.0e-05-warmup_ratio=0.040-min_lr=0.000-factor=0.920",
298
  "trial_params": {
299
- "factor": 0.92,
300
- "learning_rate": 2.9820202963061836e-05,
301
- "min_lr": 1.722197529042705e-09,
302
  "warmup_ratio": 0.04
303
  }
304
  }
 
1
  {
2
+ "best_metric": 0.5058771542200619,
3
+ "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25/trial-number=18-learning_rate=4.6e-05-warmup_ratio=0.040-min_lr=0.000-factor=0.820/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": 0.6691174507141113,
14
+ "learning_rate": 4.606381292021688e-05,
15
+ "loss": 0.9843,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
+ "grad_norm": 0.477989137172699,
21
+ "learning_rate": 4.606381292021688e-05,
22
+ "loss": 0.1813,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
+ "grad_norm": 0.28420594334602356,
28
+ "learning_rate": 4.606381292021688e-05,
29
+ "loss": 0.0718,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
+ "grad_norm": 0.27486521005630493,
35
+ "learning_rate": 4.606381292021688e-05,
36
+ "loss": 0.0395,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
+ "grad_norm": 0.2175276130437851,
42
+ "learning_rate": 4.606381292021688e-05,
43
+ "loss": 0.0251,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
+ "grad_norm": 0.1922473907470703,
49
+ "learning_rate": 4.606381292021688e-05,
50
+ "loss": 0.0177,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
+ "grad_norm": 0.18892481923103333,
56
+ "learning_rate": 4.606381292021688e-05,
57
+ "loss": 0.0139,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
+ "grad_norm": 0.1161535456776619,
63
+ "learning_rate": 4.606381292021688e-05,
64
+ "loss": 0.0111,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
+ "grad_norm": 0.16154514253139496,
70
+ "learning_rate": 4.606381292021688e-05,
71
+ "loss": 0.0088,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
+ "grad_norm": 0.16088169813156128,
77
+ "learning_rate": 4.606381292021688e-05,
78
+ "loss": 0.0078,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
+ "eval_all_ligands_equal": 0.5058771542200619,
84
+ "eval_e3_equal": 0.7961113566062749,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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)": 0.9840919133893062,
88
+ "eval_e3_heavy_atoms_difference": 0.6767123287671233,
89
+ "eval_e3_heavy_atoms_difference_norm": 0.015499968999404092,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
+ "eval_e3_valid": 0.9840919133893062,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
92
  "eval_has_all_attachment_points": 0.9769332744144941,
93
+ "eval_has_three_substructures": 0.9985859478568272,
94
+ "eval_heavy_atoms_difference": 7.977021652673442,
95
+ "eval_heavy_atoms_difference_norm": 0.105252234591077,
96
+ "eval_linker_equal": 0.7311533362792753,
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)": 0.9948740609809986,
100
+ "eval_linker_heavy_atoms_difference": 0.3779938135218736,
101
+ "eval_linker_heavy_atoms_difference_norm": 0.0009991271739602798,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
+ "eval_linker_valid": 0.9948740609809986,
104
+ "eval_loss": 0.2940564453601837,
105
+ "eval_num_fragments": 3.0001767565178965,
106
+ "eval_poi_equal": 0.7464427750773309,
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)": 0.9214317277949624,
110
+ "eval_poi_heavy_atoms_difference": 2.363411400795404,
111
+ "eval_poi_heavy_atoms_difference_norm": 0.07635871742465364,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
+ "eval_poi_valid": 0.9214317277949624,
114
+ "eval_reassembly": 0.5125939019001325,
115
+ "eval_reassembly_nostereo": 0.5362792752982766,
116
+ "eval_runtime": 1595.0598,
117
+ "eval_samples_per_second": 7.094,
118
+ "eval_steps_per_second": 0.111,
119
  "eval_tanimoto_similarity": 0.0,
120
+ "eval_valid": 0.9042863455589925,
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=18-learning_rate=4.6e-05-warmup_ratio=0.040-min_lr=0.000-factor=0.820",
144
  "trial_params": {
145
+ "factor": 0.8200000000000001,
146
+ "learning_rate": 4.606381292021688e-05,
147
+ "min_lr": 9.570957186046748e-10,
148
  "warmup_ratio": 0.04
149
  }
150
  }
last-checkpoint/training_args.bin CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:6c0c65a253d9e4d46458ef023c347b220bca27764a4e8ce84f3b6c7e7314cf12
3
  size 7480
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:2e04b41249f2af71631a96b3a173f413442176c6aa411f0cd997e7794a68d4b4
3
  size 7480