ribesstefano commited on
Commit
6080a1a
·
verified ·
1 Parent(s): 0cda51d

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 sha256:775dd05908e3c3a4ec250a8fdc7e7f19c1955e6971d9b03ff9a35b4d1a70c090
3
  size 409608164
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:0d116c9eb76cf725a0da12be840484e9223ab6c093e357240fa46f54d920e933
3
  size 409608164
last-checkpoint/optimizer.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:a9afbf574d7f8b62dded10b31bc1f4457117abd30a3a10bc64ef08b2575177d6
3
  size 814647162
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:2bf324463a943a5a3bca5238600831d9e19481b5930cd25a01c7ea87963f90b4
3
  size 814647162
last-checkpoint/rng_state.pth CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:1e9c3eab11f39985ac48cd8fdd62267ede6217cbbe6299930f3d3cc0333fa569
3
  size 14244
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:defd95987060bb52acf2b4d5e12bfa429b2a639f6776fe57d33ac145ff7e1883
3
  size 14244
last-checkpoint/scheduler.pt CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:98f204002c58afa2bf7009b998d4ee2a87cbfcdb0187e0ca9734f62204d69357
3
  size 1192
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:d5ac6c986d54dd42cc857ccb77c884b23c5bc8aaf1ee6757c7ed6a835e6f3d61
3
  size 1192
last-checkpoint/trainer_state.json CHANGED
@@ -1,278 +1,124 @@
1
  {
2
- "best_metric": 0.51064958020327,
3
- "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25-rand-smiles/trial-number=1-learning_rate=2.0e-05-warmup_ratio=0.090-min_lr=0.000-factor=0.140/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": 0.9366918206214905,
14
- "learning_rate": 1.9637600609931647e-05,
15
- "loss": 1.3552,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
- "grad_norm": 0.7903795838356018,
21
- "learning_rate": 1.9637600609931647e-05,
22
- "loss": 0.3992,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
- "grad_norm": 0.6279132962226868,
28
- "learning_rate": 1.9637600609931647e-05,
29
- "loss": 0.2193,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
- "grad_norm": 0.4536708891391754,
35
- "learning_rate": 1.9637600609931647e-05,
36
- "loss": 0.1436,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
- "grad_norm": 0.38390129804611206,
42
- "learning_rate": 1.9637600609931647e-05,
43
- "loss": 0.0988,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
- "grad_norm": 0.33358627557754517,
49
- "learning_rate": 1.9637600609931647e-05,
50
- "loss": 0.072,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
- "grad_norm": 0.2700892388820648,
56
- "learning_rate": 1.9637600609931647e-05,
57
- "loss": 0.055,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
- "grad_norm": 0.25509464740753174,
63
- "learning_rate": 1.9637600609931647e-05,
64
- "loss": 0.0438,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
- "grad_norm": 0.2741105854511261,
70
- "learning_rate": 1.9637600609931647e-05,
71
- "loss": 0.0358,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
- "grad_norm": 0.27503982186317444,
77
- "learning_rate": 1.9637600609931647e-05,
78
- "loss": 0.0298,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
- "eval_all_ligands_equal": 0.3385771100309324,
84
- "eval_e3_equal": 0.7543084401237296,
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)": 0.9961113566062748,
88
- "eval_e3_heavy_atoms_difference": 0.2403004860804242,
89
- "eval_e3_heavy_atoms_difference_norm": 0.0009850356807857721,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
- "eval_e3_valid": 0.9961113566062748,
92
- "eval_has_all_attachment_points": 0.9883340698188245,
93
- "eval_has_three_substructures": 0.9992045956694653,
94
- "eval_heavy_atoms_difference": 6.7087052585064075,
95
