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model/high_energy/checkpoints/config.yaml

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+batch_size: 1000
+epochs: 3500
+eval_every_n_epochs: 5
+smilesmodel_finetune: False
+smilesmodel_finetune_path: "/public/home/hpc212307003/molclr_cnn/nist_w2v/pretrained_gin/checkpoints/model.pth"
+fine_tune_from: "/home/xieting/graph_transformer_esa/runs/dem4_esa_casmi22_40/"
+log_every_n_steps: 2
+learning_rate: 1e-05
+weight_decay: 0.0001
+fp16_precision: True
+truncation: True
+
+model_config:
+  num_layer: 5
+  emb_dim: 300
+  feat_dim: 512
+  drop_ratio: 0.3
+  pool : mean
+  spec_embed_dim: 256
+  dropout: 0.1
+  layers: 3
+  embed_dim: 256
+  
+dataset:
+  s: 1
+  num_workers: 0
+  valid_size: 0.1
+  ms2_file: "/home/xieting/cl_data/hcd3_0.01test/train_hcd_posh_40.mgf"
+  smi_file: "/home/xieting/cl_data/hcd3_0.01test/train_hcd_posh_40_smi.npy"
+
+loss:
+  temperature: 0.1
+  use_cosine_similarity: True
+  alpha_weight: 0.75

model/low_energy/checkpoints/config.yaml

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+batch_size: 1000
+epochs: 3500
+eval_every_n_epochs: 5
+smilesmodel_finetune: False
+smilesmodel_finetune_path: "/public/home/hpc212307003/molclr_cnn/nist_w2v/pretrained_gin/checkpoints/model.pth"
+fine_tune_from: "/home/xieting/graph_transformer_esa/runs/dem4_esa_4.5_10/"
+log_every_n_steps: 2
+learning_rate: 1e-05
+weight_decay: 0.0001
+fp16_precision: True
+truncation: True
+
+model_config:
+  num_layer: 5
+  emb_dim: 300
+  feat_dim: 512
+  drop_ratio: 0.3
+  pool : mean
+  spec_embed_dim: 256
+  dropout: 0.1
+  layers: 3
+  embed_dim: 256
+  
+dataset:
+  s: 1
+  num_workers: 0
+  valid_size: 0.1
+  ms2_file: "/home/xieting/cl_data/hcd3_0.01test/train_hcd_posh_10.mgf"
+  smi_file: "/home/xieting/cl_data/hcd3_0.01test/train_hcd_posh_10_smi.npy"
+
+loss:
+  temperature: 0.1
+  use_cosine_similarity: True
+  alpha_weight: 0.75

model/median_energy/checkpoints/config.yaml

@@ -0,0 +1,34 @@
+batch_size: 1000
+epochs: 3500
+eval_every_n_epochs: 5
+smilesmodel_finetune: False
+smilesmodel_finetune_path: "/public/home/hpc212307003/molclr_cnn/nist_w2v/pretrained_gin/checkpoints/model.pth"
+fine_tune_from: "/home/xieting/graph_transformer_esa/runs/dem4_esa_4.5_20/"
+log_every_n_steps: 2
+learning_rate: 1e-05
+weight_decay: 0.0001
+fp16_precision: True
+truncation: True
+
+model_config:
+  num_layer: 5
+  emb_dim: 300
+  feat_dim: 512
+  drop_ratio: 0.3
+  pool : mean
+  spec_embed_dim: 256
+  dropout: 0.1
+  layers: 3
+  embed_dim: 256
+  
+dataset:
+  s: 1
+  num_workers: 0
+  valid_size: 0.1
+  ms2_file: "/home/xieting/cl_data/hcd3_0.01test/train_hcd_posh_20.mgf"
+  smi_file: "/home/xieting/cl_data/hcd3_0.01test/train_hcd_posh_20_smi.npy"
+
+loss:
+  temperature: 0.1
+  use_cosine_similarity: True
+  alpha_weight: 0.75