ribesstefano commited on
Commit
8ce17fb
·
verified ·
1 Parent(s): 5e7fb51

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 sha256:31c731ab87ef520c3117511325377a97ad15dae205398f02dd514384b602391c
3
  size 409608164
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:b82a301955ba2f9aa82bc36a51700c2c354faa17ac4f30bc0aa4339fd6c6cc84
3
  size 409608164
last-checkpoint/optimizer.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:f71cd535304c2b198acff97c548e4ee56f03d5adfcbd904755b7b5913a41ff61
3
  size 814647162
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:679f7566bcb90cff383d136ac5615185bbb042c5fdd60a6a54161b0486810ca0
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:a81971f92b5a7d51fd883bb2a9836249c0ca486f06f6b05ff9ab1e0e69716d27
3
  size 14244
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:2270c457ff62ab3539634227f4be5896e72a1b0aeb7296f63fc6037e55d6aafd
3
  size 14244
last-checkpoint/scheduler.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:4b7b070ada8df300c245e6daa26454039d86686f1bc260ce873c14c0e22ed613
3
  size 1064
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:efc7b8261dc9f0cd1aff039568c605f93169128d3740989947948ba3d1781e01
3
  size 1064
last-checkpoint/trainer_state.json CHANGED
@@ -1,278 +1,124 @@
1
  {
2
- "best_metric": 0.41882456915598765,
3
- "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_cosine-opt25-rand-smiles/trial-number=17-learning_rate=2.3e-05-warmup_ratio=0.070-num_cycles=5.500/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": 1.1214300394058228,
14
- "learning_rate": 1.66041292757749e-05,
15
- "loss": 3.0065,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
- "grad_norm": 0.7123772501945496,
21
- "learning_rate": 1.6680127157646984e-05,
22
- "loss": 0.577,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
- "grad_norm": 0.728777289390564,
28
- "learning_rate": 1.586004103408713e-07,
29
- "loss": 0.3074,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
- "grad_norm": 0.6285669803619385,
35
- "learning_rate": 1.3012154594856692e-05,
36
- "loss": 0.2741,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
- "grad_norm": 0.5516284704208374,
42
- "learning_rate": 2.2258211750211904e-05,
43
- "loss": 0.2059,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
- "grad_norm": 0.5238842964172363,
49
- "learning_rate": 4.171131747579263e-06,
50
- "loss": 0.1392,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
- "grad_norm": 0.3185393214225769,
56
- "learning_rate": 5.162865531391757e-06,
57
- "loss": 0.1204,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
- "grad_norm": 0.4352491497993469,
63
- "learning_rate": 2.2688596596301756e-05,
64
- "loss": 0.1114,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
- "grad_norm": 0.4045301377773285,
70
- "learning_rate": 1.1776811003545574e-05,
71
- "loss": 0.0844,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
- "grad_norm": 0.33092254400253296,
77
- "learning_rate": 4.274544366418573e-07,
78
- "loss": 0.0672,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
- "eval_all_ligands_equal": 0.11011931064958021,
84
- "eval_e3_equal": 0.5928413610251878,
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)": 0.9980556783031375,
88
- "eval_e3_heavy_atoms_difference": -0.3526292532037119,
89
- "eval_e3_heavy_atoms_difference_norm": -0.028914826481674143,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
- "eval_e3_valid": 0.9980556783031375,
92
- "eval_has_all_attachment_points": 0.9870083959346001,
93
- "eval_has_three_substructures": 0.9987627043747238,
94
