Inception Resnet v2 bad test accuracy with transfer learning

Question

I want to binary classify breast cancer histopathological images from the BreakHis dataset ( https://www.kaggle.com/ambarish/breakhis ) using transfer learning and the Inception Resnet v2. The goal is to freeze all layers and train the fully connected layer by adding two neurons to the model. In particular, initially I want to consider the images related to the magnificant factor 40X (Benign: 625, Malignant: 1370). Here is a summary of what I do:

• I read the images and resize them to 150x150
• I partition the dataset into training, validation and test set
• I load the pre-trained network Inception Resnet v2
• I freeze all the layers I add the two neurons for binary classification (1 = "benign", 0 = "malignant")
• I compile the model using as activation function the Adam method
• I carry out the training
• I make the prediction
• I calculate the accuracy

This is the code:

data = dataset[dataset["Magnificant"]=="40X"]
def preprocessing(dataset, img_size):
    # images
    X = []
    # labels 
    y = []
    
    i = 0
    for image in list(dataset["Path"]):
        # Ridimensiono e leggo le immagini
        X.append(cv2.resize(cv2.imread(image, cv2.IMREAD_COLOR), 
                            (img_size, img_size), interpolation=cv2.INTER_CUBIC))
        basename = os.path.basename(image)
        
        # Get labels
        if dataset.loc[i][2] == "benign":
            y.append(1)
        else:
            y.append(0)
        i = i+1
    return X, y

X, y = preprocessing(data, 150)
X = np.array(X)
y = np.array(y)
# Splitting
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.3, stratify = y_40, shuffle=True, random_state=1)
X_train, X_val, y_train, y_val = train_test_split(X_train, y_train, test_size=0.25, random_state=1) 

conv_base = InceptionResNetV2(weights='imagenet', include_top=False, input_shape=[150, 150, 3])   

# Freezing
for layer in conv_base.layers:
    layer.trainable = False

model = models.Sequential()
model.add(conv_base)
model.add(layers.Flatten())
model.add(layers.Dense(1, activation='sigmoid'))

opt = tf.keras.optimizers.Adam(learning_rate=0.0002)

loss = tf.keras.losses.BinaryCrossentropy(from_logits=True)

model.compile(loss=loss, optimizer=opt, metrics = ["accuracy", tf.metrics.AUC()])

batch_size = 32

train_datagen = ImageDataGenerator(rescale=1./255)
val_datagen = ImageDataGenerator(rescale=1./255) 
train_generator = train_datagen.flow(X_train, y_train, batch_size=batch_size) 
val_generator = val_datagen.flow(X_val, y_val, batch_size=batch_size)

ntrain =len(X_train)
nval = len(X_val)
len(y_train)
epochs = 70
history = model.fit_generator(train_generator,
                              steps_per_epoch=ntrain // batch_size,
                              epochs=epochs,
                              validation_data=val_generator,
                              validation_steps=nval // batch_size)

This is the output of the training at the last epoch:

Epoch 70/70
32/32 [==============================] - 3s 84ms/step - loss: 0.0499 - accuracy: 0.9903 - auc_5: 0.9996 - val_loss: 0.5661 - val_accuracy: 0.8250 - val_auc_5: 0.8521

I make the prediction:

test_datagen = ImageDataGenerator(rescale=1./255) 
x = X_test
y_pred = model.predict(test_datagen.flow(x))

y_p = []
for i in range(len(y_pred)):
    if y_pred[i] > 0.5:
        y_p.append(1)
    else:
        y_p.append(0)

I calculate the accuracy:

from sklearn.metrics import accuracy_score
accuracy =  accuracy_score(y_test, y_p)
print(accuracy)

This is the accuracy value I get: 0.5459098497495827

Why do I get such low accuracy, I have done several tests but I always get similar results?

Update

I have made the following changes but I always get the same results (place only the modified parts of the code):

X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.3, stratify = y, shuffle=True, random_state=42)
X_train, X_val, y_train, y_val = train_test_split(X_train, y_train, test_size=0.25, stratify = y_train, shuffle=True, random_state=1)

model = models.Sequential()
model.add(conv_base)
model.add(layers.Flatten())
model.add(layers.Dropout(0.5))
model.add(layers.Dense(1, activation='sigmoid'))

callback = tf.keras.callbacks.EarlyStopping(monitor='loss', patience=3)

ntrain =len(X_train)
nval = len(X_val)
len(y_train)
epochs = 70
history = model.fit_generator(train_generator,
                              steps_per_epoch=ntrain // batch_size,
                              epochs=epochs,
                              validation_data=val_generator,
                              validation_steps=nval // batch_size, callbacks=[callback]) 

Update 2

I also changed from_logits from True to False, but of course that's not the problem yet. I always get 57% accuracy.

