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8027e0e
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Parent(s):
b58cc31
test
Browse files
workdir/gradio/affinity_default.yaml
ADDED
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1 |
+
target: Chembl_Rank
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+
base_path: /data/jiaxianyan/1-git/UltraFlow
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+
root_dir: /data/jiaxianyan/1-git/UltraFlow/log
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seed: 2023
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train:
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gpu_memory_need: 10000
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repeat: 5
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optimizer:
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type: Adam
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lr: 0.001
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weight_decay: 0.000
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dropout: 0.0
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scheduler:
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type: plateau
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factor: 0.6
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# factor: 0.95
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patience: 10
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min_lr: 1e-4
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gpus:
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- 1
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resume_train: false
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#resume_epoch: latest
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resume_epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022
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resume_now: 2023-07-02_13:18:36
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batch_size: 128
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shuffle: true
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num_workers: 4
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use_memory_efficient_dataset: v2 # [v1, v2, false] , v1 split dataset, v2 do not prepare graph in advance
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pretrain_epochs: 100
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finetune_epochs: 1000
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early_stop: 70
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log_interval:
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eval: true
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save: true
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ranking_loss: pair_wise_v2 # [null, pair_wise_v1,pair_wise_v2]
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ranking_loss_lambda: 1.0
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pairwise_two_tower_regression_loss: false
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use_pretrain_model: true
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pretrain_ranking_loss: pairwise_v2 # [pairwise_v1, pairwise_v2], v1: image deepth prediction, v2: recommend system
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41 |
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pretrain_sampling_method: pairwise_v1 # [pointwise, pairwise_v1]
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pretrain_ranking_loss_lambda: 1.0
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pretrain_regression_loss_lambda: 0.3
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pretrain_regression_loss_lambda_degrade_ratio: 1.0
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pretrain_regression_loss_lambda_degrade_epoch: 1
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pretrain_use_assay_description: false
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pretrain_assay_mlp_share: true
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48 |
+
pretrain_mtl_IC50_lambda: 1.0 # 0.2404, 0.3819
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49 |
+
pretrain_mtl_Kd_lambda: 1.0 # 0.4957
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+
pretrain_mtl_Ki_lambda: 1.0 # 0.2639
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pretrain_mtl_K_lambda: 1.0 # 0.6181
