What am I doing wrong with using scikit-learn from nltk to check the accuracy of the naive bayes classifier?
...readFile definition not needed
#divide the data into training and testing sets
data = readFile('Data_test/')
training_set = list_nltk[:2000000]
testing_set = list_nltk[2000000:]
#applied Bag of words as a way to select and extract feature
count_vect = CountVectorizer()
X_train_counts = count_vect.fit_transform(training_set.split('\n'))
#apply tfd
tf_transformer = TfidfTransformer(use_idf=False).fit(X_train_counts)
X_train_tf = tf_transformer.transform(X_train_counts)
#Train the data
clf = MultinomialNB().fit(X_train_tf, training_set.split('\n'))
#now test the accuracy of the naive bayes classifier
test_data_features = count_vect.transform(testing_set)
X_new_tfidf = tf_transformer.transform(test_data_features)
predicted = clf.predict(X_new_tfidf)
print "%.3f" % nltk.classify.accuracy(clf, predicted)
The problem is when I print the nltk.classify.accuracy, it takes forever and I am suspecting this is because I have done something wrong but since I get no error, I can't figure out what it is that is wrong.
Use instead the accuracy_score of the sklearn metrics.
>>> from sklearn.metrics import accuracy_score
>>> y_pred = [0, 2, 1, 3]
>>> y_true = [0, 1, 2, 3]
>>> accuracy_score(y_true, y_pred)
0.5
I think you're mixing some things about Supervised Learning.See this answer and try to understand the top of this page.
Your data should be in this form (before doing the Vectorization) :
X = [["The cat is sleeping"], ..., ["The man is dead"]]
Y = [1, ..., 0]
Your have an error at least in this line
clf = MultinomialNB().fit(X_train_tf, training_set.split('\n'))
You need to have your training labels and vectorized data in there but you have the original and vectorized data.
It should look like this:
clf = MultinomialNB().fit(X_train_tf, y_train)
But you don't even have the label y_train data anywhere in your code as far I can tell.
Related
I'm trying to use the TensorFlow's Boston housing price example to learn how to use TensorFlow/Keras for regressions, but I keep running into a problem using my own data, even when I make as small of changes as possible. After giving up on writing everything myself, I simply changed the two lines of the code that input the data:
boston_housing = keras.datasets.boston_housing
(train_data, train_labels), (test_data, test_labels) = boston_housing.load_data()
to something that, after looking online, should also create numpy arrays from my csv:
np_array = genfromtxt('trainingdata.csv', delimiter=',')
np_array = np.delete(np_array, (0), axis=0) # Remove header
test_np_array = np_array[:800,:]
tr_np_array = np_array[800:,:] # Separate out test and train data
train_labels = tr_np_array[:, 20] # Get the last row for the labels
test_labels = test_np_array[:, 20]
train_data = np.delete(tr_np_array, (20), axis=1)
test_data = np.delete(test_np_array, (20), axis=1) # Remove the last row so the data is only the features
Everything I can look at seems right – the shapes of the arrays are all correct, the arrays do seem to be correct-looking numpy arrays, the features do seem to become normalized, etc. and yet when I set verbose to 1 on model.fit(...), the very first lines of output show a problem with loss:
Epoch 1/500
32/2560 [..............................] - ETA: 18s - loss: nan - mean_absolute_error: nan
2016/2560 [======================>.......] - ETA: 0s - loss: nan - mean_absolute_error: nan
2560/2560 [==============================] - 0s 133us/step - loss: nan - mean_absolute_error: nan - val_loss: nan - val_mean_absolute_error: nan
I'm especially confused because every other place on stack overflow where I've seen the "TensorFlow loss is 'NaN'" error, it has generally a) been with a custom loss function, and b) once the model has trained for a while, not (as here) within the first 52 passes. Where that's not the case, it's because the data wasn't normalized, but I do that later in the code, and the normalization works for the housing pricing example and prints out numbers clustered around 0. At this point, my best guess is that it's a problem with the genfromtxt command, but if anyone can see what I'm doing wrong or where I might find my issue, I'd be incredibly appreciative.
