Training Configuration of pre-trained MPNN_CNN #122

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opened 2025-10-14 17:49:08 -06:00 by navan · 0 comments

navan commented

2025-10-14 17:49:08 -06:00

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Originally created by @pykao on 12/2/2020

Hi Kexin Huang,

I am using the provided pre-trained MPNN_CNN model. When I looked into its model configuration file, it looks wired to me.

{'input_dim_drug': 1024,
'input_dim_protein': 8420,
'hidden_dim_drug': 128,
'hidden_dim_protein': 256,
'cls_hidden_dims': [1024, 1024, 512],
'batch_size': 16,
'train_epoch': 1,
'LR': 0.001,
'drug_encoding': 'MPNN',
'target_encoding': 'CNN',
'result_folder': './result/',
'binary': False,
'mpnn_hidden_size': 128,
'mpnn_depth': 3,
'cnn_target_filters': [32, 64, 96],
'cnn_target_kernels': [4, 8, 12],
'num_workers': 0,
'decay': 0}

Did you only train this model for only 1 epoch with batch size 16?

Best regards,
Po-Yu Kao

*Originally created by @pykao on 12/2/2020* Hi Kexin Huang, I am using the provided pre-trained MPNN_CNN model. When I looked into its model configuration file, it looks wired to me. {'input_dim_drug': 1024, 'input_dim_protein': 8420, 'hidden_dim_drug': 128, 'hidden_dim_protein': 256, 'cls_hidden_dims': [1024, 1024, 512], 'batch_size': 16, 'train_epoch': 1, 'LR': 0.001, 'drug_encoding': 'MPNN', 'target_encoding': 'CNN', 'result_folder': './result/', 'binary': False, 'mpnn_hidden_size': 128, 'mpnn_depth': 3, 'cnn_target_filters': [32, 64, 96], 'cnn_target_kernels': [4, 8, 12], 'num_workers': 0, 'decay': 0} Did you only train this model for only 1 epoch with batch size 16? Best regards, Po-Yu Kao