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52 |
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multi_task: IC50K # [IC50KdKi, IC50K, false]
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53 |
+
finetune_times: 5
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+
finetune_new_affinity_head: false
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55 |
+
use_FLAG: false
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FLAG_step_size: 0.01
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FLAG_m: 4
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58 |
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FLAG_v: v_inter
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59 |
+
encoder_ablation: null # [ligand, protein, interact, null]
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60 |
+
interact_ablate_op: min # [max, sum, mean, min]
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61 |
+
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62 |
+
test:
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63 |
+
#now: 2023-01-05_20:57:03
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64 |
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#epoch: 66
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65 |
+
#now: 2023-01-07_02:00:41
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#epoch: 129
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+
#now: 2023-01-07_13:50:41
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#epoch: 87
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69 |
+
#now: 2023-01-07_22:14:28
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70 |
+
#epoch: 107 # pointwise_pretrain
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71 |
+
#now: 2023-01-09_23:17:57
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72 |
+
#epoch: 63 # pairwise_smaplev1_loss_v1_regression
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73 |
+
#now: 2023-01-10_11:20:07
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74 |
+
#epoch: 20 # pointwise_chembl_smina
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75 |
+
#now: 2023-01-11_18:49:32
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76 |
+
#epoch: 39 # pw_lsv1_sampv1
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#now: 2023-01-12_02:05:49
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78 |
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#epoch: 29 # pw_lsv1_sampv1_reg
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79 |
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#now: 2023-01-12_01:41:19
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80 |
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#epoch: 41 # pw_lsv2_sampv1
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81 |
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#now: 2023-01-12_02:11:13
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82 |
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#epoch: best_loss # pw_lsv2_sampv1_reg
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83 |
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#now: 2023-01-12_02:14:41
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84 |
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#epoch: 35 # pw_lsv2_sampv1_reg_deg
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#now: 2023-01-12_02:18:41
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#epoch: best_loss # pointwise
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#now: 2023-01-12_14:53:48
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88 |
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#epoch: latest # pw_lsv2_sampv1_reg
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#now: 2023-01-13_19:42:09
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#epoch: latest # pointwise_100
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#now: 2023-01-13_17:10:44
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#epoch: latest # pw_lsv2_sampv1_reg0.1
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#now: 2023-01-13_20:24:01
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#epoch: latest # pw_lsv2_sampv1_reg
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#now: 2023-01-13_23:45:08
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#epoch: latest # pw_lsv2_sampv1_reg_deg098
