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Table 2 Hyper-parameters values explored for Bernoulli Naïve Bayes, k-nearest neighbor, random forest, support vector machines and deep neural networks

From: Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data

Hyper-parameters

Values explored

Parameter

Bernoulli Naïve Bayes

 Alpha

1, 0.5, 0.1

Laplace/Lidstone smoothing parameter

 Fit_prior

True, false

Class prior probabilities. In case of false, a uniform prior was used

k-Nearest neighbor

 Nn

1, 3, 5, 7, 9, 11

Number of nearest neighbors

Random forest

 Ntrees

10, 50, 100, 300, 700, 1000

Number of trees

 Criterion

Gini, entropy

Functions used to measure the quality of each split

 Max_features

Sqrt(n_features), log2(n_features)

Number of features considered for each split

Support vector machines

 Kernel

rbf

Radial basis function

 C

103, 102, 10, 1

Cost

 γ

10−5, 10−4, 10−3, 10−2, 10−1

Gamma

 Kernel

Linear

Linear kernel

 C

103, 102, 10, 1, 10−1, 10−2, 10−3, 10−4

Cost

Deep neural networks

 η

1, 10−1, 10−2, 10−3, 10−4

Learning rate for the stochastic gradient descent (“SGD”)

 Momentum (μ)

0.9

Weight of the previous update

 Weight decay

0.0005

 

 Epochs

300

Number of training epochs

 Batch size

256

mini-batch training size

 Hidden layers

1, 2, 3, 4

Number of hidden layers

 Number neurons

5, 10, 50, 100, 200, 500, 700, 1000, 1500, 2000, 2500, 3000, 3500

Number of neurons per hidden layer

 Activation function

ReLU, Sigmoid, Tanh

Neuron activation functions

 Regularization

No, Dropout

Regularization techniques

 Dropout

(0%, 20%, 50%) input layer, 50% hidden layers

% of neurons “dropped” using the Drop-out technique

 Weight and bias initiation

Gaussian {SD: 0.01}

Function used to initiate weights and biases.

 Loss function

SoftmaxWithLoss

Function used to minimize loss

 Output function

Softmax

Function used to calculate probability for predictions

 Number of classes

2

Binary classification