Keras 2.x killed off a bunch of useful metrics that I need to use, so I copied the functions from the old metrics.py file into my code, then included them as follows.
def precision(y_true, y_pred): #taken from old keras source code
true_positives = K.sum(K.round(K.clip(y_true * y_pred, 0, 1)))
predicted_positives = K.sum(K.round(K.clip(y_pred, 0, 1)))
precision = true_positives / (predicted_positives + K.epsilon())
return precision
def recall(y_true, y_pred): #taken from old keras source code
true_positives = K.sum(K.round(K.clip(y_true * y_pred, 0, 1)))
possible_positives = K.sum(K.round(K.clip(y_true, 0, 1)))
recall = true_positives / (possible_positives + K.epsilon())
return recall
...
model.compile(loss='categorical_crossentropy', optimizer='adam',
metrics=['accuracy', precision, recall])
and this results in
ValueError: Unknown metric function:precision
What am I doing wrong? I can't see anything I'm doing wrong according to Keras documentation.
edit:
Here is the full Traceback:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Library/Python/2.7/site-packages/keras/models.py", line 274, in
load_model
sample_weight_mode=sample_weight_mode)
File "/Library/Python/2.7/site-packages/keras/models.py", line 824, in
compile
**kwargs)
File "/Library/Python/2.7/site-packages/keras/engine/training.py", line
934, in compile
handle_metrics(output_metrics)
File "/Library/Python/2.7/site-packages/keras/engine/training.py", line
901, in handle_metrics
metric_fn = metrics_module.get(metric)
File "/Library/Python/2.7/site-packages/keras/metrics.py", line 75, in get
return deserialize(str(identifier))
File "/Library/Python/2.7/site-packages/keras/metrics.py", line 67, in
deserialize
printable_module_name='metric function')
File "/Library/Python/2.7/site-packages/keras/utils/generic_utils.py",
line 164, in deserialize_keras_object
':' + function_name)
ValueError: Unknown metric function:precision
<FATAL> : Failed to load Keras model from file:
model.h5
***> abort program execution
Traceback (most recent call last):
File "classification.py", line 84, in <module>
'H:!V:FilenameModel=model.h5:NumEpochs=20:BatchSize=32')
#:VarTransform=D,G
TypeError: none of the 3 overloaded methods succeeded. Full details:
TMVA::MethodBase* TMVA::Factory::BookMethod(TMVA::DataLoader* loader,
TString theMethodName, TString methodTitle, TString theOption = "") =>
could not convert argument 2
TMVA::MethodBase* TMVA::Factory::BookMethod(TMVA::DataLoader* loader,
TMVA::Types::EMVA theMethod, TString methodTitle, TString theOption = "") =>
FATAL error (C++ exception of type runtime_error)
TMVA::MethodBase* TMVA::Factory::BookMethod(TMVA::DataLoader*,
TMVA::Types::EMVA, TString, TString, TMVA::Types::EMVA, TString) =>
takes at least 6 arguments (4 given)
From the traceback it seems that the problem occurs when you try to load the saved model:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Library/Python/2.7/site-packages/keras/models.py", line 274, in
load_model
sample_weight_mode=sample_weight_mode)
...
ValueError: Unknown metric function:precision
<FATAL> : Failed to load Keras model from file:
model.h5
Take a look at this issue: https://github.com/keras-team/keras/issues/10104
You need to add your custom objects when loading the model. For example:
dependencies = {
'auc_roc': auc_roc
}
model = keras.models.load_model(self.output_directory + 'best_model.hdf5', custom_objects=dependencies)
My suggestion would be implementing your metrics in Keras callback.
Because:
It can achieve the same thing as metrics does.
It can also provide you model saving strategy.
class Checkpoint(keras.callbacks.Callback):
def __init__(self, test_data, filename):
self.test_data = test_data
self.filename = filename
def on_train_begin(self, logs=None):
self.pre = [0.]
self.rec = [0.]
print('Test on %s begins' % self.filename)
def on_train_end(self, logs={}):
print('Best Precison: %s' % max(self.pre))
print('Best Recall: %s' % max(self.rec))
return
def on_epoch_end(self, epoch, logs={}):
x, y = self.test_data
self.pre.append(precision(x, y))
self.rec.append(recall(x, y))
# print your precision or recall as you want
print(...)
