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Akrem Sellami
Mapping individual differences using multi-view representation learning
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6aed35a0
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6aed35a0
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5 years ago
by
Akrem Sellami
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multi_view_representation_learning/mdae_concat_three_layers.py
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6aed35a0
"""""""""""""""
Monomodal Autoenconder code
"""""""""""""""
import
keras
from
keras.layers
import
Input
,
Dense
,
concatenate
from
keras.models
import
Model
from
keras.layers
import
Dropout
from
keras.callbacks
import
EarlyStopping
import
matplotlib.pyplot
as
plt
plt
.
switch_backend
(
'
agg
'
)
import
sys
as
os
import
os
from
sklearn.preprocessing
import
StandardScaler
,
MinMaxScaler
from
sklearn.decomposition
import
PCA
from
sklearn.metrics
import
mean_squared_error
from
math
import
sqrt
from
keras.optimizers
import
SGD
,
Adadelta
,
Adam
import
numpy
as
np
from
sklearn.model_selection
import
KFold
from
keras.callbacks
import
ModelCheckpoint
from
keras.models
import
load_model
# loading multimodal fMRI data
def
load_data
(
sub
,
view
):
# Import Task fMRI data
if
view
==
1
:
view_tfmri
=
np
.
load
(
os
.
path
.
join
(
path
,
"
tfmri/{}/gii_matrix_fsaverage5.npy
"
.
format
(
sub
)))
return
view_tfmri
# Import Resting-State fMRI data
if
view
==
2
:
view_rsfmri
=
np
.
load
(
os
.
path
.
join
(
path
,
"
rsfmri/{}/correlation_matrix_fsaverage5.npy
"
.
format
(
sub
)))
return
view_rsfmri
# Import concatenated fMRI data
if
view
==
3
:
view_rsfmri
=
np
.
load
(
os
.
path
.
join
(
path
,
"
rsfmri/{}/correlation_matrix_fsaverage5.npy
"
.
format
(
sub
)))
view_tfmri
=
np
.
load
(
os
.
path
.
join
(
path
,
"
tfmri/{}/gii_matrix_fsaverage5.npy
"
.
format
(
sub
)))
fmri_data
=
np
.
concatenate
([
view_tfmri
,
view_rsfmri
],
axis
=
1
)
return
fmri_data
# Path
path
=
"
/home/asellami/data_fsaverage5
"
print
(
'
View 1: task-fMRI
'
)
print
(
'
View 2: resting-state fMRI
'
)
print
(
'
View=3: concatenated views (task-fMRI + rest-fMRI)
'
)
# activation functions
hidden_layer
=
'
linear
'
output_layer
=
'
linear
'
# MSE (tfmri+ rsfmri)
mse_train
=
[]
mse_test
=
[]
# RMSE (tfmri+ rsfmri)
rmse_train
=
[]
rmse_test
=
[]
#
# Standard deviation MSE (tfmri+ rsfmri)
std_mse_train
=
[]
std_mse_test
=
[]
# Standard deviation RMSE (tfmri+ rsfmri)
std_rmse_train
=
[]
std_rmse_test
=
[]
# MSE (tfmri)
mse_tfmri_train
=
[]
mse_tfmri_test
=
[]
# RMSE (tfmri)
rmse_tfmri_train
=
[]
rmse_tfmri_test
=
[]
# std mse (tfmri)
std_mse_tfmri_train
=
[]
std_mse_tfmri_test
=
[]
# std rmse (tfmri)
std_rmse_tfmri_train
=
[]
std_rmse_tfmri_test
=
[]
# MSE (rsfmri)
mse_rsfmri_train
=
[]
mse_rsfmri_test
=
[]
# RMSE (rsfmri)
rmse_rsfmri_train
=
[]
rmse_rsfmri_test
=
[]
# std mse (rsfmri)
std_mse_rsfmri_train
=
[]
std_mse_rsfmri_test
=
[]
# std rmse (rsfmri)
std_rmse_rsfmri_train
=
[]
std_rmse_rsfmri_test
=
[]
# missing data
missing_data
=
[
36
]
index_subjects
=
np
.
arange
(
3
,
43
)
index_subjects
=
np
.
delete
(
index_subjects
,
np
.