- "eval_heavy_atoms_difference_norm": 0.08811903753594401,
96
- "eval_linker_equal": 0.5086168802474591,
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)": 0.997613787008396,
100
- "eval_linker_heavy_atoms_difference": 1.5927529827662394,
101
- "eval_linker_heavy_atoms_difference_norm": 0.06277030655434478,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
- "eval_linker_valid": 0.997613787008396,
104
- "eval_loss": 0.29202571511268616,
105
- "eval_num_fragments": 3.0004418912947415,
106
- "eval_poi_equal": 0.6781263809102961,
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)": 0.9418471056120195,
110
- "eval_poi_heavy_atoms_difference": 1.9634997790543527,
111
- "eval_poi_heavy_atoms_difference_norm": 0.061116057900993816,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
- "eval_poi_valid": 0.9418471056120195,
114
- "eval_reassembly": 0.3447635881573133,
115
- "eval_reassembly_nostereo": 0.37136544410075123,
116
- "eval_runtime": 1565.4444,
117
- "eval_samples_per_second": 7.228,
118
- "eval_steps_per_second": 0.113,
119
- "eval_tanimoto_similarity": 0.0,
120
- "eval_valid": 0.9377817057003976,
121
- "step": 5000
122
- },
123
- {
124
- "epoch": 0.542513316235944,
125
- "grad_norm": 0.2893636226654053,
126
- "learning_rate": 1.9637600609931647e-05,
127
- "loss": 0.0252,
128
- "step": 5500
129
- },
130
- {
131
- "epoch": 0.5918327086210298,
132
- "grad_norm": 0.2260722666978836,
133
- "learning_rate": 1.9637600609931647e-05,
134
- "loss": 0.0219,
135
- "step": 6000
136
- },
137
- {
138
- "epoch": 0.6411521010061156,
139
- "grad_norm": 0.22679904103279114,
140
- "learning_rate": 1.9637600609931647e-05,
141
- "loss": 0.0189,
142
- "step": 6500
143
- },
144
- {
145
- "epoch": 0.6904714933912014,
146
- "grad_norm": 0.18228673934936523,
147
- "learning_rate": 1.9637600609931647e-05,
148
- "loss": 0.0169,
149
- "step": 7000
150
- },
151
- {
152
- "epoch": 0.7397908857762873,
153
- "grad_norm": 0.18237416446208954,
154
- "learning_rate": 1.9637600609931647e-05,
155
- "loss": 0.0151,
156
- "step": 7500
157
- },
158
- {
159
- "epoch": 0.7397908857762873,
160
- "eval_all_ligands_equal": 0.4684931506849315,
161
- "eval_e3_equal": 0.7885108263367212,
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)": 0.9929297392841361,
165
- "eval_e3_heavy_atoms_difference": 0.3597878921785241,
166
- "eval_e3_heavy_atoms_difference_norm": 0.00521588791052724,
167
- "eval_e3_tanimoto_similarity": 0.0,
168
- "eval_e3_valid": 0.9929297392841361,
169
- "eval_has_all_attachment_points": 0.9863013698630136,
170
- "eval_has_three_substructures": 0.9988510826336722,
171
- "eval_heavy_atoms_difference": 5.797967300044189,
172
- "eval_heavy_atoms_difference_norm": 0.07490685834023805,
173
- "eval_linker_equal": 0.6817498895271763,
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)": 0.9955810870525851,
177
- "eval_linker_heavy_atoms_difference": 0.4904109589041096,
178
- "eval_linker_heavy_atoms_difference_norm": 0.006170812304541001,
179
- "eval_linker_tanimoto_similarity": 0.0,
180
- "eval_linker_valid": 0.9955810870525851,
181
- "eval_loss": 0.2942061424255371,
182
- "eval_num_fragments": 2.9999116217410515,
183
- "eval_poi_equal": 0.7197525408749448,
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)": 0.9391073795846222,
187
- "eval_poi_heavy_atoms_difference": 1.726646045072912,
188
- "eval_poi_heavy_atoms_difference_norm": 0.04955859868875608,
189
- "eval_poi_tanimoto_similarity": 0.0,
190
- "eval_poi_valid": 0.9391073795846222,
191
- "eval_reassembly": 0.4752098983650022,
192
- "eval_reassembly_nostereo": 0.5030490499337164,
193
- "eval_runtime": 1518.3153,
194
- "eval_samples_per_second": 7.452,
195
