I used the code below to train my model.
# Data Preparation
objDataset = pd.read_csv('objdbase.csv')
X = objDataset.drop(columns=['Substance'])
y = objDataset['Substance']
# Prediction
def predicts(fingerprint):
models = DecisionTreeClassifier()
models.fit(X, y)
predictions = models.predict([fingerprint])
print(f'The substance is likely {predictions}')
I want the model, if it receives a dataset that is not among the ones in the database, to say something like: "Target not recognized". How do I modify the algorithm to be able to perform that?
The prediction will give you the probability of a certain result.
A model is not a method to check if something exists or not
I am new in Keras and I learned fitting and evaluating the model.
After evaluating the model one can see the actual predictions made by model.
I am wondering Is it also possible to see the predictions during fitting in Keras? Till now I cant find any code doing this.
Since this question doesn't specify "epochs", and since using callbacks may represent extra computation, I don't think it's exactly a duplication.
With tensorflow, you can use a custom training loop with eager execution turned on. A simple tutorial for creating a custom training loop: https://www.tensorflow.org/tutorials/eager/custom_training_walkthrough
Basically you will:
#transform your data in to a Dataset:
dataset = tf.data.Dataset.from_tensor_slices(
(x_train, y_train)).shuffle(some_buffer).batch(batchSize)
#the above is buggy in some versions regarding shuffling, you may need to shuffle
#again between each epoch
#create an optimizer
optimizer = tf.keras.optimizers.Adam()
#create an epoch loop:
for e in range(epochs):
#create a batch loop
for i, (x, y_true) in enumerate(dataset):
#create a tape to record actions
with tf.GradientTape() as tape:
#take the model's predictions
y_pred = model(x)
#calculate loss
loss = tf.keras.losses.binary_crossentropy(y_true, y_pred)
#calculate gradients
gradients = tape.gradient(loss, model.trainable_weights)
#apply gradients
optimizer.apply_gradients(zip(gradients, model.trainable_weights)
You can use the y_pred var for doing anything, including getting its numpy_pred = y_pred.numpy() value.
The tutorial gives some more details about metrics and validation loop.
Usually the learning cycle contains:
optim.zero_grad()
loss(m, op).backward()
optim.step()
But what should be the cycle when the data does not fit in the graphics card?
First option:
for ip, op in DataLoader(TensorDataset(inputs, outputs),
batch_size=int(1e4), pin_memory=True):
m = model(ip.to(dev))
op = op.to(dev)
optim.zero_grad()
loss(m, op).backward()
optim.step()
Second option:
optim.zero_grad()
for ip, op in DataLoader(TensorDataset(inputs, outputs),
batch_size=int(1e4), pin_memory=True):
m = model(ip.to(dev))
op = op.to(dev)
loss(m, op).backward()
optim.step()
The third option:
Accumulate gradients after calling backward().
The first option is correct and corresponds to batch gradient descent.
The second option will not work because m and op are being overwritten at each step, so your optimizer step will only correspond to optimizing based on the final batch.
The proper way of training a model using Stochastic Gradient Descent (SGD) is following these steps:
instantiate a model, and randomly init its weights. This is done only once.
instantiate the dataset and the dataloader, defining appropriate batch_size.
Iterate over the all examples, batch by batch. At each iteration
3.a Compute a stochastic estimate of the loss using only a batch, rather than the entire set (aka "forward pass")
3.b Compute the gradient of the loss w.r.t the model's parameters (aka "backward pass")
3.c Update the weights based on the current gradient
This is how the code should look like
model = MyModel(...) # instantiate a model once
dl = DataLoader(TensorDataset(inputs, outputs), batch_size=int(1e4), pin_memory=True)
for ei in range(num_epochs):
for ip, op in dl:
optim.zero_grad()
predict = model(ip.to(dev)) # forward pass
loss = criterion(predict, op.to(dev)) # estimate current loss
loss.backward() # backward pass - propagate gradients
optim.step() # update the weights based on current batch
Note that during training you iterate several times over the entire training set. Each such iteration is usually referred to as an "epoch".
I'm implementing a Multilayer Perceptron in Keras and using scikit-learn to perform cross-validation. For this, I was inspired by the code found in the issue Cross Validation in Keras
from sklearn.cross_validation import StratifiedKFold
def load_data():
# load your data using this function
def create model():
# create your model using this function
def train_and_evaluate__model(model, data[train], labels[train], data[test], labels[test)):
# fit and evaluate here.
if __name__ == "__main__":
X, Y = load_model()
kFold = StratifiedKFold(n_splits=10)
for train, test in kFold.split(X, Y):
model = None
model = create_model()
train_evaluate(model, X[train], Y[train], X[test], Y[test])
In my studies on neural networks, I learned that the knowledge representation of the neural network is in the synaptic weights and during the network tracing process, the weights that are updated to thereby reduce the network error rate and improve its performance. (In my case, I'm using Supervised Learning)
For better training and assessment of neural network performance, a common method of being used is cross-validation that returns partitions of the data set for training and evaluation of the model.
My doubt is...