argwhere
(
index_subjects
==
missing_data
))
#ar = np.arange(75,101)
#dimensions = ar[ar%2==0]
dimensions
=
[
1
,
3
,
5
,
8
,
10
,
13
,
15
,
18
,
20
,
23
,
25
,
28
,
30
,
33
,
35
,
38
,
40
,
42
,
45
,
48
,
50
]
batch_1
=
dimensions
[
0
:
6
]
batch_2
=
dimensions
[
6
:
12
]
batch_3
=
dimensions
[
12
:
17
]
batch_4
=
dimensions
[
17
:
21
]
for
dim
in
batch_1
:
# create directory
directory
=
'
{}
'
.
format
(
dim
)
if
not
os
.
path
.
exists
(
directory
):
os
.
makedirs
(
directory
)
# Cross Validation
kf
=
KFold
(
n_splits
=
10
)
print
(
kf
.
get_n_splits
(
index_subjects
))
print
(
"
number of splits:
"
,
kf
)
print
(
"
number of features:
"
,
dimensions
)
cvscores_mse_test
=
[]
cvscores_rmse_test
=
[]
cvscores_mse_train
=
[]
cvscores_rmse_train
=
[]
cvscores_mse_tfmri_train
=
[]
cvscores_mse_tfmri_test
=
[]
cvscores_rmse_tfmri_train
=
[]
cvscores_rmse_tfmri_test
=
[]
cvscores_mse_rsfmri_train
=
[]
cvscores_mse_rsfmri_test
=
[]
cvscores_rmse_rsfmri_train
=
[]
cvscores_rmse_rsfmri_test
=
[]
fold
=
0
for
train_index
,
test_index
in
kf
.
split
(
index_subjects
):
fold
+=
1
# create directory
directory
=
'
{}/fold_{}
'
.
format
(
dim
,
fold
)
if
not
os
.
path
.
exists
(
directory
):
os
.
makedirs
(
directory
)
print
(
f
"
Fold #
{
fold
}
"
)
print
(
"
TRAIN:
"
,
index_subjects
[
train_index
],
"
TEST:
"
,
index_subjects
[
test_index
])
# load training and testing data
print
(
'
Load training data...
'
)
train_tfmri_data
=
np
.
concatenate
([
load_data
(
sub
,
1
)
for
sub
in
index_subjects
[
train_index
]])
train_rsfmri_data
=
np
.
concatenate
([
load_data
(
sub
,
2
)
for
sub
in
index_subjects
[
train_index
]])
print
(
"
Shape of the training data:
"
,
train_tfmri_data
.
shape
)
print
(
'
Load testdata...
'
)
test_tfmri_data
=
np
.
concatenate
([
load_data
(
sub
,
1
)
for
sub
in
index_subjects
[
test_index
]])
test_rsfmri_data
=
np
.
concatenate
([
load_data
(
sub
,
2
)
for
sub
in
index_subjects
[
test_index
]])
print
(
"
Shape of the test data:
"
,
test_tfmri_data
.
shape
)
# Data normalization to range [-1, 1]
print
(
"
Data normalization to range [0, 1]
"
)
scaler
=
MinMaxScaler
()
normalized_train_tfmri_data
=
scaler
.
fit_transform
(
train_tfmri_data
)
normalized_test_tfmri_data
=
scaler
.
fit_transform
(
test_tfmri_data
)
normalized_train_rsfmri_data
=
scaler
.
fit_transform
(
train_rsfmri_data
)
normalized_test_rsfmri_data
=
scaler
.
fit_transform
(
test_rsfmri_data
)
# Apply linear autoencoder
# Inputs Shape
input_view_tfmri
=
Input
(
shape
=
(
normalized_train_tfmri_data
[
0
].
shape
))
input_view_rsfmri
=
Input
(
shape
=
(
normalized_train_rsfmri_data
[
0
].
shape
))
#input_train_data = Input(shape=(normalized_train_data[0].shape))
# Encoder Model
# First view
encoded_tfmri
=
Dense
(
100
,
activation
=
hidden_layer
)(
input_view_tfmri
)
# Layer 1, View 1
encoded_tfmri
=
Dense
(
dim
,
activation
=
hidden_layer
)(
encoded_tfmri
)
print
(
"
encoded tfmri shape
"
,
encoded_tfmri
.
shape
)
# Second view
encoded_rsfmri
=
Dense
(
100
,
activation
=
hidden_layer
)(
input_view_rsfmri
)
# Layer 1, View 2
encoded_rsfmri
=
Dense
(
dim
,
activation
=
hidden_layer
)(
encoded_rsfmri
)
print
(
"
encoded rsfmri shape
"
,
encoded_rsfmri
.