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#now: 2023-01-14_01:37:03
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#epoch: latest # pw_lsv2_sampv1_reg_deg003
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#now: 2023-01-14_22:52:00
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#epoch: latest # pw_lsv2_sampv1_reg_deg001
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#now: 2023-01-14_22:43:09
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#epoch: latest # pw_lsv2_sampv1_reg_deg03
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#now: 2023-01-14_22:58:01
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#epoch: latest # pw_lsv1_sampv1
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#now: 2023-01-14_23:59:19
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#epoch: latest # pw_lsv2_sampv1_reg_deg097
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#now: 2023-01-15_00:32:04
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#epoch: latest # pw_lsv2_sampv1_reg_deg096
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#now: 2023-01-15_00:56:11
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#epoch: latest # pw_lsv2_sampv1_reg_deg095
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#now: 2023-01-15_01:05:33
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#epoch: latest # pw_lsv2_sampv1_reg_deg099
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#now: 2023-01-15_01:09:30
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#epoch: latest # pw_lsv2_sampv1_reg01_GIN
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#now: 2023-01-16_02:50:27
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#epoch: latest # pw_lsv2_sampv1_reg01_GAT
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#now: 2023-01-16_02:56:21
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#epoch: latest # pw_lsv2_sampv1_reg01_GCN
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#now: 2023-01-16_02:59:20
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#epoch: latest # pw_lsv2_sampv1_reg03_GCN
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#now: 2023-01-17_02:54:28
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#epoch: latest # pw_lsv2_sampv1_reg01_EGNN
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#now: 2023-01-16_10:41:20
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#epoch: latest # pw_lsv2_sampv1_reg1_GCN
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#now: 2023-01-17_02:08:52
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#epoch: latest # pointwise_GCN
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#now: 2023-01-16_16:17:22
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#epoch: latest # pointwise_GIN
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#now: 2023-01-16_16:24:47
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#epoch: latest # pointwise_GAT
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#now: 2023-01-16_16:22:16
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#epoch: latest # pointwise_EGNN
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#now: 2023-01-16_16:28:39
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#epoch: latest # pw_lsv2_sampv1_reg_deg098_GCN
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#now: 2023-01-17_03:08:31
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#epoch: latest # pw_lsv2_sampv1_reg_deg099_GCN
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#now: 2023-01-17_03:26:00
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#epoch: latest # pw_lsv2_sampv1_reg_deg097_GCN
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#now: 2023-01-17_03:19:57
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#epoch: latest # pw_lsv2_sampv1_reg_1_GAT
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#now: 2023-01-17_10:59:53
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#epoch: latest # pw_lsv2_sampv1_reg_1_EGNN
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#now: 2023-01-17_10:49:58
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#epoch: latest # pw_lsv2_sampv1_reg_1_GIN
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#now: 2023-01-17_20:25:44
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#epoch: latest # pw_lsv2_sampv1_reg_03_assay_noshare_cls_IGN
