Upload 3 files
Browse filesfeat: kinase_phosphorylation_site checkpoint
kinase_phosphorylation_site/2025-01-21__22-15-51/checkpoints/best_valid_kinase_phosphorylation_site_f1.pth
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version https://git-lfs.github.com/spec/v1
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oid sha256:620d4f5381aa67f21b3da70f4dd3683cbf136fae1cb4cfebafcb0dd89a6a61ee
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size 5178807909
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kinase_phosphorylation_site/2025-01-21__22-15-51/config.yaml
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fix_seed: 0
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checkpoints_every: 512
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tensorboard_log: True
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tqdm_progress_bar: False
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result_path: ./results/kinase_phosphorylation_site/
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resume:
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enable: False
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resume_path: path/to/checkpoints
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restart_optimizer: True
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restart_steps: True
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prot2token_model:
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compile_model: True
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positional_encoding_type: learned # absolute, learned
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protein_encoder:
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model_type: esm_v2 # esm_v2, t5
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model_name: facebook/esm2_t33_650M_UR50D # facebook/esm2_t33_650M_UR50D, facebook/esm2_t30_150M_UR50D, facebook/esm2_t12_35M_UR50D, facebook/esm2_t6_8M_UR50D, Rostlab/prot_t5_base_mt_uniref50
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max_len: 2048
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max_label_index: 1280
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drop_positional_encoding: True
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quantization_4_bit: False # use with tune_embedding enable
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tune_embedding: False # only for esm
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fine_tune:
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enable: True
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last_layers_trainable: 8
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lora:
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enable: False
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r: 8
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lora_alpha: 32
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lora_dropout: 0.05
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decoder:
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latest_flash_attention: False
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dimension: 640
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dim_feedforward: 2560
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num_heads: 16
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num_layers: 16
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max_len: 384
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activation_function: gelu
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decoder_context_dropout: 0.0
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train_settings:
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skip: False
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data_path: ../../datasets/Joint_training/
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num_epochs: 256
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start_metric_epoch: 96
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shuffle: True
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loss: crossentropy # crossentropy or focal
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mixed_precision: bf16 # no, fp16, bf16, fp8
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device: cuda
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batch_size: 16
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num_workers: 4
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grad_accumulation: 2
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max_task_samples: 20000
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valid_settings:
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data_path: ../../datasets/Joint_training/
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do_every: 1
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batch_size: 1 # 1 when perplexity = False
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perplexity: False
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device: cuda
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num_workers: 2
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test_settings:
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enable: True
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data_path: ../../datasets/Joint_training/
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batch_size: 1
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device: cuda
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num_workers: 0
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inference_type: inference_greedy # inference_beam_search, inference_greedy
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beam_search:
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top_k: 1
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beam_width: 3
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temperature: 1.0
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monitoring_metrics:
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kinase_group: macro_f1
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kinase_interaction: f1
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kinase_phosphorylation_site: f1
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tasks:
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kinase_group: False
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kinase_interaction: False
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kinase_phosphorylation_site: True
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kinase_phosphorylation_site/2025-01-21__22-15-51/decoder_tokenizer.yaml
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|
| 1 |
+
'1': 24
|
| 2 |
+
'10': 33
|
| 3 |
+
'100': 123
|
| 4 |
+
'1000': 1023
|
| 5 |
+
'1001': 1024
|
| 6 |
+
'1002': 1025
|
| 7 |
+
'1003': 1026
|
| 8 |
+
'1004': 1027
|
| 9 |
+
'1005': 1028
|
| 10 |
+
'1006': 1029
|
| 11 |
+
'1007': 1030
|
| 12 |
+
'1008': 1031
|
| 13 |
+
'1009': 1032
|
| 14 |
+
'101': 124
|
| 15 |
+
'1010': 1033
|
| 16 |
+
'1011': 1034
|
| 17 |
+
'1012': 1035
|
| 18 |
+
'1013': 1036
|
| 19 |
+
'1014': 1037
|
| 20 |
+
'1015': 1038
|
| 21 |
+
'1016': 1039
|
| 22 |
+
'1017': 1040
|
| 23 |
+
'1018': 1041
|
| 24 |
+
'1019': 1042
|
| 25 |
+
'102': 125
|
| 26 |
+
'1020': 1043
|
| 27 |
+
'1021': 1044
|
| 28 |
+
'1022': 1045
|
| 29 |
+
'1023': 1046
|
| 30 |
+
'1024': 1047
|
| 31 |
+
'1025': 1048
|
| 32 |
+
'1026': 1049
|
| 33 |
+
'1027': 1050
|
| 34 |
+
'1028': 1051
|
| 35 |
+
'1029': 1052
|
| 36 |
+
'103': 126
|
| 37 |
+
'1030': 1053
|
| 38 |
+
'1031': 1054
|
| 39 |
+
'1032': 1055
|
| 40 |
+
'1033': 1056
|
| 41 |
+
'1034': 1057
|
| 42 |
+
'1035': 1058
|
| 43 |
+
'1036': 1059
|
| 44 |
+
'1037': 1060
|
| 45 |
+
'1038': 1061
|
| 46 |
+
'1039': 1062
|
| 47 |
+
'104': 127
|
| 48 |
+
'1040': 1063
|
| 49 |
+
'1041': 1064
|
| 50 |
+
'1042': 1065
|
| 51 |
+
'1043': 1066
|
| 52 |
+
'1044': 1067
|
| 53 |
+
'1045': 1068
|
| 54 |
+
'1046': 1069
|
| 55 |
+
'1047': 1070
|
| 56 |
+
'1048': 1071
|
| 57 |
+
'1049': 1072
|
| 58 |
+
'105': 128
|
| 59 |
+
'1050': 1073
|
| 60 |
+
'1051': 1074
|
| 61 |
+
'1052': 1075
|
| 62 |
+
'1053': 1076
|
| 63 |
+
'1054': 1077
|
| 64 |
+
'1055': 1078
|
| 65 |
+
'1056': 1079
|
| 66 |
+
'1057': 1080
|
| 67 |
+
'1058': 1081
|
| 68 |
+
'1059': 1082
|
| 69 |
+
'106': 129
|
| 70 |
+
'1060': 1083
|
| 71 |
+
'1061': 1084
|
| 72 |
+
'1062': 1085
|
| 73 |
+
'1063': 1086
|
| 74 |
+
'1064': 1087
|
| 75 |
+
'1065': 1088
|
| 76 |
+
'1066': 1089
|
| 77 |
+
'1067': 1090
|
| 78 |
+
'1068': 1091
|
| 79 |
+
'1069': 1092
|
| 80 |
+
'107': 130
|
| 81 |
+
'1070': 1093
|
| 82 |
+
'1071': 1094
|
| 83 |
+
'1072': 1095
|
| 84 |
+
'1073': 1096
|
| 85 |
+
'1074': 1097
|
| 86 |
+
'1075': 1098
|
| 87 |
+
'1076': 1099
|
| 88 |
+
'1077': 1100
|
| 89 |
+
'1078': 1101
|
| 90 |
+
'1079': 1102
|
| 91 |
+
'108': 131
|
| 92 |
+
'1080': 1103
|
| 93 |
+
'1081': 1104
|
| 94 |
+
'1082': 1105
|
| 95 |
+
'1083': 1106
|
| 96 |
+
'1084': 1107
|
| 97 |
+
'1085': 1108
|
| 98 |
+
'1086': 1109
|
| 99 |
+
'1087': 1110
|
| 100 |
+
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