shape
)
# Shared representation with concatenation
shared_layer
=
concatenate
([
encoded_tfmri
,
encoded_rsfmri
])
# Layer 3: Bottelneck layer
print
(
"
Shared Layer
"
,
shared_layer
.
shape
)
#output_shared_layer=Dense(dim, activation=hidden_layer)(shared_layer)
#print("Output Shared Layer", output_shared_layer.shape)
# Decoder Model
decoded_tfmri
=
Dense
(
dim
,
activation
=
hidden_layer
)(
shared_layer
)
decoded_tfmri
=
Dense
(
100
,
activation
=
hidden_layer
)(
decoded_tfmri
)
decoded_tfmri
=
Dense
(
normalized_train_tfmri_data
[
0
].
shape
[
0
],
activation
=
output_layer
,
name
=
"
dec_tfmri
"
)(
decoded_tfmri
)
print
(
"
decoded_tfmri
"
,
decoded_tfmri
.
shape
)
# Second view
decoded_rsfmri
=
Dense
(
dim
,
activation
=
hidden_layer
)(
shared_layer
)
decoded_rsfmri
=
Dense
(
100
,
activation
=
hidden_layer
)(
decoded_rsfmri
)
decoded_rsfmri
=
Dense
(
normalized_train_rsfmri_data
[
0
].
shape
[
0
],
activation
=
output_layer
,
name
=
"
dec_rsfmri
"
)(
decoded_rsfmri
)
print
(
"
decoded_rsfmri
"
,
decoded_rsfmri
.
shape
)
# This model maps an input to its reconstruction
multimodal_autoencoder
=
Model
(
inputs
=
[
input_view_tfmri
,
input_view_rsfmri
],
outputs
=
[
decoded_tfmri
,
decoded_rsfmri
])
adam
=
Adam
(
lr
=
0.001
,
beta_1
=
0.9
,
beta_2
=
0.999
,
amsgrad
=
False
)
multimodal_autoencoder
.
compile
(
optimizer
=
adam
,
loss
=
'
mse
'
)
print
(
multimodal_autoencoder
.
summary
())
# fit Autoencoder on training set
history
=
multimodal_autoencoder
.
fit
([
normalized_train_tfmri_data
,
normalized_train_rsfmri_data
],
[
normalized_train_tfmri_data
,
normalized_train_rsfmri_data
],
epochs
=
70
,
batch_size
=
1000
,
shuffle
=
True
,
validation_data
=
([
normalized_test_tfmri_data
,
normalized_test_rsfmri_data
],
[
normalized_test_tfmri_data
,
normalized_test_rsfmri_data
]))
# list all data in history
print
(
history
.
history
.
keys
())
# save models
# Save the results weights
# This model maps an inputs to its encoded representation
# First view
encoder_tfmri
=
Model
(
input_view_tfmri
,
encoded_tfmri
)
encoder_tfmri
.
summary
()
# Second view
encoder_rsfmri
=
Model
(
input_view_rsfmri
,
encoded_rsfmri
)
encoder_rsfmri
.
summary
()
# This model maps a two inputs to its bottelneck layer (shared layer)
encoder_shared_layer
=
Model
(
inputs
=
[
input_view_tfmri
,
input_view_rsfmri
],
outputs
=
shared_layer
)
encoder_shared_layer
.
summary
()
# Separate Decoder model
# create a placeholder for an encoded (32-dimensional) input
encoded_input
=
Input
(
shape
=
(
dim
,))
# retrieve the layers of the autoencoder model
# First view
# decoder_tfmri_layer1 = multimodal_autoencoder.layers[-6] # Index of the first layer (after bottelneck layer)
# decoder_tfmri_layer2 = multimodal_autoencoder.layers[-4]
# decoder_tfmri_layer3 = multimodal_autoencoder.layers[-2]
# # create the decoder model
# decoder_tfmri = Model(encoded_input, decoder_tfmri_layer3(decoder_tfmri_layer2(decoder_tfmri_layer1(encoded_input))))
# decoder_tfmri.summary()
# # Second view
# decoder_rsfmri_layer1 = multimodal_autoencoder.layers[-5]
# decoder_rsfmri_layer2 = multimodal_autoencoder.layers[-3]
#decoder_rsfmri_layer3 = multimodal_autoencoder.layers[-1]
# create the decoder model
# decoder_rsfmri = Model(encoded_input, decoder_rsfmri_layer3(decoder_rsfmri_layer2(decoder_rsfmri_layer1(encoded_input))))
# decoder_rsfmri.summary()
multimodal_autoencoder
.
