ribesstefano commited on
Commit
5fdd7b5
·
verified ·
1 Parent(s): e8372e5

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:d42eb3cc3676aa5ab3aba53c2f41a55a65a12a81571a83830360833de78681cb
3
  size 409608164
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f5145c2cc7d97ae3d9a124fc843bd98b3ed8f6f8784b198e6ff821ea49461e95
3
  size 409608164
last-checkpoint/optimizer.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:d857951e70a8a0628eb3e8bc8d0d7413567222c40804a0c5602d7980cd82395e
3
  size 814647162
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:a7abd2543c0f4161003949ca3b0a09f32ee52189eb6cf1ce1b0d339218db56fb
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:fc2928b365c0ef1120237fc40be202f53b478c2918d560736b898e24618aee8b
3
  size 14244
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:56116cd4c05fa65ee5b68ac09ebd53a9cecc2c132b0229f70f547f950f24eb44
3
  size 14244
last-checkpoint/scheduler.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:5442f58e6023536ebb399e7159e58225a0952bc1b64060575c79ec6328ce14bb
3
  size 1064
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:b8cec5d697af01fd16026abee650745e0dfef8562ef22eba2f073c03e205449e
3
  size 1064
last-checkpoint/trainer_state.json CHANGED
@@ -1,278 +1,124 @@
1
  {
2
- "best_metric": 0.5703049049933716,
3
- "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_cosine_restarts-opt25/trial-number=11-learning_rate=1.0e-04-warmup_ratio=0.080-num_cycles=3/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": 0.6575852632522583,
14
- "learning_rate": 0.000100182631515627,
15
- "loss": 1.1484,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
- "grad_norm": 0.343759149312973,
21
- "learning_rate": 8.597337690594066e-05,
22
- "loss": 0.1449,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
- "grad_norm": 0.2601257562637329,
28
- "learning_rate": 6.420018709015348e-05,
29
- "loss": 0.0439,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
- "grad_norm": 0.13981187343597412,
35
- "learning_rate": 3.9703875822711815e-05,
36
- "loss": 0.0221,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
- "grad_norm": 0.1797427237033844,
42
- "learning_rate": 1.793068600692463e-05,
43
- "loss": 0.0141,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
- "grad_norm": 0.13262967765331268,
49
- "learning_rate": 3.721431397238288e-06,
50
- "loss": 0.011,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
- "grad_norm": 0.24220901727676392,
56
- "learning_rate": 0.00010366882009194501,
57
- "loss": 0.0124,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
- "grad_norm": 0.15627698600292206,
63
- "learning_rate": 9.565686145691327e-05,
64
- "loss": 0.0201,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
- "grad_norm": 0.12300624698400497,
70
- "learning_rate": 7.792804718464899e-05,
71
- "loss": 0.0093,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
- "grad_norm": 0.09846580028533936,
77
- "learning_rate": 5.442400864406504e-05,
78
- "loss": 0.006,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
- "eval_all_ligands_equal": 0.5189571365444101,
84
- "eval_e3_equal": 0.7959346000883782,
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)": 0.9897481219619974,
88
- "eval_e3_heavy_atoms_difference": 0.609191338930623,
89
- "eval_e3_heavy_atoms_difference_norm": 0.013221863982469433,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
- "eval_e3_valid": 0.9897481219619974,
92
- "eval_has_all_attachment_points": 0.987273530711445,
93
- "eval_has_three_substructures": 0.9997348652231551,
94