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#now: 2023-01-18_03:15:54
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#epoch: latest # pw_lsv2_sampv1_reg_03_assay_share_first_last_avg_IGN
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#now: 2023-01-18_02:55:27
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#epoch: latest # pw_lsv2_sampv1_reg_03_assay_share_cls_IGN
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+
#now: 2023-01-18_02:53:45
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#epoch: latest # pw_lsv2_sampv1_reg_03_assay_noshare_first_last_avg_IGN
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#now: 2023-01-18_03:25:44
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#epoch: latest # pw_lsv2_sampv1_reg_03_GAT
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#now: 2023-01-18_03:39:46
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#epoch: latest # IGN_Pointwise_KdKi
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#now: 2023-01-19_15:20:08
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#epoch: latest # pw_lsv2_sampv1_reg_03_IGN_ASRP_ASSAY_cls_share_KdKi
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#now: 2023-01-19_16:36:54
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#epoch: latest # pw_lsv2_sampv1_reg_03_IGN_ASRP_KdKi
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#now: 2023-01-19_16:35:05
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#epoch: latest # pw_lsv2_sampv1_reg_03_IGN_ASRP_MTL_KdKi
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#now: 2023-01-19_20:13:09
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#epoch: latest # IGN_Pointwise_MTL_KdKi
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#now: 2023-01-20_00:32:14
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#epoch: latest # IGN_BioLinkBERT_large_first_last_avg
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#now: 2023-01-20_03:57:31
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#epoch: latest # IGN_BioLinkBERT_large_cls
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#now: 2023-01-20_03:54:29
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#epoch: latest # IGN_first_last_avg
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#now: 2023-01-20_03:36:13
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#epoch: latest # IGN_cls
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#now: 2023-01-20_03:33:14
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#epoch: latest # IGN_ASRP_reg1_MTL
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#now: 2023-01-20_02:26:15
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#epoch: latest # IGN_ASRP_reg1
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#now: 2023-01-20_01:00:28
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#epoch: latest # IGN_BioLinkBERT_large_last2avg
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#now: 2023-01-20_11:26:29
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#epoch: latest # IGN_BioLinkBERT_large_last_avg
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#now: 2023-01-20_16:37:28
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#epoch: latest # IGN_MTL_new_lambda
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#now: 2023-01-20_18:14:21
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#epoch: latest # IGN_ASRP_reg01
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185 |
+
#now: 2023-01-20_15:58:41
|
186 |
+
#epoch: latest # IGN_ASRP_reg01_MTL
|
187 |
+
#now:
|
188 |
+
#epoch: latest # IGN_ASRP_reg1_decay098
|
189 |
+
#now: 2023-01-20_17:25:17
|
190 |
+
#epoch: latest # IGN_ASRP_reg0
|
191 |
+
#now: 2023-01-20_17:04:29
|
192 |
+
#epoch: latest # IGN_ASRP_reg1_decay097
|
193 |
+
#now: 2023-01-20_17:22:09
|
194 |
+
#epoch: latest # GIN_ASRP_reg03_MTL_bio_cls
|
195 |
+
#now: 2023-01-21_02:54:26
|
196 |
+
#epoch: latest # GIN_pointwise_baseline
|
197 |
+
#now: 2023-01-21_02:57:48
|
198 |
+
#epoch: latest # IGN_ASRP_MTL_new_bio_cls_reg03
|
199 |
+
#now: 2023-01-21_02:40:35
|
200 |
+
#epoch: latest # IGN_ASRP_MTL_new_bio_cls_reg_deg098
|
201 |
+
#now: 2023-01-21_02:37:49
|
202 |
+
#epoch: latest # IGN_ASRP_MTL_new_bio_cls_reg_deg097
|
203 |
+
#now: 2023-01-21_02:30:27
|
204 |
+
#epoch: latest # GCN_ASRP_MTL_new_bio_cls_reg_deg03
|
205 |
+
#now: 2023-01-21_02:51:12
|
206 |
+
#2023-01-20_14:31:13epoch: latest # GCN_pointwise_baseline
