How to compute f1 score for each epoch in Keras

https://medium.com/@thongonary/how-to-compute-f1-score-for-each-epoch-in-keras-a1acd17715a2

https://datascience.stackexchange.com/questions/13746/how-to-define-a-custom-performance-metric-in-keras/20192

In training a neural network, f1 score is an important metric to evaluate the performance of classification models, especially for unbalanced classes where the binary accuracy is useless (see Accuracy Paradox).

Keras used to implement the f1 score in its metrics; however, the developers decided to remove it in Keras 2.0, since this quantity is evaluated for each batch, which is more misleading than helpful. Fortunately, Keras allows us to access the validation data during training via a Callback function, on which we can extend to compute the desired quantities.

Here is a sample code to compute and print out the f1 score, recall, and precision at the end of each epoch, using the whole validation data:

import numpy as np
from keras.callbacks import Callback
from sklearn.metrics import confusion_matrix, f1_score, precision_score, recall_score

class Metrics(Callback):

def on_train_begin(self, logs={}):
 self.val_f1s = []
 self.val_recalls = []
 self.val_precisions = []

def on_epoch_end(self, epoch, logs={}):
 val_predict = (np.asarray(self.model.predict(self.model.validation_data[0]))).round()
 val_targ = self.model.validation_data[1]
 _val_f1 = f1_score(val_targ, val_predict)
 _val_recall = recall_score(val_targ, val_predict)
 _val_precision = precision_score(val_targ, val_predict)
 self.val_f1s.append(_val_f1)
 self.val_recalls.append(_val_recall)
 self.val_precisions.append(_val_precision)
 print “ — val_f1: %f — val_precision: %f — val_recall %f” %(_val_f1, _val_precision, _val_recall)
 return

metrics = Metrics()

on_train_begin is initialized at the beginning of the training. Here we initiate 3 lists to hold the values of the interested quantities, which are computed in on_epoch_end. Later on, we can access these lists as usual instance variables, for example:

print (metrics.val_f1s)

Define the model, and add the callback parameter in the fit function:

model.fit(training_data, training_target, 
 validation_data=(validation_data, validation_target),
 nb_epoch=10,
 batch_size=64,
 callbacks=[metrics])

The printout during training would look like this:

Epoch 1/10
32320/32374 [============================>.] - ETA: 0s - loss: 0.0414 - val_f1: 0.375000 - val_precision: 0.782609 - val_recall 0.246575
32374/32374 [==============================] - 23s - loss: 0.0414 - val_loss: 0.0430

That’s it. Have fun training!