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  1. workdir/gradio/affinity_default.yaml +523 -0
workdir/gradio/affinity_default.yaml ADDED
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+ 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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+
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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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+ 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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+ pretrain_mtl_IC50_lambda: 1.0 # 0.2404, 0.3819
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+ 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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+ multi_task: IC50K # [IC50KdKi, IC50K, false]
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+ finetune_times: 5
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+ finetune_new_affinity_head: false
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+ use_FLAG: false
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+ FLAG_step_size: 0.01
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+ FLAG_m: 4
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+ FLAG_v: v_inter
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+ encoder_ablation: null # [ligand, protein, interact, null]
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+ interact_ablate_op: min # [max, sum, mean, min]
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+
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+ test:
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+ #now: 2023-01-05_20:57:03
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+ #epoch: 66
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+ #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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+ #now: 2023-01-07_22:14:28
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+ #epoch: 107 # pointwise_pretrain
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+ #now: 2023-01-09_23:17:57
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+ #epoch: 63 # pairwise_smaplev1_loss_v1_regression
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+ #now: 2023-01-10_11:20:07
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+ #epoch: 20 # pointwise_chembl_smina
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+ #now: 2023-01-11_18:49:32
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+ #epoch: 39 # pw_lsv1_sampv1
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+ #now: 2023-01-12_02:05:49
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+ #epoch: 29 # pw_lsv1_sampv1_reg
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+ #now: 2023-01-12_01:41:19
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+ #epoch: 41 # pw_lsv2_sampv1
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+ #now: 2023-01-12_02:11:13
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+ #epoch: best_loss # pw_lsv2_sampv1_reg
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+ #now: 2023-01-12_02:14:41
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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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+ #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
167
+ #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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+ #now: 2023-01-20_15:58:41
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+ #epoch: latest # IGN_ASRP_reg01_MTL
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+ #now:
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+ #epoch: latest # IGN_ASRP_reg1_decay098
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+ #now: 2023-01-20_17:25:17
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+ #epoch: latest # IGN_ASRP_reg0
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+ #now: 2023-01-20_17:04:29
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+ #epoch: latest # IGN_ASRP_reg1_decay097
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+ #now: 2023-01-20_17:22:09
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+ #epoch: latest # GIN_ASRP_reg03_MTL_bio_cls
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+ #now: 2023-01-21_02:54:26
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+ #epoch: latest # GIN_pointwise_baseline
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+ #now: 2023-01-21_02:57:48
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+ #epoch: latest # IGN_ASRP_MTL_new_bio_cls_reg03
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+ #now: 2023-01-21_02:40:35
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+ #epoch: latest # IGN_ASRP_MTL_new_bio_cls_reg_deg098
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+ #now: 2023-01-21_02:37:49
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+ #epoch: latest # IGN_ASRP_MTL_new_bio_cls_reg_deg097
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+ #now: 2023-01-21_02:30:27
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+ #epoch: latest # GCN_ASRP_MTL_new_bio_cls_reg_deg03
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+ #now: 2023-01-21_02:51:12
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+ #2023-01-20_14:31:13epoch: latest # GCN_pointwise_baseline
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+ #now: 2023-01-21_03:00:26
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+ #epoch: latest # IGN_IC50KdKi_pointwise_baseline
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+ #now: 2023-01-20_14:31:13
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+ #epoch: latest # IGN_IC50KdKi_pointwise_MTL_baseline
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+ #now: 2023-01-20_15:04:28
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+ #epoch: latest # IGN_KdKi_MTL_new_ASRP_reg_deg097
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+ #now: 2023-01-21_12:56:41
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+ #epoch: latest # IGN_IC50K_MTL
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+ #now: 2023-01-21_16:32:41
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+ #epoch: latest # IGN_IC50K_MTL_new_lambda
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+ #now: 2023-01-21_16:47:33
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+ #epoch: latest # IGN_IC50KiKd_ASRP_reg_deg097
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+ #now: 2023-01-21_12:31:31
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+ #epoch: latest # IGN_IC50K_Pointwise_IC5001_MTL
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+ #now: 2023-01-22_20:09:05
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+ #epoch: latest # IGN_IC50K_ASRP_reg_deg097_MTL_new_lambda
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+ #now: 2023-01-22_00:22:25
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+ #epoch: latest # IGN_IC50K_ASRP_reg_deg097_MTL
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+ #now: 2023-01-22_00:32:35
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+ #epoch: latest # IGN_IC50K_ASRP_reg_deg098_MTL
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+ #now: 2023-01-22_14:12:10
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+ #epoch: latest # IGN_IC50K_ASRP_reg03_MTL
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+ #now: 2023-01-22_14:22:52
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+ #finetune_epoch_list: [103, 162, 76] # ASRP_IC50
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+ #now: 2023-01-15_22:37:29
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+ #finetune_epoch_list: [182, 96, 149] # pointwise_IC50
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+ #now: 2023-01-14_17:39:58
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+ #finetune_epoch_list: [125, 211] # ASRP_reg03_IC50K_MTL
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+ #now: 2023-01-23_19:34:56
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+ #finetune_epoch_list: [100_bs_128_lr_0.001] # ASRP_reg03_IC50K_MTL
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+ #now: 2023-01-23_19:55:02
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+ #epoch: latest # resume training GIN
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+ #now: 2023-01-23_23:27:05
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+ #epoch: latest # resume training EGNN
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+ #now: 2023-01-23_23:31:09
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+ #epoch: latest # resume training GCN
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+ #now: 2023-01-23_23:33:01
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+ #epoch: latest # resume training GAT
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+ #now: 2023-01-23_23:35:01
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+ #epoch: latest # resume training AttentiveFP ASRP reg 1 MTL