save
(
'
{}/fold_{}/multimodal_autoencoder.h5
'
.
format
(
dim
,
fold
))
encoder_shared_layer
.
save
(
'
{}/fold_{}/encoder_shared_layer.h5
'
.
format
(
dim
,
fold
))
encoder_tfmri
.
save
(
'
{}/fold_{}/encoder_tfmri.h5
'
.
format
(
dim
,
fold
))
encoder_rsfmri
.
save
(
'
{}/fold_{}/encoder_rsfmri.h5
'
.
format
(
dim
,
fold
))
# decoder_tfmri.save('{}/fold_{}/decoder_tfmri.h5'.format(dim, fold))
# decoder_rsfmri.save('{}/fold_{}/decoder_rsfmri.h5'.format(dim, fold))
# plot our loss
plt
.
plot
(
history
.
history
[
'
loss
'
],
label
=
'
loss_fold_{}
'
.
format
(
fold
))
plt
.
plot
(
history
.
history
[
'
val_loss
'
],
label
=
'
val_loss_fold_{}
'
.
format
(
fold
))
print
(
"
vector of val_loss
"
,
history
.
history
[
'
val_loss
'
])
plt
.
title
(
'
model train vs validation loss
'
)
plt
.
ylabel
(
'
loss
'
)
plt
.
xlabel
(
'
epoch
'
)
plt
.
legend
()
plt
.
savefig
(
'
{}/fold_{}/loss.png
'
.
format
(
dim
,
fold
))
plt
.
savefig
(
'
{}/fold_{}/loss.pdf
'
.
format
(
dim
,
fold
))
plt
.
close
()
# Reconstruction of training data
print
(
"
Reconstruction of training data...
"
)
[
X_train_new_tfmri
,
X_train_new_rsfmri
]
=
multimodal_autoencoder
.
predict
([
normalized_train_tfmri_data
,
normalized_train_rsfmri_data
])
# Training
# tfmri
print
(
"
Max value of predicted training tfmri data
"
,
np
.
max
(
X_train_new_tfmri
))
print
(
"
Min value of predicted training tfmri data
"
,
np
.
min
(
X_train_new_tfmri
))
print
(
"
Reconstructed tfmri matrix shape:
"
,
X_train_new_tfmri
.
shape
)
val_mse_train_tfmri
=
mean_squared_error
(
normalized_train_tfmri_data
,
X_train_new_tfmri
)
cvscores_mse_tfmri_train
.
append
(
val_mse_train_tfmri
)
print
(
'
Reconstruction MSE of tfmri:
'
,
val_mse_train_tfmri
)
val_rmse_tfmri
=
sqrt
(
val_mse_train_tfmri
)
print
(
'
Reconstruction RMSE of tfmri :
'
,
val_rmse_tfmri
)
cvscores_rmse_tfmri_train
.
append
(
val_rmse_tfmri
)
#rsfmri
print
(
"
Max value of predicted training rsfmri data
"
,
np
.
max
(
X_train_new_rsfmri
))
print
(
"
Min value of predicted training rsfmri data
"
,
np
.
min
(
X_train_new_rsfmri
))
print
(
"
Reconstructed rsfmri matrix shape:
"
,
X_train_new_rsfmri
.
shape
)
val_mse_train_rsfmri
=
mean_squared_error
(
normalized_train_rsfmri_data
,
X_train_new_rsfmri
)
cvscores_mse_rsfmri_train
.
append
(
val_mse_train_rsfmri
)
print
(
'
Reconstruction MSE of rsfmri:
'
,
val_mse_train_rsfmri
)
val_rmse_rsfmri
=
sqrt
(
val_mse_train_rsfmri
)
print
(
'
Reconstruction RMSE of rsfmri :
'
,
val_rmse_rsfmri
)
cvscores_rmse_rsfmri_train
.
append
(
val_rmse_rsfmri
)
#sum of MSE (tfmri + rsfmri)
cvscores_mse_train
.
append
(
np
.
sum
([
val_mse_train_tfmri
,
val_mse_train_rsfmri
]))
# sum of RMSE (tfmri + rsfmri)
cvscores_rmse_train
.
append
(
sqrt
(
np
.
sum
([
val_mse_train_tfmri
,
val_mse_train_rsfmri
])))
# Reconstruction of test data
print
(
"
Reconstruction of test data...