|
207 |
+
#now: 2023-01-21_03:00:26
|
208 |
+
#epoch: latest # IGN_IC50KdKi_pointwise_baseline
|
209 |
+
#now: 2023-01-20_14:31:13
|
210 |
+
#epoch: latest # IGN_IC50KdKi_pointwise_MTL_baseline
|
211 |
+
#now: 2023-01-20_15:04:28
|
212 |
+
#epoch: latest # IGN_KdKi_MTL_new_ASRP_reg_deg097
|
213 |
+
#now: 2023-01-21_12:56:41
|
214 |
+
#epoch: latest # IGN_IC50K_MTL
|
215 |
+
#now: 2023-01-21_16:32:41
|
216 |
+
#epoch: latest # IGN_IC50K_MTL_new_lambda
|
217 |
+
#now: 2023-01-21_16:47:33
|
218 |
+
#epoch: latest # IGN_IC50KiKd_ASRP_reg_deg097
|
219 |
+
#now: 2023-01-21_12:31:31
|
220 |
+
#epoch: latest # IGN_IC50K_Pointwise_IC5001_MTL
|
221 |
+
#now: 2023-01-22_20:09:05
|
222 |
+
#epoch: latest # IGN_IC50K_ASRP_reg_deg097_MTL_new_lambda
|
223 |
+
#now: 2023-01-22_00:22:25
|
224 |
+
#epoch: latest # IGN_IC50K_ASRP_reg_deg097_MTL
|
225 |
+
#now: 2023-01-22_00:32:35
|
226 |
+
#epoch: latest # IGN_IC50K_ASRP_reg_deg098_MTL
|
227 |
+
#now: 2023-01-22_14:12:10
|
228 |
+
#epoch: latest # IGN_IC50K_ASRP_reg03_MTL
|
229 |
+
#now: 2023-01-22_14:22:52
|
230 |
+
#finetune_epoch_list: [103, 162, 76] # ASRP_IC50
|
231 |
+
#now: 2023-01-15_22:37:29
|
232 |
+
#finetune_epoch_list: [182, 96, 149] # pointwise_IC50
|
233 |
+
#now: 2023-01-14_17:39:58
|
234 |
+
#finetune_epoch_list: [125, 211] # ASRP_reg03_IC50K_MTL
|
235 |
+
#now: 2023-01-23_19:34:56
|
236 |
+
#finetune_epoch_list: [100_bs_128_lr_0.001] # ASRP_reg03_IC50K_MTL
|
237 |
+
#now: 2023-01-23_19:55:02
|
238 |
+
#epoch: latest # resume training GIN
|
239 |
+
#now: 2023-01-23_23:27:05
|
240 |
+
#epoch: latest # resume training EGNN
|
241 |
+
#now: 2023-01-23_23:31:09
|
242 |
+
#epoch: latest # resume training GCN
|
243 |
+
#now: 2023-01-23_23:33:01
|
244 |
+
#epoch: latest # resume training GAT
|
245 |
+
#now: 2023-01-23_23:35:01
|
246 |
+
#epoch: latest # resume training AttentiveFP ASRP reg 1 MTL
|
247 |
+
#now: 2023-01-24_00:04:18
|
248 |
+
#epoch: latest # IC50K ASRP reg03 MTL GIN
|
249 |
+
#now: 2023-01-24_13:11:09
|
250 |
+
#epoch: latest # IC50K ASRP reg03 MTL GCN
|
251 |
+
#now: 2023-01-24_13:29:10
|
252 |
+
#epoch: latest # IC50K ASRP reg03 MTL GAT
|
253 |
+
#now: 2023-01-24_13:35:25
|
254 |
+
#epoch: latest # IC50K ASRP reg03 MTL EGNN
|
255 |
+
#now: 2023-01-24_13:32:19
|
256 |
+
#epoch: latest # IC50K ASRP reg1 MTL AttentiveFP
|
257 |
+
#now: 2023-01-24_13:40:54
|
258 |
+
#epoch: latest # IC50K ASRP reg0 MTL AttentiveFP
|
259 |
+
#now: 2023-01-24_21:47:05
|
260 |
+
#epoch: latest # IC50K ARRP K reg001 AttentiveFP
|
261 |
+
#now: 2023-01-26_01:06:33
|
262 |
+
#epoch: latest # IC50K ASRP reg deg096 MTL AttentiveFP
|
263 |
+
#now: 2023-01-25_17:19:26
|
264 |
+
#epoch: latest # IC50K ASRP reg deg099 MTL AttentiveFP
|
265 |
+
#now: 2023-01-25_17:00:41
|
266 |
+
#epoch: latest # IC50K ASRP reg01 MTL AttentiveFP
|
267 |
+
#now: 2023-01-25_17:27:33
|
268 |
+
#epoch: latest # IC50K ASRP reg001 MTL AttentiveFP
|
269 |
+
#now: 2023-01-25_17:34:35
|
270 |
+
#epoch: latest # IC50K ASRP K reg deg099 AttentiveFP
|
271 |
+
#now: 2023-01-25_20:11:34
|
272 |
+
#epoch: latest # IC50K ASRP K reg deg096 AttentiveFP
|
273 |
+
#now: 2023-01-25_20:44:22
|
274 |
+
#epoch: latest # IC50K ASRP Pointwise EGNN
|
275 |
+
#now: 2023-01-27_01:48:42
|
276 |
+
#epoch: latest # IC50K ASRP Pointwise GAT
|
277 |
+
#now: 2023-01-27_01:43:00
|
278 |
+
#epoch: latest # IC50K ASRP Pointwise GIN
|
279 |
+
#now: 2023-01-27_01:40:44
|
280 |
+
#epoch: latest # IC50K ASRP Pointwise GCN
|
281 |
+
#now: 2023-01-27_01:29:01
|
282 |
+
#epoch: latest # IC50K ASRP reg deg095 AttentiveFP
|
283 |
+
#now: 2023-01-27_11:48:44
|
284 |
+
#epoch: latest # IC50K ASRP K reg deg095 AttentiveFP
|
285 |
+
#now: 2023-01-27_12:04:37
|
286 |
+
#epoch: latest # IC50K ASRP reg deg098 MTL GCN
|
287 |
+
#now: 2023-01-27_17:46:03
|
288 |
+
#epoch: latest # IC50K ASRP reg deg097 MTL GCN
|
289 |
+
#now: 2023-01-27_17:56:52
|
290 |
+
#epoch: latest # IC50K ASRP reg deg096 MTL GCN
|
291 |
+
#now: 2023-01-27_18:14:49
|
292 |
+
#epoch: latest # IC50K ASRP reg deg096 MTL GIN
|
293 |
+
#now: 2023-01-27_19:42:01
|
294 |
+
#epoch: latest # IC50K ASRP reg deg097 MTL GIN
|
295 |
+
#now: 2023-01-27_21:08:11
|
296 |
+
#epoch: latest # IC50K ASRP reg deg096 MTL AttentiveFP Flag correct batch 512 seed 43
|
297 |
+
#now: 2023-03-28_23:20:01
|
298 |
+
#epoch: latest # IC50K ASRP reg deg097 MTL AttentiveFP Flag correct batch 512 seed 43
