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Table 5 Architectures, parameters, and hyperparameters explored for DNNs

From: Multi-channel PINN: investigating scalable and transferable neural networks for drug discovery

Base model

 

Value

Description

PINN

Separated layers

1, 2, 3, 4

The number of separated layers for PINN

Concatenated layers

1, 2

The number of concatenated layers for PINN

Number of nodes

256, 512, 1024, 2048

The number of nodes for layers

Dilated CNN

Filters

4, 8, 16, 32

The number of filters for Dilated CNN

Kernel size

6, 8, 12, 22

The length of the convolution window for Dilated CNN

Embedding

16, 32

Dimension of dense embedding for low level representations

LSTM, BLSTM

Units

128, 256

The units to represent hidden layers for RNN

DNN

Lr

0.0005

Initial learning rate

Initializer

\([ - \sqrt{ 3 / fan_{in}}, \sqrt{ 3 / fan_{in}}]\)

Initial weight value called Lecun uniform distribution

Optimizer

Adam

Optimizer for stochastic gradient descent

Weight decay

0.0, 0.00001

Learning rate decay over each update

Activation function

ReLU, ELU

Neuron activation function

Drop out

0.25, 0.5

The rate of drop out

Batch

1024

Batch size for training

Epochs_training

400

Training epochs on a training task

Epochs_finetune

200

Finetuning epochs for a pretrained model on a test task