"
)
[
X_test_new_tfmri
,
X_test_new_rsfmri
]
=
multimodal_autoencoder
.
predict
([
normalized_test_tfmri_data
,
normalized_test_rsfmri_data
])
# Test
# tfmri
print
(
"
Max value of predicted testing tfmri data
"
,
np
.
max
(
X_test_new_tfmri
))
print
(
"
Min value of predicted testing tfmri data
"
,
np
.
min
(
X_test_new_tfmri
))
print
(
"
Reconstructed tfmri matrix shape:
"
,
X_test_new_tfmri
.
shape
)
val_mse_test_tfmri
=
mean_squared_error
(
normalized_test_tfmri_data
,
X_test_new_tfmri
)
cvscores_mse_tfmri_test
.
append
(
val_mse_test_tfmri
)
print
(
'
Reconstruction MSE of tfmri:
'
,
val_mse_test_tfmri
)
val_rmse_tfmri
=
sqrt
(
val_mse_test_tfmri
)
print
(
'
Reconstruction RMSE of tfmri :
'
,
val_rmse_tfmri
)
cvscores_rmse_tfmri_test
.
append
(
val_rmse_tfmri
)
# rsfmri
print
(
"
Max value of predicted testing rsfmri data
"
,
np
.
max
(
X_test_new_rsfmri
))
print
(
"
Min value of predicted testing rsfmri data
"
,
np
.
min
(
X_test_new_rsfmri
))
print
(
"
Reconstructed rsfmri matrix shape:
"
,
X_test_new_rsfmri
.
shape
)
val_mse_test_rsfmri
=
mean_squared_error
(
normalized_test_rsfmri_data
,
X_test_new_rsfmri
)
cvscores_mse_rsfmri_test
.
append
(
val_mse_test_rsfmri
)
print
(
'
Reconstruction MSE of rsfmri:
'
,
val_mse_test_rsfmri
)
val_rmse_rsfmri
=
sqrt
(
val_mse_test_rsfmri
)
print
(
'
Reconstruction RMSE of rsfmri :
'
,
val_rmse_rsfmri
)
cvscores_rmse_rsfmri_test
.
append
(
val_rmse_rsfmri
)
# sum of MSE (tfmri + rsfmri)
cvscores_mse_test
.
append
(
np
.
sum
([
val_mse_test_tfmri
,
val_mse_test_rsfmri
]))
# sum of MSE (tfmri + rsfmri)
cvscores_rmse_test
.
append
(
sqrt
(
np
.
sum
([
val_mse_test_tfmri
,
val_mse_test_rsfmri
])))
# Save MSE, RMSE (tfmri +rsfmr)
print
(
"
shape of vector mse train
"
,
np
.
array
([
cvscores_mse_train
]).
shape
)
print
(
cvscores_mse_train
)
np
.
save
(
'
{}/cvscores_mse_train.npy
'
.
format
(
dim
),
np
.
array
([
cvscores_mse_train
]))
print
(
"
shape of mse vector(test):
"
,
np
.
array
([
cvscores_mse_test
]).
shape
)
print
(
cvscores_mse_test
)
np
.
save
(
'
{}/cvscores_mse_test.npy
'
.
format
(
dim
),
np
.
array
([
cvscores_mse_test
]))
print
(
"
shape of rmse vector (train):
"
,
np
.
array
([
cvscores_rmse_train
]).
shape
)
print
(
cvscores_rmse_train
)
np
.
save
(
'
{}/cvscores_rmse_train.npy
'
.
format
(
dim
),
np
.
array
([
cvscores_rmse_train
]))
print
(
"
shape of rmse vector (test):
"
,
np
.
array
([
cvscores_rmse_test
]).
shape
)
print
(
cvscores_rmse_test
)
np
.
save
(
'
{}/cvscores_rmse_test.npy
'
.
format
(
dim
),
np
.
array
([
cvscores_rmse_test
]))
print
(
"
%.3f%% (+/- %.5f%%)
"
%
(
np
.
mean
(
cvscores_mse_test
),
np
.