|
299 |
+
#now: 2023-03-30_21:39:55
|
300 |
+
#epoch: latest # IC50K ASRP reg deg098 MTL AttentiveFP Flag correct batch 512 seed 43
|
301 |
+
#now: 2023-03-30_21:46:44
|
302 |
+
#epoch: latest # IC50K ASRP reg deg099 MTL AttentiveFP Flag correct batch 512 seed 43
|
303 |
+
#now: 2023-03-30_21:54:54
|
304 |
+
#epoch: latest # IC50K ASRP reg 03 MTL AttentiveFP Flag correct batch 512 seed 43
|
305 |
+
#now: 2023-03-31_03:57:32
|
306 |
+
#epoch: latest # IC50K ASRP reg deg096 MTL AttentiveFP Flag correct batch 256 seed 2022
|
307 |
+
#now: 2023-04-04_16:31:48
|
308 |
+
#epoch: latest # IC50K ASRP reg deg097 MTL AttentiveFP Flag correct batch 256 seed 2022
|
309 |
+
#now: 2023-04-02_18:52:38
|
310 |
+
#epoch: latest # IC50K ASRP reg deg098 MTL AttentiveFP Flag correct batch 256 seed 2022
|
311 |
+
#now: 2023-04-03_21:29:07
|
312 |
+
#epoch: latest # IC50K ASRP reg deg099 MTL AttentiveFP Flag correct batch 256 seed 2022
|
313 |
+
#now: 2023-04-02_20:44:06
|
314 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022
|
315 |
+
#now: 2023-04-03_21:24:55
|
316 |
+
#epoch: latest_300 # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 batch256 resume
|
317 |
+
#now: 2023-04-10_00:08:29
|
318 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 batch512 resume
|
319 |
+
#now: 2023-04-10_00:38:19
|
320 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 top_2
|
321 |
+
#now: 2023-04-09_11:11:49
|
322 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 top_3
|
323 |
+
#now: 2023-04-09_11:01:41
|
324 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 43 top_3
|
325 |
+
#now: 2023-04-11_00:45:49
|
326 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 top_5
|
327 |
+
#now: 2023-04-09_13:40:20
|
328 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 4M
|
329 |
+
#now: 2023-04-09_00:38:24
|
330 |
+
epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 adbf
|
331 |
+
now: 2023-04-12_01:18:25
|
332 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 adbf w_sum_v2
|
333 |
+
#now: 2023-05-17_22:38:25
|
334 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 blind
|
335 |
+
#now: 2023-04-13_00:23:30
|
336 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2023 blind
|
337 |
+
#now: 2023-04-13_00:38:20
|
338 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 top_9 mbp e thre03
|
339 |
+
#now: 2023-05-11_20:01:47
|
340 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 top_9 mbp e thre03 pretrain
|
341 |
+
#now: 2023-05-15_22:00:09
|
342 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 top_9 mbp e min
|
343 |
+
#now: 2023-05-11_19:35:57
|
344 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 top_9 mbp e min pretrain
|
345 |
+
#now: 2023-05-15_21:33:54
|
346 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 top_9 random
|
347 |
+
#now: 2023-05-13_15:22:02
|
348 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 w_sum_v2
|
349 |
+
#now: 2023-05-11_19:40:11
|
350 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 multi_head 4
|
351 |
+
#now: 2023-05-11_20:40:43
|
352 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 multi_head 6
|
353 |
+
#now: 2023-05-11_20:44:59
|
354 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 multi_head_v2 4
|
355 |
+
#now: 2023-05-13_01:13:14
|
356 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 multi_head_v2 6
|
357 |
+
#now: 2023-05-13_01:16:17
|
358 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL EGNN Flag correct batch 256 seed 2022
|
359 |
+
#now: 2023-04-06_17:11:06
|
360 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL 2-layer GCN Flag correct batch 256 seed 2022
|
361 |
+
#now: 2023-04-06_17:15:53
|
362 |
+
#epoch: latest # IC50K ASRP reg deg 096 MTL 2-layer GCN Flag correct batch 256 seed 2022
|
363 |
+
#now: 2023-04-24_17:18:37
|
364 |
+
#epoch: latest # IC50K ASRP reg deg 096 MTL 3-layer GCN Flag correct batch 256 seed 2022
|
365 |
+
#now: 2023-04-09_23:04:26
|
366 |
+
#epoch: latest # IC50K ASRP reg reg 001 MTL 2-layer GCN Flag correct batch 256 seed 2022
|
367 |
+
#now: 2023-04-12_05:29:04
|
368 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL GIN Flag correct batch 256 seed 2022
|
369 |
+
#now: 2023-04-10_17:19:32
|
370 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL GIN Flag correct batch 512 seed 2022
|
371 |
+
#now: 2023-04-11_19:45:16
|
372 |
+