  "eval_steps_per_second": 0.117,
196
  "eval_tanimoto_similarity": 0.0,
197
- "eval_valid": 0.9309765797613787,
198
- "step": 7500
199
- },
200
- {
201
- "epoch": 0.789110278161373,
202
- "grad_norm": 0.17814092338085175,
203
- "learning_rate": 1.9637600609931647e-05,
204
- "loss": 0.0131,
205
- "step": 8000
206
- },
207
- {
208
- "epoch": 0.8384296705464589,
209
- "grad_norm": 0.17906583845615387,
210
- "learning_rate": 1.9637600609931647e-05,
211
- "loss": 0.0121,
212
- "step": 8500
213
- },
214
- {
215
- "epoch": 0.8877490629315447,
216
- "grad_norm": 0.17858368158340454,
217
- "learning_rate": 1.9637600609931647e-05,
218
- "loss": 0.0109,
219
- "step": 9000
220
- },
221
- {
222
- "epoch": 0.9370684553166305,
223
- "grad_norm": 0.20851778984069824,
224
- "learning_rate": 1.9637600609931647e-05,
225
- "loss": 0.01,
226
- "step": 9500
227
- },
228
- {
229
- "epoch": 0.9863878477017163,
230
- "grad_norm": 0.19188041985034943,
231
- "learning_rate": 1.9637600609931647e-05,
232
- "loss": 0.0094,
233
- "step": 10000
234
- },
235
- {
236
- "epoch": 0.9863878477017163,
237
- "eval_all_ligands_equal": 0.51064958020327,
238
- "eval_e3_equal": 0.7939019001325673,
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": 0.2714980114891737,
243
- "eval_e3_heavy_atoms_difference_norm": 0.0006646498648945236,
244
- "eval_e3_tanimoto_similarity": 0.0,
245
- "eval_e3_valid": 0.9930181175430844,
246
- "eval_has_all_attachment_points": 0.9847989394608926,
247
- "eval_has_three_substructures": 0.9993813521873619,
248
- "eval_heavy_atoms_difference": 4.782942996022978,
249
- "eval_heavy_atoms_difference_norm": 0.061200538749235575,
250
- "eval_linker_equal": 0.7305346884666372,
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)": 0.9962881131241714,
254
- "eval_linker_heavy_atoms_difference": 0.2067167476800707,
255
- "eval_linker_heavy_atoms_difference_norm": -0.00944347093296283,
256
- "eval_linker_tanimoto_similarity": 0.0,
257
- "eval_linker_valid": 0.9962881131241714,
258
- "eval_loss": 0.31269723176956177,
259
- "eval_num_fragments": 2.9999116217410515,
260
- "eval_poi_equal": 0.7448519664162616,
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)": 0.9511268228015908,
264
- "eval_poi_heavy_atoms_difference": 1.479275298276624,
265
- "eval_poi_heavy_atoms_difference_norm": 0.039726793829409066,
266
- "eval_poi_tanimoto_similarity": 0.0,
267
- "eval_poi_valid": 0.9511268228015908,
268
- "eval_reassembly": 0.5191338930623066,
269
- "eval_reassembly_nostereo": 0.5487406098099867,
270
- "eval_runtime": 1509.6271,
271
- "eval_samples_per_second": 7.495,
272
- "eval_steps_per_second": 0.117,
273
- "eval_tanimoto_similarity": 0.0,
274
- "eval_valid": 0.9428192664604508,
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=1-learning_rate=2.0e-05-warmup_ratio=0.090-min_lr=0.000-factor=0.140",
298
  "trial_params": {
299
- "factor": 0.14,
300
- "learning_rate": 1.9637600609931647e-05,
301
- "min_lr": 2.625658863416167e-10,
302
- "warmup_ratio": 0.09
303
  }
304
  }
 
1
  {
2
+ "best_metric": 0.5083517454706142,
3
+ "best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25-rand-smiles/trial-number=2-learning_rate=4.8e-05-warmup_ratio=0.020-min_lr=0.000-factor=0.550/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": 0.6996342539787292,
14
+ "learning_rate": 4.8207210410584316e-05,
15
+ "loss": 0.9734,
16
  "step": 500
17
  },
18
  {
19
  "epoch": 0.09863878477017163,
20
+ "grad_norm": 0.4646381139755249,
21
+ "learning_rate": 4.8207210410584316e-05,
22
+ "loss": 0.189,
23
  "step": 1000
24
  },
25
  {
26
  "epoch": 0.14795817715525744,
27
+ "grad_norm": 0.29534122347831726,
28
+ "learning_rate": 4.8207210410584316e-05,