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+ #now: 2023-01-24_00:04:18
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+ #epoch: latest # IC50K ASRP reg03 MTL GIN
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+ #now: 2023-01-24_13:11:09
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+ #epoch: latest # IC50K ASRP reg03 MTL GCN
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+ #now: 2023-01-24_13:29:10
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+ #epoch: latest # IC50K ASRP reg03 MTL GAT
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+ #now: 2023-01-24_13:35:25
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+ #epoch: latest # IC50K ASRP reg03 MTL EGNN
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+ #now: 2023-01-24_13:32:19
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+ #epoch: latest # IC50K ASRP reg1 MTL AttentiveFP
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+ #now: 2023-01-24_13:40:54
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+ #epoch: latest # IC50K ASRP reg0 MTL AttentiveFP
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+ #now: 2023-01-24_21:47:05
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+ #epoch: latest # IC50K ARRP K reg001 AttentiveFP
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+ #now: 2023-01-26_01:06:33
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+ #epoch: latest # IC50K ASRP reg deg096 MTL AttentiveFP
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+ #now: 2023-01-25_17:19:26
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+ #epoch: latest # IC50K ASRP reg deg099 MTL AttentiveFP
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+ #now: 2023-01-25_17:00:41
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+ #epoch: latest # IC50K ASRP reg01 MTL AttentiveFP
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+ #now: 2023-01-25_17:27:33
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+ #epoch: latest # IC50K ASRP reg001 MTL AttentiveFP
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+ #now: 2023-01-25_17:34:35
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+ #epoch: latest # IC50K ASRP K reg deg099 AttentiveFP
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+ #now: 2023-01-25_20:11:34
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+ #epoch: latest # IC50K ASRP K reg deg096 AttentiveFP
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+ #now: 2023-01-25_20:44:22
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+ #epoch: latest # IC50K ASRP Pointwise EGNN
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+ #now: 2023-01-27_01:48:42
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+ #epoch: latest # IC50K ASRP Pointwise GAT
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+ #now: 2023-01-27_01:43:00
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+ #epoch: latest # IC50K ASRP Pointwise GIN
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+ #now: 2023-01-27_01:40:44
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+ #epoch: latest # IC50K ASRP Pointwise GCN
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+ #now: 2023-01-27_01:29:01
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+ #epoch: latest # IC50K ASRP reg deg095 AttentiveFP
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+ #now: 2023-01-27_11:48:44
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+ #epoch: latest # IC50K ASRP K reg deg095 AttentiveFP
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+ #now: 2023-01-27_12:04:37
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+ #epoch: latest # IC50K ASRP reg deg098 MTL GCN
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+ #now: 2023-01-27_17:46:03
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+ #epoch: latest # IC50K ASRP reg deg097 MTL GCN
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+ #now: 2023-01-27_17:56:52
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+ #epoch: latest # IC50K ASRP reg deg096 MTL GCN
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+ #now: 2023-01-27_18:14:49
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+ #epoch: latest # IC50K ASRP reg deg096 MTL GIN
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+ #now: 2023-01-27_19:42:01
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+ #epoch: latest # IC50K ASRP reg deg097 MTL GIN
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+ #now: 2023-01-27_21:08:11
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+ #epoch: latest # IC50K ASRP reg deg096 MTL AttentiveFP Flag correct batch 512 seed 43
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+ #now: 2023-03-28_23:20:01
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+ #epoch: latest # IC50K ASRP reg deg097 MTL AttentiveFP Flag correct batch 512 seed 43
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+ #now: 2023-03-30_21:39:55
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+ #epoch: latest # IC50K ASRP reg deg098 MTL AttentiveFP Flag correct batch 512 seed 43
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+ #now: 2023-03-30_21:46:44
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+ #epoch: latest # IC50K ASRP reg deg099 MTL AttentiveFP Flag correct batch 512 seed 43
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+ #now: 2023-03-30_21:54:54
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+ #epoch: latest # IC50K ASRP reg 03 MTL AttentiveFP Flag correct batch 512 seed 43
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+ #now: 2023-03-31_03:57:32
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+ #epoch: latest # IC50K ASRP reg deg096 MTL AttentiveFP Flag correct batch 256 seed 2022
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+ #now: 2023-04-04_16:31:48
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+ #epoch: latest # IC50K ASRP reg deg097 MTL AttentiveFP Flag correct batch 256 seed 2022
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+ #now: 2023-04-02_18:52:38
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+ #epoch: latest # IC50K ASRP reg deg098 MTL AttentiveFP Flag correct batch 256 seed 2022
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+ #now: 2023-04-03_21:29:07
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+ #epoch: latest # IC50K ASRP reg deg099 MTL AttentiveFP Flag correct batch 256 seed 2022
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+ #now: 2023-04-02_20:44:06
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+ #epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022
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+ #now: 2023-04-03_21:24:55
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+ #epoch: latest_300 # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 batch256 resume
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+ #now: 2023-04-10_00:08:29
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+ #epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 batch512 resume
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+ #now: 2023-04-10_00:38:19
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+ #epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 top_2
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+ #now: 2023-04-09_11:11:49
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+ #epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 top_3
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+ #now: 2023-04-09_11:01:41
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+ #epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 43 top_3
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+ #now: 2023-04-11_00:45:49
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+ #epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 top_5
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+ #now: 2023-04-09_13:40:20
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+ #epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 4M
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+ #now: 2023-04-09_00:38:24
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+ epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 adbf
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+ now: 2023-04-12_01:18:25
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+ #epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 adbf w_sum_v2
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+ #now: 2023-05-17_22:38:25
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+ #epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2022 blind
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+ #now: 2023-04-13_00:23:30
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+ #epoch: latest # IC50K ASRP reg reg 03 MTL AttentiveFP Flag correct batch 256 seed 2023 blind
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+ #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
+