Edit:
Here is the full code for the program. Commenting out lines 13 through 26 and uncommenting lines 10 and 11 make the program work perfectly. Commenting out lines 13 and 14 and uncommenting 16 and 17 was my attempt at using pandas, but that led to the same errors.
import tensorflow as tf
from tensorflow import keras
import numpy as np
from numpy import genfromtxt
import pandas as pd
print(tf.__version__)
# boston_housing = keras.datasets.boston_housing # Line 10
# (train_data, train_labels), (test_data, test_labels) = boston_housing.load_data()
np_array = genfromtxt('trainingdata.csv', delimiter=',') # Line 13
np_array = np.delete(np_array, (0), axis=0)
# df = pd.read_csv('trainingdata.csv') # Line 16
# np_array = df.get_values()
test_np_array = np_array[:800,:]
tr_np_array = np_array[800:,:]
train_labels = tr_np_array[:, 20]
test_labels = test_np_array[:, 20]
train_data = np.delete(tr_np_array, (20), axis=1)
test_data = np.delete(test_np_array, (20), axis=1) # Line 26
order = np.argsort(np.random.random(train_labels.shape))
train_data = train_data[order]
train_labels = train_labels[order]
mean = train_data.mean(axis=0)
std = train_data.std(axis=0)
train_data = (train_data - mean) / std
test_data = (test_data - mean) / std
labels_mean = train_labels.mean(axis=0)
labels_std = train_labels.std(axis=0)
train_labels = (train_labels - labels_mean) / labels_std
test_labels = (test_labels - labels_mean) / labels_std
def build_model():
model = keras.Sequential([
keras.layers.Dense(64, activation=tf.nn.relu,
input_shape=(train_data.shape[1],)),
keras.layers.Dense(64, activation=tf.nn.relu),
keras.layers.Dense(1)
])
optimizer = tf.train.RMSPropOptimizer(0.001)
model.compile(loss='mse',
optimizer=optimizer,
metrics=['mae'])
return model
model = build_model()
model.summary()
EPOCHS = 500
early_stop = keras.callbacks.EarlyStopping(monitor='val_loss', patience=20)
history = model.fit(train_data, train_labels, epochs=EPOCHS,
validation_split=0.2, verbose=1,
callbacks=[early_stop])
[loss, mae] = model.evaluate(test_data, test_labels, verbose=0)
print("Testing set Mean Abs Error: ${:7.2f}".format(mae * 1000 * labels_std))
I need help in understanding the accuracy and dataset output format for Deep Learning model.
I did some training for deep learning based on this site : https://machinelearningmastery.com/deep-learning-with-python2/
I did the example for pima-indian-diabetes dataset, and iris flower dataset. I train my computer for pima-indian-diabetes dataset using script from this : http://machinelearningmastery.com/tutorial-first-neural-network-python-keras/
Then I train my computer for iris-flower dataset using below script.
# import package
import numpy
from pandas import read_csv
from keras.models import Sequential
from keras.layers import Dense
from keras.wrappers.scikit_learn import KerasClassifier
from keras.utils import np_utils
from sklearn.model_selection import cross_val_score, KFold
from sklearn.preprocessing import LabelEncoder
from sklearn.pipeline import Pipeline
from keras.callbacks import ModelCheckpoint
# fix random seed for reproductibility
seed = 7
numpy.random.seed(seed)
# load dataset
dataframe = read_csv("iris_2.csv", header=None)
dataset = dataframe.values
X = dataset[:,0:4].astype(float)
Y = dataset[:,4]
# encode class value as integers
encoder = LabelEncoder()
encoder.fit(Y)
encoded_Y = encoder.transform(Y)
### one-hot encoder ###
dummy_y = np_utils.to_categorical(encoded_Y)
# define base model
def baseline_model():
# create model
model = Sequential()
model.add(Dense(4, input_dim=4, init='normal', activation='relu'))
model.add(Dense(3, init='normal', activation='sigmoid'))
# Compile model
model.compile(loss='categorical_crossentropy', optimizer='adam', metrics=['accuracy'])
model_json = model.to_json()
with open("iris.json", "w") as json_file:
json_file.write(model_json)
model.save_weights('iris.h5')
return model
estimator = KerasClassifier(build_fn=baseline_model, nb_epoch=1000, batch_size=6, verbose=0)
kfold = KFold(n_splits=10, shuffle=True, random_state=seed)
results = cross_val_score(estimator, X, dummy_y, cv=kfold)
print("Accuracy: %.2f%% (%.2f%%)" % (results.mean()*100, results.std()*100))
Everything works fine until I decided to try on other dataset from this link : https://archive.ics.uci.edu/ml/datasets/Glass+Identification
At first I train this new dataset using the pime-indian-diabetes dataset script's example and change the value for X and Y variable to this
dataset = numpy.loadtxt("glass.csv", delimiter=",")
X = dataset[:,0:10]
Y = dataset[:,10]
and also the value for the neuron layer to this
model = Sequential()
model.add(Dense(10, input_dim=10, init='uniform', activation='relu'))
model.add(Dense(10, init='uniform', activation='relu'))
model.add(Dense(1, init='uniform', activation='sigmoid'))
the result produce accuracy = 32.71%
Then I changed the output column of this dataset which is originally in integer (1~7) to string (a~g) and use the example's script for the iris-flower dataset by doing some modification to it