- "eval_heavy_atoms_difference": 3.68519664162616,
95
- "eval_heavy_atoms_difference_norm": 0.047260073323281075,
96
- "eval_linker_equal": 0.7496243923994698,
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)": 0.9977021652673442,
100
- "eval_linker_heavy_atoms_difference": 0.32470172337604947,
101
- "eval_linker_heavy_atoms_difference_norm": -0.001965493580026269,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
- "eval_linker_valid": 0.9977021652673442,
104
- "eval_loss": 0.3125883936882019,
105
- "eval_num_fragments": 3.0000883782589485,
106
- "eval_poi_equal": 0.7557224922669024,
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)": 0.9706584180291649,
110
- "eval_poi_heavy_atoms_difference": 0.7122403888643394,
111
- "eval_poi_heavy_atoms_difference_norm": 0.010501165767226064,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
- "eval_poi_valid": 0.9706584180291649,
114
- "eval_reassembly": 0.5268228015908086,
115
- "eval_reassembly_nostereo": 0.552364118426867,
116
- "eval_runtime": 1535.8187,
117
- "eval_samples_per_second": 7.367,
118
- "eval_steps_per_second": 0.115,
119
  "eval_tanimoto_similarity": 0.0,
120
- "eval_valid": 0.9590808661069377,
121
  "step": 5000
122
- },
123
- {
124
- "epoch": 0.542513316235944,
125
- "grad_norm": 0.07069461047649384,
126
- "learning_rate": 3.037037763348429e-05,
127
- "loss": 0.004,
128
- "step": 5500
129
- },
130
- {
131
- "epoch": 0.5918327086210298,
132
- "grad_norm": 0.05461514741182327,
133
- "learning_rate": 1.1114976351929146e-05,
134
- "loss": 0.003,
135
- "step": 6000
136
- },
137
- {
138
- "epoch": 0.6411521010061156,
139
- "grad_norm": 0.06773870438337326,
140
- "learning_rate": 9.388408882665784e-07,
141
- "loss": 0.0026,
142
- "step": 6500
143
- },
144
- {
145
- "epoch": 0.6904714933912014,
146
- "grad_norm": 0.17225702106952667,
147
- "learning_rate": 0.00010179964060387911,
148
- "loss": 0.0115,
149
- "step": 7000
150
- },
151
- {
152
- "epoch": 0.7397908857762873,
153
- "grad_norm": 0.0747770220041275,
154
- "learning_rate": 8.955148497015824e-05,
155
- "loss": 0.0072,
156
- "step": 7500
157
- },
158
- {
159
- "epoch": 0.7397908857762873,
160
- "eval_all_ligands_equal": 0.5173663278833407,
161
- "eval_e3_equal": 0.8022094564737074,
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)": 0.9894829871851525,
165
- "eval_e3_heavy_atoms_difference": 0.6038886433937252,
166
- "eval_e3_heavy_atoms_difference_norm": 0.012404143305947432,
167
- "eval_e3_tanimoto_similarity": 0.0,
168
- "eval_e3_valid": 0.9894829871851525,
169
- "eval_has_all_attachment_points": 0.9878921785240831,
170
- "eval_has_three_substructures": 0.9992045956694653,
171
- "eval_heavy_atoms_difference": 4.957578435704817,
172
- "eval_heavy_atoms_difference_norm": 0.06262525333255187,
173
- "eval_linker_equal": 0.7567830313742819,
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)": 0.996464869642068,
177
- "eval_linker_heavy_atoms_difference": 0.40980998674326113,
178
- "eval_linker_heavy_atoms_difference_norm": 0.006682600227663089,
179
- "eval_linker_tanimoto_similarity": 0.0,
180
- "eval_linker_valid": 0.996464869642068,
181
- "eval_loss": 0.30381327867507935,
182
- "eval_num_fragments": 2.999381352187362,
183
- "eval_poi_equal": 0.7467962881131242,
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)": 0.9570481661511269,
187
- "eval_poi_heavy_atoms_difference": 1.3366327883340698,
188
- "eval_poi_heavy_atoms_difference_norm": 0.031869690411330115,
189
- "eval_poi_tanimoto_similarity": 0.0,
190
- "eval_poi_valid": 0.9570481661511269,
