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Refactor ANN.py for compatibility with modern TensorFlow #6

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Refactor ANN.py for compatibility with modern TensorFlow #6

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16 changes: 11 additions & 5 deletions scripts/ANN.py
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Original file line number Diff line number Diff line change
@@ -1,14 +1,16 @@
# Import libraries
import os
import numpy as np
from Bio.Alphabet import IUPAC
from keras.optimizers import Adam
# from Bio.Alphabet import IUPAC <-- REMOVED (Deprecated)
from tensorflow.keras.optimizers import Adam # <-- UPDATED for modern Tensorflow
from contextlib import redirect_stdout

# Import custom functions
from utils import one_hot_encoder, create_ann, \
plot_ROC_curve, plot_PR_curve, calc_stat

# Define the protein alphabet manually since Bio.Alphabet is removed
PROTEIN_ALPHABET = "ACDEFGHIKLMNPQRSTVWY"

def ANN_classification(dataset, filename, save_model=False):
"""
Expand Down Expand Up @@ -37,13 +39,16 @@ def ANN_classification(dataset, filename, save_model=False):
X_val = dataset.val.loc[:, 'AASeq'].values

# One hot encode the sequences
X_train = [one_hot_encoder(s=x, alphabet=IUPAC.protein) for x in X_train]
# UPDATED: Using PROTEIN_ALPHABET string instead of IUPAC.protein
X_train = [one_hot_encoder(s=x, alphabet=PROTEIN_ALPHABET) for x in X_train]
X_train = [x.flatten('F') for x in X_train]
X_train = np.asarray(X_train)
X_test = [one_hot_encoder(s=x, alphabet=IUPAC.protein) for x in X_test]

X_test = [one_hot_encoder(s=x, alphabet=PROTEIN_ALPHABET) for x in X_test]
X_test = [x.flatten('F') for x in X_test]
X_test = np.asarray(X_test)
X_val = [one_hot_encoder(s=x, alphabet=IUPAC.protein) for x in X_val]

X_val = [one_hot_encoder(s=x, alphabet=PROTEIN_ALPHABET) for x in X_val]
X_val = [x.flatten('F') for x in X_val]
X_val = np.asarray(X_val)

Expand All @@ -56,6 +61,7 @@ def ANN_classification(dataset, filename, save_model=False):
ANN_classifier = create_ann()

# Compiling the ANN
# Note: Learning rate is small, suitable for fine-tuning or noisy data
ada_optimizer = Adam(learning_rate=0.0001)
ANN_classifier.compile(
optimizer=ada_optimizer, loss='binary_crossentropy',
Expand Down