In this code snippet:
for train, test in kFold.split(X, Y):
model = None
model = create_model()
train_evaluate(model, X[train], Y[train], X[test], Y[test])
We define, train and evaluate a new neural net for each of the generated partitions?
If my goal is to fine-tune the network for the entire dataset, why is it not correct to define a single neural network and train it with the generated partitions?
That is, why is this piece of code like this?
for train, test in kFold.split(X, Y):
model = None
model = create_model()
train_evaluate(model, X[train], Y[train], X[test], Y[test])
and not so?
model = None
model = create_model()
for train, test in kFold.split(X, Y):
train_evaluate(model, X[train], Y[train], X[test], Y[test])
Is my understanding of how the code works wrong? Or my theory?
If my goal is to fine-tune the network for the entire dataset
It is not clear what you mean by "fine-tune", or even what exactly is your purpose for performing cross-validation (CV); in general, CV serves one of the following purposes:
Model selection (choose the values of hyperparameters)
Model assessment
Since you don't define any search grid for hyperparameter selection in your code, it would seem that you are using CV in order to get the expected performance of your model (error, accuracy etc).
Anyway, for whatever reason you are using CV, the first snippet is the correct one; your second snippet
model = None
model = create_model()
for train, test in kFold.split(X, Y):
train_evaluate(model, X[train], Y[train], X[test], Y[test])
will train your model sequentially over the different partitions (i.e. train on partition #1, then continue training on partition #2 etc), which essentially is just training on your whole data set, and it is certainly not cross-validation...
That said, a final step after the CV which is often only implied (and frequently missed by beginners) is that, after you are satisfied with your chosen hyperparameters and/or model performance as given by your CV procedure, you go back and train again your model, this time with the entire available data.
You can use wrappers of the Scikit-Learn API with Keras models.
Given inputs x and y, here's an example of repeated 5-fold cross-validation:
from sklearn.model_selection import RepeatedKFold, cross_val_score
from tensorflow.keras.models import *
from tensorflow.keras.layers import *
from tensorflow.keras.wrappers.scikit_learn import KerasRegressor
def buildmodel():
model= Sequential([
Dense(10, activation="relu"),
Dense(5, activation="relu"),
Dense(1)
])
model.compile(optimizer='adam', loss='mse', metrics=['mse'])
return(model)
estimator= KerasRegressor(build_fn=buildmodel, epochs=100, batch_size=10, verbose=0)
kfold= RepeatedKFold(n_splits=5, n_repeats=100)
results= cross_val_score(estimator, x, y, cv=kfold, n_jobs=2) # 2 cpus
results.mean() # Mean MSE
I think many of your questions will be answered if you read about nested cross-validation. This is a good way to "fine tune" the hyper parameters of your model. There's a thread here:
https://stats.stackexchange.com/questions/65128/nested-cross-validation-for-model-selection
The biggest issue to be aware of is "peeking" or circular logic. Essentially - you want to make sure that none of data used to assess model accuracy is seen during training.
One example where this might be problematic is if you are running something like PCA or ICA for feature extraction. If doing something like this, you must be sure to run PCA on your training set, and then apply the transformation matrix from the training set to the test set.
The main idea of testing your model performance is to perform the following steps:
Train a model on a training set.
Evaluate your model on a data not used during training process in order to simulate a new data arrival.
So basically - the data you should finally test your model should mimic the first data portion you'll get from your client/application to apply your model on.
So that's why cross-validation is so powerful - it makes every data point in your whole dataset to be used as a simulation of new data.
And now - to answer your question - every cross-validation should follow the following pattern:
for train, test in kFold.split(X, Y
model = training_procedure(train, ...)
score = evaluation_procedure(model, test, ...)
because after all, you'll first train your model and then use it on a new data. In your second approach - you cannot treat it as a mimicry of a training process because e.g. in second fold your model would have information kept from the first fold - which is not equivalent to your training procedure.
Of course - you could apply a training procedure which uses 10 folds of consecutive training in order to finetune network. But this is not cross-validation then - you'll need to evaluate this procedure using some kind of schema above.
The commented out functions make this a little less obvious, but the idea is to keep track of your model performance as you iterate through your folds and at the end provide either those lower level performance metrics or an averaged global performance. For example:
The train_evaluate function ideally would output some accuracy score for each split, which could be combined at the end.
def train_evaluate(model, x_train, y_train, x_test, y_test):
model.fit(x_train, y_train)
return model.score(x_test, y_test)
X, Y = load_model()
kFold = StratifiedKFold(n_splits=10)
scores = np.zeros(10)
idx = 0
for train, test in kFold.split(X, Y):
model = create_model()
scores[idx] = train_evaluate(model, X[train], Y[train], X[test], Y[test])
idx += 1
print(scores)
print(scores.mean())
So yes you do want to create a new model for each fold as the purpose of this exercise is to determine how your model as it is designed performs on all segments of the data, not just one particular segment that may or may not allow the model to perform well.