29
+ "loss": 0.0806,
30
  "step": 1500
31
  },
32
  {
33
  "epoch": 0.19727756954034326,
34
+ "grad_norm": 0.25903186202049255,
35
+ "learning_rate": 4.8207210410584316e-05,
36
+ "loss": 0.046,
37
  "step": 2000
38
  },
39
  {
40
  "epoch": 0.24659696192542907,
41
+ "grad_norm": 0.1971054971218109,
42
+ "learning_rate": 4.8207210410584316e-05,
43
+ "loss": 0.0305,
44
  "step": 2500
45
  },
46
  {
47
  "epoch": 0.2959163543105149,
48
+ "grad_norm": 0.21787063777446747,
49
+ "learning_rate": 4.8207210410584316e-05,
50
+ "loss": 0.0225,
51
  "step": 3000
52
  },
53
  {
54
  "epoch": 0.3452357466956007,
55
+ "grad_norm": 0.1680845320224762,
56
+ "learning_rate": 4.8207210410584316e-05,
57
+ "loss": 0.0172,
58
  "step": 3500
59
  },
60
  {
61
  "epoch": 0.3945551390806865,
62
+ "grad_norm": 0.18149493634700775,
63
+ "learning_rate": 4.8207210410584316e-05,
64
+ "loss": 0.0143,
65
  "step": 4000
66
  },
67
  {
68
  "epoch": 0.4438745314657723,
69
+ "grad_norm": 0.1732591688632965,
70
+ "learning_rate": 4.8207210410584316e-05,
71
+ "loss": 0.0119,
72
  "step": 4500
73
  },
74
  {
75
  "epoch": 0.49319392385085814,
76
+ "grad_norm": 0.1654258370399475,
77
+ "learning_rate": 4.8207210410584316e-05,
78
+ "loss": 0.0102,
79
  "step": 5000
80
  },
81
  {
82
  "epoch": 0.49319392385085814,
83
+ "eval_all_ligands_equal": 0.5083517454706142,
84
+ "eval_e3_equal": 0.7987627043747239,
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)": 0.9861246133451171,
88
+ "eval_e3_heavy_atoms_difference": 0.49421122403888645,
89
+ "eval_e3_heavy_atoms_difference_norm": 0.00927130830353229,
90
  "eval_e3_tanimoto_similarity": 0.0,
91
+ "eval_e3_valid": 0.9861246133451171,
92
+ "eval_has_all_attachment_points": 0.9825894829871852,
93
+ "eval_has_three_substructures": 0.999116217410517,
94
+ "eval_heavy_atoms_difference": 5.2900574458683165,
95
+ "eval_heavy_atoms_difference_norm": 0.0676014805881027,
96
+ "eval_linker_equal": 0.7308882015024304,
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)": 0.9969067609368095,
100
+ "eval_linker_heavy_atoms_difference": 0.46805125939019,
101
+ "eval_linker_heavy_atoms_difference_norm": 0.005183485274385287,
102
  "eval_linker_tanimoto_similarity": 0.0,
103
+ "eval_linker_valid": 0.9969067609368095,
104
+ "eval_loss": 0.29249435663223267,
105
+ "eval_num_fragments": 2.99946973044631,
106
+ "eval_poi_equal": 0.7437030490499337,
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)": 0.9570481661511269,
110
+ "eval_poi_heavy_atoms_difference": 1.4901458241272647,
111
+ "eval_poi_heavy_atoms_difference_norm": 0.041714774874027596,
112
  "eval_poi_tanimoto_similarity": 0.0,
113
+ "eval_poi_valid": 0.9570481661511269,
114
+ "eval_reassembly": 0.5154220061864782,
115
+ "eval_reassembly_nostereo": 0.5402562969509501,
116
+ "eval_runtime": 1509.5435,
117
+ "eval_samples_per_second": 7.496,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
118
  "eval_steps_per_second": 0.117,
119
  "eval_tanimoto_similarity": 0.0,
120
+ "eval_valid": 0.9424657534246575,
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=2-learning_rate=4.8e-05-warmup_ratio=0.020-min_lr=0.000-factor=0.550",
144
  "trial_params": {
145
+ "factor": 0.55,
146
+ "learning_rate": 4.8207210410584316e-05,
147
+ "min_lr": 3.4399207522159007e-12,
148
+ "warmup_ratio": 0.02
149
  }
150
  }
last-checkpoint/training_args.bin CHANGED
@@ -1,3 +1,3 @@
1
  version https://git-lfs.github.com/spec/v1
2
- oid sha256:60a7aec275bcf811429dfbc78d6576e73abbb33c21daf6b6653852b729ab5c9a
3
  size 7544
 
1
  version https://git-lfs.github.com/spec/v1
2
+ oid sha256:6063fbd0753d44cd280186a06657d1da6da2b725bde8658b24f8f30e8c30c281
3
  size 7544