std
(
cvscores_mse_test
)))
mse_train
.
append
(
np
.
mean
(
cvscores_mse_train
))
std_mse_train
.
append
(
np
.
std
(
cvscores_mse_train
))
mse_test
.
append
(
np
.
mean
(
cvscores_mse_test
))
std_mse_test
.
append
(
np
.
std
(
cvscores_mse_test
))
rmse_train
.
append
(
np
.
mean
(
cvscores_rmse_train
))
std_rmse_train
.
append
(
np
.
std
(
cvscores_rmse_train
))
rmse_test
.
append
(
np
.
mean
(
cvscores_rmse_test
))
std_rmse_test
.
append
(
np
.
std
(
cvscores_rmse_test
))
# Save MSE, RMSE (tfmri)
print
(
"
shape of vector mse train (tfmri)
"
,
np
.
array
([
cvscores_mse_tfmri_train
]).
shape
)
print
(
cvscores_mse_tfmri_train
)
np
.
save
(
'
{}/cvscores_mse_tfmri_train.npy
'
.
format
(
dim
),
np
.
array
([
cvscores_mse_tfmri_train
]))
print
(
"
shape of mse vector(test):
"
,
np
.
array
([
cvscores_mse_tfmri_test
]).
shape
)
print
(
cvscores_mse_tfmri_test
)
np
.
save
(
'
{}/cvscores_mse_tfmri_test.npy
'
.
format
(
dim
),
np
.
array
([
cvscores_mse_tfmri_test
]))
print
(
"
shape of rmse vector (train):
"
,
np
.
array
([
cvscores_rmse_tfmri_train
]).
shape
)
print
(
cvscores_rmse_tfmri_train
)
np
.
save
(
'
{}/cvscores_rmse_tfmri_train.npy
'
.
format
(
dim
),
np
.
array
([
cvscores_rmse_tfmri_test
]))
print
(
"
shape of rmse vector tfmri (test):
"
,
np
.
array
([
cvscores_rmse_tfmri_test
]).
shape
)
print
(
cvscores_rmse_tfmri_test
)
np
.
save
(
'
{}/cvscores_rmse_tfmri_test.npy
'
.
format
(
dim
),
np
.
array
([
cvscores_rmse_tfmri_test
]))
mse_tfmri_train
.
append
(
np
.
mean
(
cvscores_mse_tfmri_train
))
std_mse_tfmri_train
.
append
(
np
.
std
(
cvscores_mse_tfmri_train
))
mse_tfmri_test
.
append
(
np
.
mean
(
cvscores_mse_tfmri_test
))
std_mse_tfmri_test
.
append
(
np
.
std
(
cvscores_mse_tfmri_test
))
rmse_tfmri_train
.
append
(
np
.
mean
(
cvscores_rmse_tfmri_train
))
std_rmse_tfmri_train
.
append
(
np
.
std
(
cvscores_rmse_tfmri_train
))
rmse_tfmri_test
.
append
(
np
.
mean
(
cvscores_rmse_tfmri_test
))
std_rmse_tfmri_test
.
append
(
np
.
std
(
cvscores_rmse_tfmri_test
))
# Save MSE, RMSE (rsfmri)
print
(
"
shape of vector mse train (rsfmri)
"
,
np
.
array
([
cvscores_mse_rsfmri_train
]).
shape
)
print
(
cvscores_mse_rsfmri_train
)
np
.
save
(
'
{}/cvscores_mse_rsfmri_train.npy
'
.
format
(
dim
),
np
.
array
([
cvscores_mse_rsfmri_train
]))
print
(
"
shape of mse vector(test):
"
,
np
.
array
([
cvscores_mse_rsfmri_test
]).
shape
)
print
(
cvscores_mse_rsfmri_test
)
np
.
save
(
'
{}/cvscores_mse_rsfmri_test.npy
'
.
format
(
dim
),
np
.
array
([
cvscores_mse_rsfmri_test
]))
print
(
"
shape of rmse vector (train):
"
,
np
.
array
([
cvscores_rmse_rsfmri_train
]).
shape
)
print
(
cvscores_rmse_rsfmri_train
)
np
.
save
(
'
{}/cvscores_rmse_rsfmri_train.npy
'
.
format
(
dim
),
np
.
array
([
cvscores_rmse_rsfmri_test
]))
print
(
"
shape of rmse vector rsfmri (test):
"
,
np
.