191
- "eval_reassembly": 0.5249668581528943,
192
- "eval_reassembly_nostereo": 0.5500662836942112,
193
- "eval_runtime": 1535.106,
194
- "eval_samples_per_second": 7.371,
195
- "eval_steps_per_second": 0.115,
196
- "eval_tanimoto_similarity": 0.0,
197
- "eval_valid": 0.9453822359699514,
198
- "step": 7500
199
- },
200
- {
201
- "epoch": 0.789110278161373,
202
- "grad_norm": 0.06744291633367538,
203
- "learning_rate": 6.894387657509068e-05,
204
- "loss": 0.004,
205
- "step": 8000
206
- },
207
- {
208
- "epoch": 0.8384296705464589,
209
- "grad_norm": 0.0616152361035347,
210
- "learning_rate": 4.455848650174181e-05,
211
- "loss": 0.0028,
212
- "step": 8500
213
- },
214
- {
215
- "epoch": 0.8877490629315447,
216
- "grad_norm": 0.030910490080714226,
217
- "learning_rate": 2.1816896643868615e-05,
218
- "loss": 0.002,
219
- "step": 9000
220
- },
221
- {
222
- "epoch": 0.9370684553166305,
223
- "grad_norm": 0.05898826941847801,
224
- "learning_rate": 5.775224268319631e-06,
225
- "loss": 0.0015,
226
- "step": 9500
227
- },
228
- {
229
- "epoch": 0.9863878477017163,
230
- "grad_norm": 0.060594432055950165,
231
- "learning_rate": 0.0,
232
- "loss": 0.0013,
233
- "step": 10000
234
- },
235
- {
236
- "epoch": 0.9863878477017163,
237
- "eval_all_ligands_equal": 0.5703049049933716,
238
- "eval_e3_equal": 0.8189129474149359,
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)": 0.9942554131683606,
242
- "eval_e3_heavy_atoms_difference": 0.36783031374281927,
243
- "eval_e3_heavy_atoms_difference_norm": 0.006249267556050742,
244
- "eval_e3_tanimoto_similarity": 0.0,
245
- "eval_e3_valid": 0.9942554131683606,
246
- "eval_has_all_attachment_points": 0.9908086610693769,
247
- "eval_has_three_substructures": 0.9999116217410517,
248
- "eval_heavy_atoms_difference": 2.9059655324790103,
249
- "eval_heavy_atoms_difference_norm": 0.03736833824404718,
250
- "eval_linker_equal": 0.8147591692443659,
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)": 0.9983208130799823,
254
- "eval_linker_heavy_atoms_difference": 0.28608042421564295,
255
- "eval_linker_heavy_atoms_difference_norm": 0.00016462975909777643,
256
- "eval_linker_tanimoto_similarity": 0.0,
257
- "eval_linker_valid": 0.9983208130799823,
258
- "eval_loss": 0.31623375415802,
259
- "eval_num_fragments": 2.9999116217410515,
260
- "eval_poi_equal": 0.7785240830755634,
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)": 0.9743703049049933,
264
- "eval_poi_heavy_atoms_difference": 0.5845338046840477,
265
- "eval_poi_heavy_atoms_difference_norm": 0.008440998215488436,
266
- "eval_poi_tanimoto_similarity": 0.0,
267
- "eval_poi_valid": 0.9743703049049933,
268
- "eval_reassembly": 0.5772867874502873,
269
- "eval_reassembly_nostereo": 0.6049491825011047,
270
- "eval_runtime": 1518.7606,
271
- "eval_samples_per_second": 7.45,
272
- "eval_steps_per_second": 0.117,
273
- "eval_tanimoto_similarity": 0.0,
274
- "eval_valid": 0.9672116659301812,
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=11-learning_rate=1.0e-04-warmup_ratio=0.080-num_cycles=3",
298
  "trial_params": {
299
- "learning_rate": 0.00010390406291286528,
300
- "num_cycles": 3,
301
- "warmup_ratio": 0.08
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_restarts-opt25/trial-number=12-learning_rate=2.2e-06-warmup_ratio=0.050-num_cycles=10/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": 2.3763999938964844,
14
+ "learning_rate": 1.4154648142539406e-06,
15
+ "loss": 3.9782,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
+ "grad_norm": 2.259150743484497,
