ribesstefano's picture
Training in progress, step 10000, checkpoint
1533b8e verified
raw
history blame
10.8 kB
{
"best_metric": 0.41069376933274415,
"best_model_checkpoint": "/mimer/NOBACKUP/groups/naiss2023-6-290/stefano/models//PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25/trial-number=4-learning_rate=1.1e-05-warmup_ratio=0.030-min_lr=0.000-factor=0.940/checkpoint-10000",
"epoch": 0.9863878477017163,
"eval_steps": 2500,
"global_step": 10000,
"is_hyper_param_search": true,
"is_local_process_zero": true,
"is_world_process_zero": true,
"log_history": [
{
"epoch": 0.049319392385085814,
"grad_norm": 1.135282278060913,
"learning_rate": 1.0718650414525622e-05,
"loss": 1.7205,
"step": 500
},
{
"epoch": 0.09863878477017163,
"grad_norm": 0.9048516750335693,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.5893,
"step": 1000
},
{
"epoch": 0.14795817715525744,
"grad_norm": 0.8448904156684875,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.3625,
"step": 1500
},
{
"epoch": 0.19727756954034326,
"grad_norm": 0.67970210313797,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.2509,
"step": 2000
},
{
"epoch": 0.24659696192542907,
"grad_norm": 0.7555980682373047,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.1866,
"step": 2500
},
{
"epoch": 0.2959163543105149,
"grad_norm": 0.5226275324821472,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.147,
"step": 3000
},
{
"epoch": 0.3452357466956007,
"grad_norm": 0.3435736298561096,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.1174,
"step": 3500
},
{
"epoch": 0.3945551390806865,
"grad_norm": 0.33571186661720276,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.0952,
"step": 4000
},
{
"epoch": 0.4438745314657723,
"grad_norm": 0.4317052662372589,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.0774,
"step": 4500
},
{
"epoch": 0.49319392385085814,
"grad_norm": 0.4251234829425812,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.0646,
"step": 5000
},
{
"epoch": 0.49319392385085814,
"eval_all_ligands_equal": 0.1314184710561202,
"eval_e3_equal": 0.6642509942554131,
"eval_e3_graph_edit_distance": 9.999999999999999e+63,
"eval_e3_graph_edit_distance_norm": 1.0,
"eval_e3_has_attachment_point(s)": 0.9954927087936367,
"eval_e3_heavy_atoms_difference": -0.1652673442333186,
"eval_e3_heavy_atoms_difference_norm": -0.0189775084827908,
"eval_e3_tanimoto_similarity": 0.0,
"eval_e3_valid": 0.9954927087936367,
"eval_has_all_attachment_points": 0.9818824569155987,
"eval_has_three_substructures": 0.9983208130799823,
"eval_heavy_atoms_difference": 9.841184268669908,
"eval_heavy_atoms_difference_norm": 0.1288377887017133,
"eval_linker_equal": 0.21767565178965975,
"eval_linker_graph_edit_distance": 9.999999999999999e+63,
"eval_linker_graph_edit_distance_norm": 1.0,
"eval_linker_has_attachment_point(s)": 0.9942554131683606,
"eval_linker_heavy_atoms_difference": 2.058241272646929,
"eval_linker_heavy_atoms_difference_norm": 0.07612205467495885,
"eval_linker_tanimoto_similarity": 0.0,
"eval_linker_valid": 0.9942554131683606,
"eval_loss": 0.300495982170105,
"eval_num_fragments": 2.999381352187362,
"eval_poi_equal": 0.5985859478568272,
"eval_poi_graph_edit_distance": 9.999999999999999e+63,
"eval_poi_graph_edit_distance_norm": 1.0,
"eval_poi_has_attachment_point(s)": 0.900309323906319,
"eval_poi_heavy_atoms_difference": 3.2072470172337604,
"eval_poi_heavy_atoms_difference_norm": 0.10008980427814149,
"eval_poi_tanimoto_similarity": 0.0,
"eval_poi_valid": 0.900309323906319,
"eval_reassembly": 0.13442333186036234,
"eval_reassembly_nostereo": 0.1504197967300044,
"eval_runtime": 1571.3971,
"eval_samples_per_second": 7.201,
"eval_steps_per_second": 0.113,
"eval_tanimoto_similarity": 0.0,
"eval_valid": 0.8950066283694211,
"step": 5000
},
{
"epoch": 0.542513316235944,
"grad_norm": 0.4560946822166443,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.0539,
"step": 5500
},
{
"epoch": 0.5918327086210298,
"grad_norm": 0.28064244985580444,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.0459,
"step": 6000
},
{
"epoch": 0.6411521010061156,
"grad_norm": 0.279048353433609,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.0399,
"step": 6500
},
{
"epoch": 0.6904714933912014,
"grad_norm": 0.28535017371177673,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.0349,
"step": 7000
},
{
"epoch": 0.7397908857762873,
"grad_norm": 0.2345045953989029,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.0311,
"step": 7500
},
{
"epoch": 0.7397908857762873,
"eval_all_ligands_equal": 0.31975254087494476,
"eval_e3_equal": 0.7414935925762263,
"eval_e3_graph_edit_distance": 9.999999999999999e+63,
"eval_e3_graph_edit_distance_norm": 1.0,
