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Léo Schneider
LC-MS-RT-prediction
Commits
aba4f1cd
Commit
aba4f1cd
authored
9 months ago
by
Schneider Leo
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seq_length args
parent
538eee31
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2 changed files
config_common.py
+3
-0
3 additions, 0 deletions
config_common.py
main_custom.py
+8
-7
8 additions, 7 deletions
main_custom.py
with
11 additions
and
7 deletions
config_common.py
+
3
−
0
View file @
aba4f1cd
import
argparse
from
tensorflow.python.keras.utils.generic_utils
import
default
def
load_args
():
parser
=
argparse
.
ArgumentParser
()
...
...
@@ -27,6 +29,7 @@ def load_args():
parser
.
add_argument
(
'
--norm_first
'
,
action
=
argparse
.
BooleanOptionalAction
)
parser
.
add_argument
(
'
--activation
'
,
type
=
str
,
default
=
'
relu
'
)
parser
.
add_argument
(
'
--file
'
,
action
=
argparse
.
BooleanOptionalAction
)
parser
.
add_argument
(
'
--seq_length
'
,
type
=
int
,
default
=
25
)
args
=
parser
.
parse_args
()
return
args
This diff is collapsed.
Click to expand it.
main_custom.py
+
8
−
7
View file @
aba4f1cd
...
...
@@ -223,28 +223,28 @@ def main(args):
data_train
,
data_val
,
data_test
=
common_dataset
.
load_data
(
path_train
=
args
.
dataset_train
,
path_val
=
args
.
dataset_val
,
path_test
=
args
.
dataset_test
,
batch_size
=
args
.
batch_size
,
length
=
25
,
pad
=
True
,
convert
=
True
,
vocab
=
'
unmod
'
)
batch_size
=
args
.
batch_size
,
length
=
args
.
seq_length
,
pad
=
True
,
convert
=
True
,
vocab
=
'
unmod
'
)
elif
args
.
forward
==
'
rt
'
:
data_train
,
data_val
,
data_test
=
dataloader
.
load_data
(
data_sources
=
[
args
.
dataset_train
,
args
.
dataset_val
,
args
.
dataset_test
],
batch_size
=
args
.
batch_size
,
length
=
25
)
batch_size
=
args
.
batch_size
,
length
=
args
.
seq_length
)
elif
args
.
forward
==
'
transfer
'
:
data_train
,
_
,
_
=
dataloader
.
load_data
(
data_sources
=
[
args
.
dataset_train
,
'
database/data_holdout.csv
'
,
'
database/data_holdout.csv
'
],
batch_size
=
args
.
batch_size
,
length
=
25
)
batch_size
=
args
.
batch_size
,
length
=
args
.
seq_length
)
_
,
data_val
,
data_test
=
common_dataset
.
load_data
(
path_train
=
args
.
dataset_val
,
path_val
=
args
.
dataset_val
,
path_test
=
args
.
dataset_test
,
batch_size
=
args
.
batch_size
,
length
=
25
,
pad
=
True
,
convert
=
True
,
vocab
=
'
unmod
'
)
batch_size
=
args
.
batch_size
,
length
=
args
.
seq_length
,
pad
=
True
,
convert
=
True
,
vocab
=
'
unmod
'
)
elif
args
.
forward
==
'
reverse
'
:
_
,
data_val
,
data_test
=
dataloader
.
load_data
(
data_sources
=
[
'
database/data_train.csv
'
,
args
.
dataset_val
,
args
.
dataset_test
],
batch_size
=
args
.
batch_size
,
length
=
25
)
batch_size
=
args
.
batch_size
,
length
=
args
.
seq_length
)
data_train
,
_
,
_
=
common_dataset
.
load_data
(
path_train
=
args
.
dataset_train
,
path_val
=
args
.
dataset_train
,
path_test
=
args
.
dataset_train
,
batch_size
=
args
.
batch_size
,
length
=
25
,
pad
=
True
,
convert
=
True
,
vocab
=
'
unmod
'
)
batch_size
=
args
.
batch_size
,
length
=
args
.
seq_length
,
pad
=
True
,
convert
=
True
,
vocab
=
'
unmod
'
)
print
(
'
\n
Data loaded
'
)
...
...
@@ -253,7 +253,8 @@ def main(args):
,
n_head
=
args
.
n_head
,
encoder_num_layer
=
args
.
encoder_num_layer
,
decoder_int_num_layer
=
args
.
decoder_int_num_layer
,
decoder_rt_num_layer
=
args
.
decoder_rt_num_layer
,
drop_rate
=
args
.
drop_rate
,
embedding_dim
=
args
.
embedding_dim
,
acti
=
args
.
activation
,
norm
=
args
.
norm_first
)
embedding_dim
=
args
.
embedding_dim
,
acti
=
args
.
activation
,
norm
=
args
.
norm_first
,
seq_length
=
args
.
seq_length
)
if
torch
.
cuda
.
is_available
():
model
=
model
.
cuda
()
optimizer
=
optim
.
Adam
(
model
.
parameters
(),
lr
=
args
.
lr
)
...
...
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