21
+ "learning_rate": 4.420955339237543e-08,
22
+ "loss": 1.6474,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
+ "grad_norm": 1.417884111404419,
28
+ "learning_rate": 1.3822352979831102e-06,
29
+ "loss": 1.4116,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
+ "grad_norm": 1.4686042070388794,
35
+ "learning_rate": 3.498093351576883e-08,
36
+ "loss": 1.1769,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
+ "grad_norm": 1.374851942062378,
42
+ "learning_rate": 1.348712939813865e-06,
43
+ "loss": 1.07,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
+ "grad_norm": 1.3333460092544556,
49
+ "learning_rate": 2.681604268390353e-08,
50
+ "loss": 0.9419,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
+ "grad_norm": 1.3361984491348267,
56
+ "learning_rate": 1.3149314939193131e-06,
57
+ "loss": 0.8707,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
+ "grad_norm": 1.3137452602386475,
63
+ "learning_rate": 1.97231022497391e-08,
64
+ "loss": 0.7844,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
+ "grad_norm": 1.387094259262085,
70
+ "learning_rate": 1.2809249753519381e-06,
71
+ "loss": 0.7308,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
+ "grad_norm": 1.45970618724823,
77
+ "learning_rate": 1.3709254203049984e-08,
78
+ "loss": 0.6691,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
+ "eval_all_ligands_equal": 0.0,
84
+ "eval_e3_equal": 0.043747238179407864,
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)": 0.9451171011931065,
88
+ "eval_e3_heavy_atoms_difference": 1.780733539549271,
89
+ "eval_e3_heavy_atoms_difference_norm": 0.011796785596124824,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
+ "eval_e3_valid": 0.9451171011931065,
92
+ "eval_has_all_attachment_points": 0.653557224922669,
93
+ "eval_has_three_substructures": 0.9476800707026072,
94
+ "eval_heavy_atoms_difference": 66.00486080424216,
95
+ "eval_heavy_atoms_difference_norm": 0.8581384495257799,
96
+ "eval_linker_equal": 0.001237295625276182,
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)": 0.907998232434821,
100
+ "eval_linker_heavy_atoms_difference": 9.123287671232877,
101
+ "eval_linker_heavy_atoms_difference_norm": 0.4624936678575905,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
+ "eval_linker_valid": 0.907998232434821,
104
+ "eval_loss": 0.729906439781189,
105
+ "eval_num_fragments": 3.038886433937251,
106
+ "eval_poi_equal": 8.837825894829872e-05,
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)": 0.26619531595227575,
110
+ "eval_poi_heavy_atoms_difference": 26.38851082633672,
111
+ "eval_poi_heavy_atoms_difference_norm": 0.8104800494182971,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
+ "eval_poi_valid": 0.26619531595227575,
114
+ "eval_reassembly": 0.0,
115
+ "eval_reassembly_nostereo": 0.0,
116
+ "eval_runtime": 1464.416,
117
+ "eval_samples_per_second": 7.727,
118
+ "eval_steps_per_second": 0.121,
119
  "eval_tanimoto_similarity": 0.0,
120
+ "eval_valid": 0.24984533804684048,
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=12-learning_rate=2.2e-06-warmup_ratio=0.050-num_cycles=10",
144
  "trial_params": {
145
+ "learning_rate": 2.182809124107808e-06,
146
+ "num_cycles": 10,
147
+ "warmup_ratio": 0.05
148
  }
149
  }
last-checkpoint/training_args.bin CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:79e8dd2f501b00cb907081399791da6f3e67acafeecf3f0d96b43e4e21e6e9c2
3
  size 7480
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:e2d81e53661da53b9a9ee62f9627e098efc364b9e2a928206d40d7422e054944
3
  size 7480