#epoch: latest # IC50K ASRP reg deg 097 MTL GIN Flag correct batch 256 seed 2022
|
373 |
+
#now: 2023-04-12_10:06:59
|
374 |
+
#now: 2023-04-25_17:04:46
|
375 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL GAT Flag correct batch 256 seed 2022
|
376 |
+
#now: 2023-04-10_17:22:42
|
377 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL GAT Flag correct batch 512 seed 2022
|
378 |
+
#now: 2023-04-11_19:39:24
|
379 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFp Flag correct batch 256 seed 2022, v2 effi
|
380 |
+
#now: 2023-04-09_03:02:28
|
381 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 memoery_efficient
|
382 |
+
#now: 2023-04-03_19:25:03
|
383 |
+
#epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 double reg
|
384 |
+
#now: 2023-04-10_14:07:38
|
385 |
+
#epoch: latest # IC50K ASRP reg reg 01 MTL AttentiveFP Flag correct batch 256 seed 2022 double reg
|
386 |
+
#now: 2023-04-10_20:11:02
|
387 |
+
#epoch: latest # IC50K ASRP reg reg 1 MTL AttentiveFP Flag correct batch 256 seed 2022
|
388 |
+
#now: 2023-04-04_22:34:44
|
389 |
+
#epoch: latest # IC50K ASRP reg reg 0 MTL AttentiveFP Flag correct batch 256 seed 2022
|
390 |
+
#now: 2023-04-05_13:37:59
|
391 |
+
#epoch: latest # IC50K ASRP reg reg 01 MTL AttentiveFP Flag correct batch 256 seed 2022
|
392 |
+
#now: 2023-04-10_20:11:02
|
393 |
+
#epoch: latest # IC50K ASRP reg reg 001 MTL AttentiveFP Flag correct batch 256 seed 2022
|
394 |
+
#now: 2023-04-24_17:04:01
|
395 |
+
#epoch: latest # IC50K ASRP rank 0 MTL AttentiveFP Flag correct batch 256 seed 2022
|
396 |
+
#now: 2023-04-06_15:00:40
|
397 |
+
#epoch: latest # IC50K ASRP reg deg03 MTL AttentiveFP Flag correct batch 256 seed 2022 afbf, remove overlap
|
398 |
+
#now: 2023-09-11_19:04:11
|
399 |
+
#epoch: latest # IC50K ASRP reg deg03 MTL AttentiveFP Flag correct batch 256 seed 2022 afbf, remove overlap, pdbbind finetune valid
|
400 |
+
#now: 2023-09-16_17:47:44
|
401 |
+
#now: 2023-09-18_18:18:01 # best
|
402 |
+
#epoch: latest # IC50K ASRP reg deg03 AttentiveFP Flag correct batch 256 seed 2022 afbf, remove overlap, pdbbind finetune valid
|
403 |
+
#now: 2023-09-25_14:59:00
|
404 |
+
#finetune_epoch_list: [44,142,51] # IGN_basic
|
405 |
+
#now: 2023-01-29_05:42:59
|
406 |
+
#finetune_epoch_list: [72,206,97] # AttentiveFP K ASRP reg deg097
|
407 |
+
#now: 2023-01-20_23:38:21
|
408 |
+
#finetune_epoch_list: [137,46,98] # AttentiveFP K pointwise
|
409 |
+
#now: 2023-01-20_04:32:20
|
410 |
+
#finetune_epoch_list: [182,96,149] # IGN IC50 pointwise
|
411 |
+
#now: 2023-01-14_17:39:58
|
412 |
+
#finetune_epoch_list: [21, 28,152] # IGN IC50 ASRP reg0
|
413 |
+
#now: 2023-01-15_22:26:14
|
414 |
+
#finetune_epoch_list: [133,74,95] # IGN IC50 ASRP reg0.01
|
415 |
+
#now: 2023-01-15_22:40:26
|
416 |
+
#finetune_epoch_list: [125,178,179] # IGN IC50 ASRP reg0.1
|
417 |
+
#now: 2023-01-14_18:26:02
|
418 |
+
#finetune_epoch_list: [103,162,76] # IGN IC50 ASRP reg0.3
|
419 |
+
#now: 2023-01-15_22:37:29
|
420 |
+
#finetune_epoch_list: [129, 89,278] # IGN IC50 ASRP reg1
|
421 |
+
#now: 2023-01-14_17:52:02
|
422 |
+
#finetune_epoch_list: [211,175,47] # IGN K ASRP reg0
|
423 |
+
#now: 2023-01-20_23:42:33
|
424 |
+
#finetune_epoch_list: [49,96,80] # IGN IC50Kikd pointwise
|
425 |
+
#now: 2023-01-21_13:57:28
|
426 |
+
#finetune_epoch_list: [63,44,138] # IGN baseline
|
427 |
+
#now: 2023-01-20_01:46:31
|
428 |
+
#finetune_epoch_list: [137,164,139] # IGN IC50KiKd ASRP
|
429 |
+
#now: 2023-01-29_13:14:16
|
430 |
+
#finetune_epoch_list: [169,93,179] # IGN IC50KiKd MTL
|
431 |
+
#now: 2023-01-27_18:32:50
|
432 |
+
epoch: best_valid_1
|
433 |
+
now: 2023-10-19_19:11:01
|
434 |
+
|
435 |
+
data:
|
436 |
+
dataset_name: chembl_in_pdbbind_smina # [chembl_in_pdbbind_smina, chembl], chembl_smina: poses are generated by smina, chembl: poses are generated by UltraDock
|
437 |
+
top_N: 1
|
438 |
+
docking_type: site_specific # [blind, site_specific, all]
|
439 |
+
poses_select_rules: mbp_error_min # [mbp_error_min, mbp_error_threshold, random, null]
|
440 |
+
confidence_threshold: 0.3
|
441 |
+
use_ic50: true
|
442 |
+
use_ki: true
|
443 |
+
use_kd: true
|
444 |
+
affinity_relation: '=' # [=, >, all], all: use > and =
|
445 |
+
assay_des_type: BioLinkBERT_large_first_last_avg # [cls, first_last_avg, BioLinkBERT_large_cls, BioLinkBERT_large_first_last_avg, BioLinkBERT_large_last2avg, BioLinkBERT_large_last_avg]
