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Patrick Skillman-Lawrence
mhc_rank
Commits
a84bccbf
Commit
a84bccbf
authored
8 years ago
by
Jeff Hammerbacher
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Remove tf-mhcflurry.py (not necessary) and clear TF exploration notebook state.
parent
79f8ff23
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notebooks/TF exploration.ipynb
+17
-134
17 additions, 134 deletions
notebooks/TF exploration.ipynb
script/tf-mhcflurry.py
+0
-20
0 additions, 20 deletions
script/tf-mhcflurry.py
with
17 additions
and
154 deletions
notebooks/TF exploration.ipynb
+
17
−
134
View file @
a84bccbf
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script/tf-mhcflurry.py
deleted
100644 → 0
+
0
−
20
View file @
79f8ff23
from
mhcflurry.dataset
import
Dataset
from
mhcflurry.peptide_encoding
import
indices_to_hotshot_encoding
file_to_explore
=
"
/root/.local/share/mhcflurry/2/class1_data/combined_human_class1_dataset.csv
"
dataset
=
Dataset
.
from_csv
(
filename
=
file_to_explore
,
sep
=
"
,
"
,
peptide_column_name
=
"
peptide
"
)
df
=
dataset
.
to_dataframe
()
df_kmers
=
dataset
.
kmer_index_encoding
()
training_hotshot
=
indices_to_hotshot_encoding
(
df_kmers
[
0
])
from
keras.models
import
Sequential
from
keras.layers
import
Dense
,
Activation
model
=
Sequential
()
model
.
add
(
Dense
(
input_dim
=
9
*
21
,
output_dim
=
1
))
# TF backend segfaults here
model
.
add
(
Activation
(
"
sigmoid
"
))
model
.
compile
(
loss
=
"
mse
"
,
optimizer
=
"
rmsprop
"
)
model
.
fit
(
training_hotshot
,
df_kmers
[
1
],
nb_epoch
=
5
,
batch_size
=
1
)
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