- "eval_heavy_atoms_difference": 5.611400795404331,
95
- "eval_heavy_atoms_difference_norm": 0.07280718278132618,
96
- "eval_linker_equal": 0.20132567388422448,
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)": 0.9957578435704817,
100
- "eval_linker_heavy_atoms_difference": 1.1542200618647813,
101
- "eval_linker_heavy_atoms_difference_norm": 0.015000989286050285,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
- "eval_linker_valid": 0.9957578435704817,
104
- "eval_loss": 0.301456481218338,
105
- "eval_num_fragments": 2.999646486964207,
106
- "eval_poi_equal": 0.5993813521873619,
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)": 0.9392841361025188,
110
- "eval_poi_heavy_atoms_difference": 1.6953601414052144,
111
- "eval_poi_heavy_atoms_difference_norm": 0.04866969285000904,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
- "eval_poi_valid": 0.9392841361025188,
114
- "eval_reassembly": 0.11259390190013256,
115
- "eval_reassembly_nostereo": 0.13442333186036234,
116
- "eval_runtime": 1600.9107,
117
- "eval_samples_per_second": 7.068,
118
- "eval_steps_per_second": 0.111,
119
  "eval_tanimoto_similarity": 0.0,
120
- "eval_valid": 0.9366327883340698,
121
  "step": 5000
122
- },
123
- {
124
- "epoch": 0.542513316235944,
125
- "grad_norm": 0.4414580762386322,
126
- "learning_rate": 1.776329188349048e-05,
127
- "loss": 0.0644,
128
- "step": 5500
129
- },
130
- {
131
- "epoch": 0.5918327086210298,
132
- "grad_norm": 0.4248468279838562,
133
- "learning_rate": 1.9300081717101823e-05,
134
- "loss": 0.0569,
135
- "step": 6000
136
- },
137
- {
138
- "epoch": 0.6411521010061156,
139
- "grad_norm": 0.2549741566181183,
140
- "learning_rate": 1.0943784305675876e-06,
141
- "loss": 0.0439,
142
- "step": 6500
143
- },
144
- {
145
- "epoch": 0.6904714933912014,
146
- "grad_norm": 0.27541837096214294,
147
- "learning_rate": 9.862523618028005e-06,
148
- "loss": 0.0401,
149
- "step": 7000
150
- },
151
- {
152
- "epoch": 0.7397908857762873,
153
- "grad_norm": 0.4759804904460907,
154
- "learning_rate": 2.3105212568338626e-05,
155
- "loss": 0.0393,
156
- "step": 7500
157
- },
158
- {
159
- "epoch": 0.7397908857762873,
160
- "eval_all_ligands_equal": 0.2690234202386213,
161
- "eval_e3_equal": 0.7056120194432169,
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)": 0.997348652231551,
165
- "eval_e3_heavy_atoms_difference": 0.10172337604949183,
166
- "eval_e3_heavy_atoms_difference_norm": -0.0070542327648459024,
167
- "eval_e3_tanimoto_similarity": 0.0,
168
- "eval_e3_valid": 0.997348652231551,
169
- "eval_has_all_attachment_points": 0.9858594785682722,
170
- "eval_has_three_substructures": 0.9992045956694653,
171
- "eval_heavy_atoms_difference": 5.296155545735749,
172
- "eval_heavy_atoms_difference_norm": 0.06857629473680947,
173
- "eval_linker_equal": 0.4202386212991604,
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)": 0.9968183826778613,
177
- "eval_linker_heavy_atoms_difference": 0.6022978347326557,
178
- "eval_linker_heavy_atoms_difference_norm": -0.0013174337936367362,
179
- "eval_linker_tanimoto_similarity": 0.0,
180
- "eval_linker_valid": 0.9968183826778613,
181
- "eval_loss": 0.29956623911857605,
182
- "eval_num_fragments": 3.0004418912947415,
183
- "eval_poi_equal": 0.6509058771542201,
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)": 0.943791427308882,
187
- "eval_poi_heavy_atoms_difference": 1.6980998674326115,
188
- "eval_poi_heavy_atoms_difference_norm": 0.04522592378769132,
189
- "eval_poi_tanimoto_similarity": 0.0,
190
- "eval_poi_valid": 0.943791427308882,
191
- "eval_reassembly": 0.27353071144498453,
192