This is the model.fit output over 30 epochs:

Epoch 1/30
32/32 [==============================] - 23s 202ms/step - loss: 0.7994 - accuracy: 0.6010 - auc: 0.5272 - val_loss: 0.5338 - val_accuracy: 0.7688 - val_auc: 0.7943
Epoch 2/30
32/32 [==============================] - 3s 87ms/step - loss: 0.5778 - accuracy: 0.7206 - auc: 0.7521 - val_loss: 0.4763 - val_accuracy: 0.7781 - val_auc: 0.8155
Epoch 3/30
32/32 [==============================] - 3s 85ms/step - loss: 0.5311 - accuracy: 0.7581 - auc: 0.7710 - val_loss: 0.4740 - val_accuracy: 0.7719 - val_auc: 0.8212
Epoch 4/30
32/32 [==============================] - 3s 85ms/step - loss: 0.4684 - accuracy: 0.7718 - auc: 0.8219 - val_loss: 0.4270 - val_accuracy: 0.8031 - val_auc: 0.8611
Epoch 5/30
32/32 [==============================] - 3s 83ms/step - loss: 0.4280 - accuracy: 0.7943 - auc: 0.8617 - val_loss: 0.4496 - val_accuracy: 0.7969 - val_auc: 0.8468
Epoch 6/30
32/32 [==============================] - 3s 88ms/step - loss: 0.4237 - accuracy: 0.8250 - auc: 0.8673 - val_loss: 0.3993 - val_accuracy: 0.7937 - val_auc: 0.8840
Epoch 7/30
32/32 [==============================] - 3s 85ms/step - loss: 0.4130 - accuracy: 0.8513 - auc: 0.8767 - val_loss: 0.4207 - val_accuracy: 0.7781 - val_auc: 0.8692
Epoch 8/30
32/32 [==============================] - 3s 85ms/step - loss: 0.3446 - accuracy: 0.8485 - auc: 0.9077 - val_loss: 0.4229 - val_accuracy: 0.7937 - val_auc: 0.8730
Epoch 9/30
32/32 [==============================] - 3s 85ms/step - loss: 0.3690 - accuracy: 0.8514 - auc: 0.9003 - val_loss: 0.4300 - val_accuracy: 0.8062 - val_auc: 0.8696
Epoch 10/30
32/32 [==============================] - 3s 100ms/step - loss: 0.3204 - accuracy: 0.8533 - auc: 0.9270 - val_loss: 0.4235 - val_accuracy: 0.7969 - val_auc: 0.8731
Epoch 11/30
32/32 [==============================] - 3s 86ms/step - loss: 0.3555 - accuracy: 0.8508 - auc: 0.9124 - val_loss: 0.4124 - val_accuracy: 0.8000 - val_auc: 0.8797
Epoch 12/30
32/32 [==============================] - 3s 85ms/step - loss: 0.3243 - accuracy: 0.8481 - auc: 0.9308 - val_loss: 0.3979 - val_accuracy: 0.7969 - val_auc: 0.8908
Epoch 13/30
32/32 [==============================] - 3s 85ms/step - loss: 0.3017 - accuracy: 0.8744 - auc: 0.9348 - val_loss: 0.4239 - val_accuracy: 0.8094 - val_auc: 0.8758
Epoch 14/30
32/32 [==============================] - 3s 89ms/step - loss: 0.3317 - accuracy: 0.8521 - auc: 0.9221 - val_loss: 0.4238 - val_accuracy: 0.8094 - val_auc: 0.8704
Epoch 15/30
32/32 [==============================] - 3s 85ms/step - loss: 0.2840 - accuracy: 0.8908 - auc: 0.9490 - val_loss: 0.4131 - val_accuracy: 0.8281 - val_auc: 0.8858
Epoch 16/30
32/32 [==============================] - 3s 85ms/step - loss: 0.2583 - accuracy: 0.8905 - auc: 0.9511 - val_loss: 0.3841 - val_accuracy: 0.8375 - val_auc: 0.9007
Epoch 17/30
32/32 [==============================] - 3s 87ms/step - loss: 0.2810 - accuracy: 0.8648 - auc: 0.9470 - val_loss: 0.3928 - val_accuracy: 0.8438 - val_auc: 0.8972
Epoch 18/30