"eval_e3_has_attachment_point(s)": 0.9930181175430844,
"eval_e3_heavy_atoms_difference": 0.23756076005302695,
"eval_e3_heavy_atoms_difference_norm": -9.951114981210329e-05,
"eval_e3_tanimoto_similarity": 0.0,
"eval_e3_valid": 0.9930181175430844,
"eval_has_all_attachment_points": 0.9832081307998233,
"eval_has_three_substructures": 0.9982324348210341,
"eval_heavy_atoms_difference": 8.244454264250994,
"eval_heavy_atoms_difference_norm": 0.10871833846438654,
"eval_linker_equal": 0.4819266460450729,
"eval_linker_graph_edit_distance": 9.999999999999999e+63,
"eval_linker_graph_edit_distance_norm": 1.0,
"eval_linker_has_attachment_point(s)": 0.9954043305346885,
"eval_linker_heavy_atoms_difference": 0.9907202828104287,
"eval_linker_heavy_atoms_difference_norm": 0.023780405382435494,
"eval_linker_tanimoto_similarity": 0.0,
"eval_linker_valid": 0.9954043305346885,
"eval_loss": 0.295632004737854,
"eval_num_fragments": 3.000353513035793,
"eval_poi_equal": 0.6684931506849315,
"eval_poi_graph_edit_distance": 9.999999999999999e+63,
"eval_poi_graph_edit_distance_norm": 1.0,
"eval_poi_has_attachment_point(s)": 0.9179849756959788,
"eval_poi_heavy_atoms_difference": 2.835528060097216,
"eval_poi_heavy_atoms_difference_norm": 0.08970608654557162,
"eval_poi_tanimoto_similarity": 0.0,
"eval_poi_valid": 0.9179849756959788,
"eval_reassembly": 0.3252319929297393,
"eval_reassembly_nostereo": 0.3522757401679187,
"eval_runtime": 1456.0998,
"eval_samples_per_second": 7.771,
"eval_steps_per_second": 0.122,
"eval_tanimoto_similarity": 0.0,
"eval_valid": 0.9111798497569598,
"step": 7500
},
{
"epoch": 0.789110278161373,
"grad_norm": 0.28123733401298523,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.0265,
"step": 8000
},
{
"epoch": 0.8384296705464589,
"grad_norm": 0.24425843358039856,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.0236,
"step": 8500
},
{
"epoch": 0.8877490629315447,
"grad_norm": 0.24540802836418152,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.0209,
"step": 9000
},
{
"epoch": 0.9370684553166305,
"grad_norm": 0.225132018327713,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.0192,
"step": 9500
},
{
"epoch": 0.9863878477017163,
"grad_norm": 0.22183990478515625,
"learning_rate": 1.0718650414525622e-05,
"loss": 0.0172,
"step": 10000
},
{
"epoch": 0.9863878477017163,
"eval_all_ligands_equal": 0.41069376933274415,
"eval_e3_equal": 0.7672116659301812,
"eval_e3_graph_edit_distance": 9.999999999999999e+63,
"eval_e3_graph_edit_distance_norm": 1.0,
"eval_e3_has_attachment_point(s)": 0.9932832523199293,
"eval_e3_heavy_atoms_difference": 0.29164825452938575,
"eval_e3_heavy_atoms_difference_norm": 0.0027889377232460147,
"eval_e3_tanimoto_similarity": 0.0,
"eval_e3_valid": 0.9932832523199293,
"eval_has_all_attachment_points": 0.983738400353513,
"eval_has_three_substructures": 0.9990278391515687,
"eval_heavy_atoms_difference": 8.101723376049492,
"eval_heavy_atoms_difference_norm": 0.10700669432541757,
"eval_linker_equal": 0.598232434821034,
"eval_linker_graph_edit_distance": 9.999999999999999e+63,
"eval_linker_graph_edit_distance_norm": 1.0,
"eval_linker_has_attachment_point(s)": 0.994962439239947,
"eval_linker_heavy_atoms_difference": 0.9996464869642068,
"eval_linker_heavy_atoms_difference_norm": 0.03566936969040077,
"eval_linker_tanimoto_similarity": 0.0,
"eval_linker_valid": 0.994962439239947,
"eval_loss": 0.29776647686958313,
"eval_num_fragments": 3.0007954043305345,
"eval_poi_equal": 0.7079982324348211,
"eval_poi_graph_edit_distance": 9.999999999999999e+63,
"eval_poi_graph_edit_distance_norm": 1.0,
"eval_poi_has_attachment_point(s)": 0.9185152452496685,
"eval_poi_heavy_atoms_difference": 2.548298718515245,
"eval_poi_heavy_atoms_difference_norm": 0.07894069428466077,
"eval_poi_tanimoto_similarity": 0.0,
"eval_poi_valid": 0.9185152452496685,
"eval_reassembly": 0.4183826778612461,
"eval_reassembly_nostereo": 0.4470172337604949,
"eval_runtime": 1468.5838,
"eval_samples_per_second": 7.705,
"eval_steps_per_second": 0.121,
"eval_tanimoto_similarity": 0.0,
"eval_valid": 0.9102076889085285,
"step": 10000
}
],
"logging_steps": 500,
"max_steps": 10000,
"num_input_tokens_seen": 0,
"num_train_epochs": 1,
"save_steps": 5000,
"stateful_callbacks": {
"TrainerControl": {
"args": {
"should_epoch_stop": false,
"should_evaluate": false,
"should_log": false,
"should_save": true,
"should_training_stop": true
},
"attributes": {}
}
},
"total_flos": 8.663036348367667e+16,
"train_batch_size": 128,
"trial_name": "trial-number=4-learning_rate=1.1e-05-warmup_ratio=0.030-min_lr=0.000-factor=0.940",
"trial_params": {
"factor": 0.9400000000000001,
"learning_rate": 1.0718650414525622e-05,
"min_lr": 3.3284513007278865e-10,
"warmup_ratio": 0.03
}
}