array
([
cvscores_rmse_rsfmri_test
]).
shape
)
print
(
cvscores_rmse_rsfmri_test
)
np
.
save
(
'
{}/cvscores_rmse_rsfmri_test.npy
'
.
format
(
dim
),
np
.
array
([
cvscores_rmse_rsfmri_test
]))
mse_rsfmri_train
.
append
(
np
.
mean
(
cvscores_mse_rsfmri_train
))
std_mse_rsfmri_train
.
append
(
np
.
std
(
cvscores_mse_rsfmri_train
))
mse_rsfmri_test
.
append
(
np
.
mean
(
cvscores_mse_rsfmri_test
))
std_mse_rsfmri_test
.
append
(
np
.
std
(
cvscores_mse_rsfmri_test
))
rmse_rsfmri_train
.
append
(
np
.
mean
(
cvscores_rmse_rsfmri_train
))
std_rmse_rsfmri_train
.
append
(
np
.
std
(
cvscores_rmse_rsfmri_train
))
rmse_rsfmri_test
.
append
(
np
.
mean
(
cvscores_rmse_rsfmri_test
))
std_rmse_rsfmri_test
.
append
(
np
.
std
(
cvscores_rmse_rsfmri_test
))
# save MSE, RMSE, and STD vectors for training and test sets
np
.
save
(
'
mse_train_mean.npy
'
,
np
.
array
([
mse_train
]))
np
.
save
(
'
rmse_train_mean.npy
'
,
np
.
array
([
rmse_train
]))
np
.
save
(
'
std_mse_train_mean.npy
'
,
np
.
array
([
std_mse_train
]))
np
.
save
(
'
std_rmse_train_mean.npy
'
,
np
.
array
([
std_rmse_train
]))
np
.
save
(
'
mse_test_mean.npy
'
,
np
.
array
([
mse_test
]))
np
.
save
(
'
rmse_test_mean.npy
'
,
np
.
array
([
rmse_test
]))
np
.
save
(
'
std_mse_test_mean.npy
'
,
np
.
array
([
std_mse_test
]))
np
.
save
(
'
std_rmse_test_mean.npy
'
,
np
.
array
([
std_rmse_test
]))
# save MSE, RMSE, and STD vectors for training and test sets (rsfmri)
np
.
save
(
'
mse_test_mean_rsfmri.npy
'
,
np
.
array
([
mse_rsfmri_test
]))
np
.
save
(
'
rmse_test_mean_rsfmri.npy
'
,
np
.
array
([
rmse_rsfmri_test
]))
np
.
save
(
'
mse_train_mean_rsfmri.npy
'
,
np
.
array
([
mse_rsfmri_train
]))
np
.
save
(
'
rmse_train_mean_rsfmri.npy
'
,
np
.
array
([
rmse_rsfmri_train
]))
np
.
save
(
'
std_mse_mean_rsfmri.npy
'
,
np
.
array
([
std_mse_rsfmri_test
]))
np
.
save
(
'
std_rmse_mean_rsfmri.npy
'
,
np
.
array
([
std_rmse_rsfmri_test
]))
# plotting the mse train
# setting x and y axis range
# plotting the mse train
plt
.
plot
(
dimensions
,
mse_train
,
label
=
"
mse_train
"
)
plt
.
plot
(
dimensions
,
mse_test
,
label
=
"
mse_test
"
)
plt
.
xlabel
(
'
Encoding dimension
'
)
plt
.
ylabel
(
'
Reconstruction error (MSE)
'
)
# showing legend
plt
.
legend
()
plt
.
savefig
(
'
reconstruction_error_mse.pdf
'
)
plt
.
savefig
(
'
reconstruction_error_mse.png
'
)
plt
.
close
()
# plotting the rmse train
# setting x and y axis range
plt
.
plot
(
dimensions
,
rmse_train
,
label
=
"
rmse_train
"
)
plt
.
plot
(
dimensions
,
rmse_test
,
label
=
"
rmse_test
"
)
plt
.
xlabel
(
'
Encoding dimension
'
)
plt
.
ylabel
(
'
Reconstruction error (RMSE)
'
)
# showing legend
plt
.
legend
()
plt
.
savefig
(
'
reconstruction_error_rmse.pdf
'
)
plt
.
savefig
(
'
reconstruction_error_rmse.png
'
)
plt
.
close
()
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