This type of approach becomes particularly powerful when applied along with a grid search over hyperparameters. In this approach you train a model with varying hyperparameters using the cross validation splits and keep track of the performance on splits and overall. In the end you will be able to get a much better idea of which hyperparameters allow the model to perform best. For a much more in depth explanation see sklearn Model Selection and pay particular attention to the sections of Cross Validation and Grid Search.
The general idea I am trying to realize is a seq2seq-model (taken from the translate.py-example in the models, based on the seq2seq-class). This trains well.
Furthermore I am using the hidden state of the rnn after all the encoding is done, right before decoding starts (I call it the “hidden state at end of encoding”). I use this hidden state at end of encoding to feed it into a further sub-graph which I call “prices” (see below). The training gradients of this sub-graph backprop not only through this additional sub-graph, but also back into the encoder-part of the rnn (which is what I want and need).
The plan is to add more such sub-graph to the hidden state at end of encoding, as I want to analyze the input phrases in a variety of ways.
Now during training when I evaluate and train both sub-graphs (encoder+prices AND encoder+decoder) at the same time, the net does NOT converge. However, if I train by executing the training in the following way (pseudo-code):
if global_step % 10 == 0:
execute-the-price-training_code
else:
execute-the-decoder-training_code
So I am not training both sub-graphs simultaneously. Now it does converge, but the encoder+decoder-part converges MUCH slower than if I ONLY train this part and never train the prices-sub-graph.
My question is: I should be able to train both sub-graphs simultaneously. But probably I have to rescale the gradients flowing back into the hidden state at end of encoding. Here we get the gradients from the prices sub-graph AND from the decoder-sub-graph. How should this rescaling be done. I didnt find any papers describing such an undertaking, but maybe I am searching with the wrong keywords.
Here is the training-part of the code:
This is the (almost original) training-op-preparation:
if not forward_only:
self.gradient_norms = []
self.updates = []
opt = tf.train.AdadeltaOptimizer(self.learning_rate)
for bucket_id in xrange(len(buckets)):
tf.scalar_summary("seq2seq loss", self.losses[bucket_id])
gradients = tf.gradients(self.losses[bucket_id], var_list_seq2seq)
clipped_gradients, norm = tf.clip_by_global_norm(gradients, max_gradient_norm)
self.gradient_norms.append(norm)
self.updates.append(opt.apply_gradients(zip(clipped_gradients, var_list_seq2seq), global_step=self.global_step))
Now, additionally, I am running a second sub-graph that takes the hidden state at end of encoding as input:
with tf.name_scope('prices') as scope:
#First layer
W_price_first_layer = tf.Variable(tf.random_normal([num_layers*size, self.prices_hidden_layer_size], stddev=0.35), name="W_price_first_layer")
B_price_first_layer = tf.Variable(tf.zeros([self.prices_hidden_layer_size]), name="B_price_first_layer")
self.output_price_first_layer = tf.add(tf.matmul(self.hidden_state, W_price_first_layer), B_price_first_layer)
self.activation_price_first_layer = tf.nn.sigmoid(self.output_price_first_layer)
#self.activation_price_first_layer = tf.nn.Relu(self.output_price_first_layer)
#Second layer to softmax (price ranges)
W_price = tf.Variable(tf.random_normal([self.prices_hidden_layer_size, self.prices_bit_size], stddev=0.35), name="W_price")
W_price_t = tf.transpose(W_price)
B_price = tf.Variable(tf.zeros([self.prices_bit_size]), name="B_price")
self.output_price_second_layer = tf.add(tf.matmul(self.activation_price_first_layer, W_price),B_price)
self.price_prediction = tf.nn.softmax(self.output_price_second_layer)
self.label_price = tf.placeholder(tf.int32, shape=[self.batch_size], name="price_label")
#Remember the prices trainables
var_list_prices = tf.get_collection(tf.GraphKeys.TRAINABLE_VARIABLES, "prices")
var_list_all = tf.trainable_variables()
#Backprop
self.loss_price = tf.nn.sparse_softmax_cross_entropy_with_logits(self.output_price_second_layer, self.label_price)
self.loss_price_scalar = tf.reduce_mean(self.loss_price)
self.optimizer_price = tf.train.AdadeltaOptimizer(self.learning_rate_prices)
self.training_op_price = self.optimizer_price.minimize(self.loss_price, var_list=var_list_all)
Thx a bunch
I expect that running two optimizers simultaneously will lead to inconsistent gradient updates on the common variables, and this might be causing your training not to converge.
Instead, if you add the scalar loss from each sub-network to the "losses collection" (e.g. via tf.contrib.losses.add_loss() or tf.add_to_collection(tf.GraphKeys.LOSSES, ...), you can use tf.contrib.losses.get_total_loss() to get a single loss value that can be passed to a single standard TensorFlow tf.train.Optimizer subclass. TensorFlow will derive the appropriate back-prop computation for your split network.
The get_total_loss() method simply computes an unweighted sum of the values that have been added to the losses collection. I'm not familiar with the literature on how or if you should scale these values, but you can use any arbitrary (differentiable) TensorFlow expression to combine the losses and pass the result to a single optimizer.