32/32 [==============================] - 3s 89ms/step - loss: 0.2622 - accuracy: 0.8923 - auc: 0.9550 - val_loss: 0.3732 - val_accuracy: 0.8438 - val_auc: 0.9089
Epoch 19/30
32/32 [==============================] - 3s 84ms/step - loss: 0.2486 - accuracy: 0.8990 - auc: 0.9579 - val_loss: 0.4077 - val_accuracy: 0.8250 - val_auc: 0.8924
Epoch 20/30
32/32 [==============================] - 3s 85ms/step - loss: 0.2412 - accuracy: 0.9074 - auc: 0.9635 - val_loss: 0.4249 - val_accuracy: 0.8219 - val_auc: 0.8787
Epoch 21/30
32/32 [==============================] - 3s 84ms/step - loss: 0.2386 - accuracy: 0.9095 - auc: 0.9657 - val_loss: 0.4177 - val_accuracy: 0.8094 - val_auc: 0.8904
Epoch 22/30
32/32 [==============================] - 3s 99ms/step - loss: 0.2313 - accuracy: 0.8996 - auc: 0.9668 - val_loss: 0.4089 - val_accuracy: 0.8406 - val_auc: 0.8890
Epoch 23/30
32/32 [==============================] - 3s 86ms/step - loss: 0.2424 - accuracy: 0.9067 - auc: 0.9654 - val_loss: 0.4033 - val_accuracy: 0.8500 - val_auc: 0.8953
Epoch 24/30
32/32 [==============================] - 3s 85ms/step - loss: 0.2315 - accuracy: 0.9045 - auc: 0.9626 - val_loss: 0.3903 - val_accuracy: 0.8250 - val_auc: 0.9030
Epoch 25/30
32/32 [==============================] - 3s 85ms/step - loss: 0.2001 - accuracy: 0.9321 - auc: 0.9788 - val_loss: 0.4276 - val_accuracy: 0.8000 - val_auc: 0.8855
Epoch 26/30
32/32 [==============================] - 3s 87ms/step - loss: 0.2118 - accuracy: 0.9212 - auc: 0.9695 - val_loss: 0.4335 - val_accuracy: 0.8125 - val_auc: 0.8897
Epoch 27/30
32/32 [==============================] - 3s 85ms/step - loss: 0.2463 - accuracy: 0.8941 - auc: 0.9665 - val_loss: 0.4112 - val_accuracy: 0.8438 - val_auc: 0.8882
Epoch 28/30
32/32 [==============================] - 3s 85ms/step - loss: 0.2130 - accuracy: 0.9033 - auc: 0.9771 - val_loss: 0.3834 - val_accuracy: 0.8406 - val_auc: 0.9021
Epoch 29/30
32/32 [==============================] - 3s 86ms/step - loss: 0.2021 - accuracy: 0.9229 - auc: 0.9754 - val_loss: 0.3855 - val_accuracy: 0.8469 - val_auc: 0.9008
Epoch 30/30
32/32 [==============================] - 3s 88ms/step - loss: 0.1859 - accuracy: 0.9314 - auc: 0.9824 - val_loss: 0.4018 - val_accuracy: 0.8375 - val_auc: 0.8928

Answer 1

You have to change from_logits=True to from_logits=False in your loss function. Once again Credits - @ Frightera .

Answer 2

It seems like your model is over-fitting somewhere. It would be best if you could check for that.

• Do the K-Fold test for 10 folds. It would show the true results
• In your metrics, do add the F1 score. The F1 value would give you a real look into the metrics of the TP in terms of both FP and FN
• Add some augmentations (apart from the rescaling one) to make the model robust to changes in the dataset.
• Tweak the training parameters (if you feel).

If these changes fail, then there might be a possibility that the model fails to learn the artifacts of the image. You should go ahead with a different model!