Convolutional Variational Autoencoder - ApogeeCVAE


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class astroNN.models.apogee_models.ApogeeCVAE[source]

Class for Convolutional Autoencoder Neural Network for stellar spectra analysis


2017-Dec-21 - Written - Henry Leung (University of Toronto)

Inheritance diagram of astroNN.models.apogee_models.ApogeeCVAE

It is a 9 layered convolutional neural net (2 convolutional layers->2 dense layers->latent space->2 dense layers->2 convolutional layers)

You can create ApogeeVAE via

from astroNN.models import ApogeeCVAE

# And then create an object of ApogeeCVAE classs
cvae_net = ApogeeCVAE()

APOGEE Spectra Analysis

Although in theory you can feed any 1D data to astroNN neural networks. This tutorial will only focus on spectra analysis.

from astroNN.models import ApogeeCVAE
from astroNN.datasets import H5Loader

# Load the train data from dataset first, x_train is spectra and y_train will be ASPCAP labels
loader = H5Loader('datasets.h5')
x_train, y_train = loader.load()

# And then create an object of Bayesian Convolutional Neural Network classs
cvae_net = ApogeeCVAE()

# Set max_epochs to 10 for a quick result. You should train more epochs normally, especially with dropout
cvae_net.max_epochs = 10

After the training, you can use ‘vae_net’ in this case and call test method to test the neural network on test data. Or you can load the folder by

from astroNN.models import load_folder
cvae_net = load_folder('astroNN_0101_run001')

# Load the test data from dataset, x_test is spectra and y_test will be ASPCAP labels
loader2 = H5Loader('datasets.h5')
loader2.load_combined = False
x_test, y_test = loader2.load()

VAE is a special case. You can either use test_encoder(x_test) to get the value in latent space or use test(x_test) to get spectra reconstruction

# Get latent space representation
latent_space_value = cvae_net.test_encoder(x_test)

# Get spectra reconstruction
spectra_recon = cvae_net.test(x_test)


You can access to Keras model method like model.predict via (in the above tutorial) vae_net.keras_model (Example: vae_net.keras_model.predict())

Example Plots on latent space using VAE.plot_latent()

../_images/C.jpg ../_images/logg.jpg

Example Plots on spectra reconstruction

x_re = cvae_net.test(x_test)

import pylab as plt

fig = plt.figure(figsize=(20, 15), dpi=150)
plt.plot(x[0], linewidth=0.9, label='APOGEE spectra')
plt.plot(x_re[0], linewidth=0.9, label='Reconstructed spectra by VAE')
plt.xlabel('Pixel', fontsize=25)
plt.ylabel('Normalized flux', fontsize=25)
plt.legend(loc='best', fontsize=25)
plt.tick_params(labelsize=20, width=1, length=10)