|
446 |
+
assay_des_dim: 1024
|
447 |
+
#finetune_dataset_name: pdbbind2016_finetune #pdbbind2020_no_add_h # pdbbind2016_finetune
|
448 |
+
finetune_dataset_name: pdbbind2020_no_add_h
|
449 |
+
generalize_dataset_name: csar_test
|
450 |
+
split_type: assay_specific # [vertical, horizontal, assay_specific]
|
451 |
+
drop_last: true
|
452 |
+
dataset_path: ./UltraFlow/data
|
453 |
+
#labels_path: ./UltraFlow/data/INDEX_general_PL_data.2016
|
454 |
+
labels_path: ./UltraFlow/data/INDEX_general_PL_data.2020
|
455 |
+
generalize_labels_path: ./UltraFlow/data/CSAR_NRC_HiQ_Set/SUMMARY_FILES/score_total.txt
|
456 |
+
generalize_csar_test: ./UltraFlow/data/csar_new_2016
|
457 |
+
vertical_train_names: ./UltraFlow/data/vertical_train_uniprots
|
458 |
+
vertical_val_names: ./UltraFlow/data/vertical_valid_uniprots
|
459 |
+
vertical_test_names: ./UltraFlow/data/vertical_test_uniprots
|
460 |
+
horizontal_train_names: ./UltraFlow/data/horizontal_train.pkl
|
461 |
+
horizontal_val_names: ./UltraFlow/data/horizontal_valid.pkl
|
462 |
+
horizontal_test_names: ./UltraFlow/data/horizontal_test.pkl
|
463 |
+
assay_specific_info: ./UltraFlow/data/vertical_total_smiles_and_uniprots
|
464 |
+
assay_specific_train: ./UltraFlow/data/assay_specific_rank_pretrain_train
|
465 |
+
assay_specific_valid: ./UltraFlow/data/assay_specific_rank_pretrain_valid
|
466 |
+
chemb_smina_asrp_train: ./UltraFlow/data/chembl_smina_asrp_train
|
467 |
+
chemb_smina_asrp_valid: ./UltraFlow/data/chembl_smina_asrp_valid
|
468 |
+
#finetune_train_names: ./UltraFlow/data/pdbbind2016_train_M
|
469 |
+
#finetune_train_names: ./UltraFlow/data/pdbbind_2020_casf_train
|
470 |
+
#finetune_train_names: ./UltraFlow/data/pdbbind2016_train
|
471 |
+
#finetune_train_names: ./UltraFlow/data/timesplit_no_lig_overlap_train
|
472 |
+
#finetune_train_names: ./UltraFlow/data/tankbind_vtrain
|
473 |
+
#finetune_train_names: ./UltraFlow/data/pdbbind2016_general_train
|
474 |
+
finetune_train_names: ./UltraFlow/data/pdbbind2016_general_gign_train
|
475 |
+
#finetune_valid_names: ./UltraFlow/data/pdbbind2016_valid_M
|
476 |
+
#finetune_valid_names: ./UltraFlow/data/pdbbind2016_valid
|
477 |
+
#finetune_valid_names: ./UltraFlow/data/pdbbind_2020_casf_valid
|
478 |
+
#finetune_valid_names: ./UltraFlow/data/timesplit_no_lig_overlap_val
|
479 |
+
#finetune_valid_names: ./UltraFlow/data/pdbbind2016_general_valid
|
480 |
+
finetune_valid_names: ./UltraFlow/data/pdbbind2016_general_gign_valid
|
481 |
+
#finetune_test_names: ./UltraFlow/data/pdbbind2016_test #290
|
482 |
+
#finetune_test_names: ./UltraFlow/data/core_set #285
|
483 |
+
#finetune_test_names: ./UltraFlow/data/timesplit_test
|
484 |
+
#finetune_test_names: ./UltraFlow/data/pdbbind_2020_casf_test
|
485 |
+
finetune_test_names: ./UltraFlow/data/pdb_after_2016
|
486 |
+
finetune_random_split: false
|
487 |
+
finetune_total_names: total # [refined, total]
|
488 |
+
finetune_refined_path: ./UltraFlow/data/pdbbind2016_refined
|
489 |
+
finetune_total_path: ./UltraFlow/data/pdbbind2016_total
|
490 |
+
ligcut: 5.0 # null # 5.0
|
491 |
+
add_chemical_bond_feats: true
|
492 |
+
use_mean_node_features: false
|
493 |
+
use_bond_d3_feature: false
|
494 |
+
protcut: 30.0 # null # 30.0
|
495 |
+
intercut: 12.0 # 8 # 12.0
|
496 |
+
chaincut: 10
|
497 |
+
prot_graph_type: residue_complete # atom_pocket # residue_complete
|
498 |
+
n_jobs: 8
|
499 |
+
lig_max_neighbors: null
|
500 |
+
prot_max_neighbors: 10
|
501 |
+
inter_min_neighbors: null
|
502 |
+
inter_max_neighbors: null
|
503 |
+
lig_type: openbabel
|
504 |
+
test_2: false # test for asrp pretraining
|
505 |
+
test_100: false # test for finetune
|
506 |
+
|
507 |
+
model:
|
508 |
+
model_type: Affinity_GNNs # [Affinity_GNNs, IGN, IGN_basic]
|
509 |
+
GNN_type: AttentiveFP # [GCN, GAT, GIN, EGNN, AttentiveFP]
|
510 |
+
out_dim: 1
|
511 |
+
aux_dim: 8
|
512 |
+
num_layers: 3
|
513 |
+
hidden_dim: 128 # 128 #256
|
514 |
+
inter_out_dim: 128 # 128 # 200
|
515 |
+
fc_hidden_dim: [128,128,128] # [128, 128, 128] # [200,200,200]
|
516 |
+
assay_des_fc_hidden_dim: [512] # [768, 512]
|
517 |
+
fintune_fc_hidden_dim: [128] # [128] # [200]
|
518 |
+
readout: w_sum # [w_sum, mean, max, sum, multi_head, w_sum_v2, multi_head_v2, w_sum_v3, multi_head_v3]
|
519 |
+
num_head: 4
|
520 |
+
attn_merge: concat # [concat, average]
|
521 |
+
dropout: 0.1
|
522 |
+
jk: sum
|
523 |
+
|