- "eval_reassembly_nostereo": 0.297039328325232,
193
- "eval_runtime": 1495.624,
194
- "eval_samples_per_second": 7.565,
195
- "eval_steps_per_second": 0.118,
196
- "eval_tanimoto_similarity": 0.0,
197
- "eval_valid": 0.9398144056562086,
198
- "step": 7500
199
- },
200
- {
201
- "epoch": 0.789110278161373,
202
- "grad_norm": 0.21357761323451996,
203
- "learning_rate": 6.84133667553644e-06,
204
- "loss": 0.0326,
205
- "step": 8000
206
- },
207
- {
208
- "epoch": 0.8384296705464589,
209
- "grad_norm": 0.25558289885520935,
210
- "learning_rate": 2.8044543687991375e-06,
211
- "loss": 0.0273,
212
- "step": 8500
213
- },
214
- {
215
- "epoch": 0.8877490629315447,
216
- "grad_norm": 0.29299396276474,
217
- "learning_rate": 2.135331805932135e-05,
218
- "loss": 0.0275,
219
- "step": 9000
220
- },
221
- {
222
- "epoch": 0.9370684553166305,
223
- "grad_norm": 0.2609122097492218,
224
- "learning_rate": 1.4891027000593144e-05,
225
- "loss": 0.026,
226
- "step": 9500
227
- },
228
- {
229
- "epoch": 0.9863878477017163,
230
- "grad_norm": 0.20302577316761017,
231
- "learning_rate": 0.0,
232
- "loss": 0.0204,
233
- "step": 10000
234
- },
235
- {
236
- "epoch": 0.9863878477017163,
237
- "eval_all_ligands_equal": 0.41882456915598765,
238
- "eval_e3_equal": 0.759169244365886,
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)": 0.9969067609368095,
242
- "eval_e3_heavy_atoms_difference": 0.032523199292973926,
243
- "eval_e3_heavy_atoms_difference_norm": -0.008456533785678375,
244
- "eval_e3_tanimoto_similarity": 0.0,
245
- "eval_e3_valid": 0.9969067609368095,
246
- "eval_has_all_attachment_points": 0.9897481219619974,
247
- "eval_has_three_substructures": 0.9994697304463102,
248
- "eval_heavy_atoms_difference": 4.253910737958463,
249
- "eval_heavy_atoms_difference_norm": 0.05558554950808673,
250
- "eval_linker_equal": 0.6033583738400353,
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)": 0.9972602739726028,
254
- "eval_linker_heavy_atoms_difference": 0.4562969509500663,
255
- "eval_linker_heavy_atoms_difference_norm": -0.0010081340677265851,
256
- "eval_linker_tanimoto_similarity": 0.0,
257
- "eval_linker_valid": 0.9972602739726028,
258
- "eval_loss": 0.3004947006702423,
259
- "eval_num_fragments": 2.9998232434821035,
260
- "eval_poi_equal": 0.7078214759169245,
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)": 0.9555457357490057,
264
- "eval_poi_heavy_atoms_difference": 1.2387980556783031,
265
- "eval_poi_heavy_atoms_difference_norm": 0.035008881003771114,
266
- "eval_poi_tanimoto_similarity": 0.0,
267
- "eval_poi_valid": 0.9555457357490057,
268
- "eval_reassembly": 0.42492266902342024,
269
- "eval_reassembly_nostereo": 0.45258506407423776,
270
- "eval_runtime": 1502.872,
271
- "eval_samples_per_second": 7.529,
272
- "eval_steps_per_second": 0.118,
273
- "eval_tanimoto_similarity": 0.0,
274
- "eval_valid": 0.9508616880247459,
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=17-learning_rate=2.3e-05-warmup_ratio=0.070-num_cycles=5.500",
298
  "trial_params": {
299
- "learning_rate": 2.321257272753331e-05,
300
- "num_cycles": 5.5,
301
- "warmup_ratio": 0.06999999999999999
302
  }
303
  }
 
1
  {
2
+ "best_metric": 0.5033141847105612,
3
+ "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_cosine-opt25-rand-smiles/trial-number=18-learning_rate=2.0e-04-warmup_ratio=0.010-num_cycles=2.500/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": 0.6453943848609924,
14
+ "learning_rate": 0.00014340124668857647,
15
+ "loss": 1.519,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
+ "grad_norm": 0.30024901032447815,
21
