DGP/ssl_vae.py

###
'''
Similar to M1 from https://github.com/dpkingma/nips14-ssl
Original Author: S. Saemundsson
Edited by: Z. Rahaie
'''
###
from vae import VariationalAutoencoder
import numpy as np
import data.asd as asd

if __name__ == '__main__':

    num_batches = 0      
    dim_z = 0             
    epochs = 0           
    learning_rate = 1e-4    
    l2_loss = 1e-5          
    seed = 12345            

    hidden_layers_px = [ sqrt(input_size), sqrt(hidden_layers_px[0]),  sqrt(hidden_layers_px[1])]  
    hidden_layers_qz = [ sqrt(input_size), sqrt(hidden_layers_px[0]), sqrt(hidden_layers_px[2]) ]  

    
    asd_path = ['nds/AutDB_ASD_cnv_dataset.txt']
    #Uses anglpy module exists kingma github (linked before) to divide the dataset
    train_x, train_y, valid_x, valid_y, test_x, test_y = asd.load_numpy(asd_path, binarize_y=True)

    x_train, y_train = train_x.T, train_y.T
    x_valid, y_valid = valid_x.T, valid_y.T
    x_test, y_test = test_x.T, test_y.T

    dim_x = x_train.shape[1]
    dim_y = y_train.shape[1]


    VAE = VariationalAutoencoder(   dim_x = dim_x, 
                                    dim_z = dim_z,
                                    hidden_layers_px = hidden_layers_px,
                                    hidden_layers_qz = hidden_layers_qz,
                                    l2_loss = l2_loss )

    #every n iterations (set to 0 to disable)

    VAE.train(  x = x_train, x_valid = x_valid, epochs = epochs, num_batches = num_batches,
                learning_rate = learning_rate, seed = seed, stop_iter = 30, print_every = 10, draw_img = 0 )
    
    weights_as_numpy = VAE.get_weights()
    
    output_weights_to_label = weights_as_numpy[6]
    
    scores = weights_as_numpy[0] * weights_as_numpy[1] * weights_as_numpy [2] * output_weights_to_label
    
    genes_index = [i for i,v in enumerate(scores) if v > 0]
    
    print(genes_index)