# Save your model when a better trained model was found
if pre > max(self.pre):
self.model.save(self.filename, overwrite=True)
print('Higher precision found. Save as %s' % self.filename)
return
after that, you can add your callback to your:
checkpoint = Checkpoint((x_test, y_test), 'precison.h5')
model.compile(loss='categorical_crossentropy', optimizer='adam', callbacks=[checkpoint])
I tested your code in Python 3.6.5, TensorFlow==1.9 and Keras==2.2.2 and it worked. I think the error could be due to Python 2 usage.
import numpy as np
import tensorflow as tf
import keras
import keras.backend as K
from keras.layers import Dense
from keras.models import Sequential, Input, Model
from sklearn import datasets
print(f"TF version: {tf.__version__}, Keras version: {keras.__version__}\n")
# dummy dataset
iris = datasets.load_iris()
x, y_ = iris.data, iris.target
def one_hot(v): return np.eye(len(np.unique(v)))[v]
y = one_hot(y_)
# model
inp = Input(shape=(4,))
dense = Dense(8, activation='relu')(inp)
dense = Dense(16, activation='relu')(dense)
dense = Dense(3, activation='softmax')(dense)
model = Model(inputs=inp, outputs=dense)
# custom metrics
def precision(y_true, y_pred): #taken from old keras source code
true_positives = K.sum(K.round(K.clip(y_true * y_pred, 0, 1)))
predicted_positives = K.sum(K.round(K.clip(y_pred, 0, 1)))
precision = true_positives / (predicted_positives + K.epsilon())
return precision
def recall(y_true, y_pred): #taken from old keras source code
true_positives = K.sum(K.round(K.clip(y_true * y_pred, 0, 1)))
possible_positives = K.sum(K.round(K.clip(y_true, 0, 1)))
recall = true_positives / (possible_positives + K.epsilon())
return recall
# training
model.compile(loss='categorical_crossentropy', optimizer='adam', metrics=['accuracy', precision, recall])
model.fit(x=x, y=y, batch_size=8, epochs=15)
Output:
TF version: 1.9.0, Keras version: 2.2.2
Epoch 1/15
150/150 [==============================] - 0s 2ms/step - loss: 1.2098 - acc: 0.2600 - precision: 0.0000e+00 - recall: 0.0000e+00
Epoch 2/15
150/150 [==============================] - 0s 135us/step - loss: 1.1036 - acc: 0.4267 - precision: 0.0000e+00 - recall: 0.0000e+00
Epoch 3/15
150/150 [==============================] - 0s 132us/step - loss: 1.0391 - acc: 0.5733 - precision: 0.0000e+00 - recall: 0.0000e+00
Epoch 4/15
150/150 [==============================] - 0s 133us/step - loss: 0.9924 - acc: 0.6533 - precision: 0.0000e+00 - recall: 0.0000e+00
Epoch 5/15
150/150 [==============================] - 0s 108us/step - loss: 0.9379 - acc: 0.6667 - precision: 0.0000e+00 - recall: 0.0000e+00
Epoch 6/15
150/150 [==============================] - 0s 134us/step - loss: 0.8802 - acc: 0.6667 - precision: 0.0533 - recall: 0.0067
Epoch 7/15
150/150 [==============================] - 0s 167us/step - loss: 0.8297 - acc: 0.7867 - precision: 0.4133 - recall: 0.0800
Epoch 8/15
150/150 [==============================] - 0s 138us/step - loss: 0.7743 - acc: 0.8200 - precision: 0.9467 - recall: 0.3667
Epoch 9/15
150/150 [==============================] - 0s 161us/step - loss: 0.7232 - acc: 0.7467 - precision: 1.0000 - recall: 0.5667
Epoch 10/15
150/150 [==============================] - 0s 134us/step - loss: 0.6751 - acc: 0.8000 - precision: 0.9733 - recall: 0.6333
Epoch 11/15
150/150 [==============================] - 0s 134us/step - loss: 0.6310 - acc: 0.8867 - precision: 0.9924 - recall: 0.6400
Epoch 12/15
150/150 [==============================] - 0s 131us/step - loss: 0.5844 - acc: 0.8867 - precision: 0.9759 - recall: 0.6600
Epoch 13/15
150/150 [==============================] - 0s 111us/step - loss: 0.5511 - acc: 0.9133 - precision: 0.9759 - recall: 0.6533
Epoch 14/15
150/150 [==============================] - 0s 134us/step - loss: 0.5176 - acc: 0.9000 - precision: 0.9403 - recall: 0.6733
Epoch 15/15
150/150 [==============================] - 0s 134us/step - loss: 0.4899 - acc: 0.8667 - precision: 0.8877 - recall: 0.6733