+ "learning_rate": 0.0001878001438351963,
22
+ "loss": 0.102,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
+ "grad_norm": 0.15960834920406342,
28
+ "learning_rate": 0.00012191951719773646,
29
+ "loss": 0.0292,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
+ "grad_norm": 0.10984167456626892,
35
+ "learning_rate": 4.1475601830154605e-05,
36
+ "loss": 0.0142,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
+ "grad_norm": 0.09457601606845856,
42
+ "learning_rate": 5.005669712982349e-07,
43
+ "loss": 0.0092,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
+ "grad_norm": 0.12721996009349823,
49
+ "learning_rate": 2.6516320374474144e-05,
50
+ "loss": 0.0085,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
+ "grad_norm": 0.17860917747020721,
56
+ "learning_rate": 0.00010204873010150722,
57
+ "loss": 0.0108,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
+ "grad_norm": 0.1712469458580017,
63
+ "learning_rate": 0.00017636456261024047,
64
+ "loss": 0.0198,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
+ "grad_norm": 0.16711823642253876,
70
+ "learning_rate": 0.00019954772889767774,
71
+ "loss": 0.0159,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
+ "grad_norm": 0.11587321758270264,
77
+ "learning_rate": 0.00015602667506056428,
78
+ "loss": 0.0109,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
+ "eval_all_ligands_equal": 0.5033141847105612,
84
+ "eval_e3_equal": 0.7938135218736191,
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)": 0.9905435262925321,
88
+ "eval_e3_heavy_atoms_difference": 0.4669023420238621,
89
+ "eval_e3_heavy_atoms_difference_norm": 0.007575271177021908,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
+ "eval_e3_valid": 0.9905435262925321,
92
+ "eval_has_all_attachment_points": 0.9913389306230668,
93
+ "eval_has_three_substructures": 0.9996464869642068,
94
+ "eval_heavy_atoms_difference": 6.135572249226691,
95
+ "eval_heavy_atoms_difference_norm": 0.07836621490514804,
96
+ "eval_linker_equal": 0.7340698188245691,
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)": 0.9969951391957579,
100
+ "eval_linker_heavy_atoms_difference": 0.7690676093680955,
101
+ "eval_linker_heavy_atoms_difference_norm": 0.025383089814494973,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
+ "eval_linker_valid": 0.9969951391957579,
104
+ "eval_loss": 0.29212433099746704,
105
+ "eval_num_fragments": 2.9995581087052585,
106
+ "eval_poi_equal": 0.7510384445426425,
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)": 0.9475033141847106,
110
+ "eval_poi_heavy_atoms_difference": 1.743791427308882,
111
+ "eval_poi_heavy_atoms_difference_norm": 0.050082263417517286,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
+ "eval_poi_valid": 0.9475033141847106,
114
+ "eval_reassembly": 0.5104728236853734,
115
+ "eval_reassembly_nostereo": 0.5452938577110031,
116
+ "eval_runtime": 1512.4575,
117
+ "eval_samples_per_second": 7.481,
118
+ "eval_steps_per_second": 0.117,
119
  "eval_tanimoto_similarity": 0.0,
120
+ "eval_valid": 0.9362792752982766,
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=2.0e-04-warmup_ratio=0.010-num_cycles=2.500",
144
  "trial_params": {
145
+ "learning_rate": 0.0002004749428706299,
146
+ "num_cycles": 2.5,
147
+ "warmup_ratio": 0.01
148
  }
149
  }
last-checkpoint/training_args.bin CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:b261af858adb9cfe0d2c1a61e005cf32851d1b6c12b154cbe6a390caaae3353b
3
  size 7480
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f6d827f97d112aeca59a21ac48c9a4653f744b8e6a9bd8e942e1f99049559f88
3
  size 7480