import numpy
from pandas import read_csv
from keras.models import Sequential
from keras.layers import Dense
from keras.wrappers.scikit_learn import KerasClassifier
from sklearn.model_selection import cross_val_score
from sklearn.preprocessing import LabelEncoder
from sklearn.model_selection import StratifiedKFold
from sklearn.preprocessing import StandardScaler
from sklearn.pipeline import Pipeline
seed = 7
numpy.random.seed(seed)
dataframe = read_csv("glass.csv", header=None)
dataset = dataframe.values
X = dataset[:,0:10].astype(float)
Y = dataset[:,10]
encoder = LabelEncoder()
encoder.fit(Y)
encoded_Y = encoder.transform(Y)
def create_baseline():
model = Sequential()
model.add(Dense(10, input_dim=10, init='normal', activation='relu'))
model.add(Dense(1, init='normal', activation='sigmoid'))
model.compile(loss='binary_crossentropy', optimizer='adam', metrics=['accuracy'])
model_json = model.to_json()
with open("glass.json", "w") as json_file:
json_file.write(model_json)
model.save_weights('glass.h5')
return model
estimator = KerasClassifier(build_fn=create_baseline, nb_epoch=1000, batch_size=10, verbose=0)
kfold = StratifiedKFold(n_splits=10, shuffle=True, random_state=seed)
results = cross_val_score(estimator, X, encoded_Y, cv=kfold)
print("Baseline: %.2f%% (%.2f%%)" % (results.mean()*100, results.std()*100))
I did not use 'dummy_y' variable as refer to this tutorial : http://machinelearningmastery.com/binary-classification-tutorial-with-the-keras-deep-learning-library/
I check that the dataset using alphabet as the output and thinking that maybe I can reuse that script to train the new glass dataset that I modified.
This time the results become like this
Baseline : 68.42% (3.03%)
From the article, that 68% and 3% means the mean and standard deviation of model accuracy.
My 1st question is when do I use integer or alphabet as the output column? and is this kind of accuracy result common when we tempered with the dataset like changing the output from integer to string/alphabet?
My 2nd question is how do I know how many neuron I have to put for each layer? Is it related to what backend I use when compiling the model(Tensorflow or Theano)?
Thank you in advance.
First question
It doesn't matter, as you can see here:
Y = range(10)
encoder = LabelEncoder()
encoder.fit(Y)
encoded_Y = encoder.transform(Y)
print encoded_Y
Y = ['a', 'b', 'c', 'd', 'e', 'f','g','h','i','j']
encoder = LabelEncoder()
encoder.fit(Y)
encoded_Y = encoder.transform(Y)
print encoded_Y
results:
[0 1 2 3 4 5 6 7 8 9]
[0 1 2 3 4 5 6 7 8 9]
Which means that your classifier sees exactly the same labels.
Second question
There is no absolutely correct answer for this question, but for sure it does not depend on your backend.
You should try and experiment with different number of neurons, number of layers, types of layers and all other network parameters in order to understand what is the best architecture to your problem.
With experience you will develop both a good intuition as for what parameters will be better for which type of problems as well as a good method for the experimentation.
The best rule of thumb (assuming you have the dataset required to sustain such a strategy) I've heard is "Make your network as large as you can until it overfit, add regularization until it does not overfit - repeat".
Per parts. First, if your output includes values of [0, 5] it is
impossible that using the sigmoid activation you can obtain that.
The sigmoid function has a range of [0, 1]. You could use an
activation = linear (without activation). But I think it's a bad approach because your problem is not to estimate a continuous value.
Second, the question you should ask yourself is not so much the type
of data you are using (in the sense of how you store the
information). Is it a string? Is it an int? Is it a float? It does
not matter, but you have to ask what kind of problem you are trying
to solve.
In this case, the problem should not be treated as a regression
(estimate a continuous value). Because your output are categorical,
numbers but categorical. Really you want to classifying between:
Type of glass: (class attribute).
When do a classification problem the following configuration is
"normally" used:
The class is encoded by one-hot encoding. It is nothing more than a vector of 0's and a single one in the corresponding class.
For instance: class 3 (0 count) and have 6 classes -> [0, 0, 0, 1, 0, 0] (as many zeros as classes you have).
As you see now, we dont have a single output, your model must be as outputs as your Y (6 classes). That way the last layer should
have as many neurons as classes. Dense (classes, ...).
You are also interested in the fact that the output is the probability of belonging to each class, that is: p (y = class_0),
... p (y_class_n). For this, the softmax activation layer is used,
which is to ensure that the sum of all the probabilities is 1.
You have to change the loss for the categorical_crossentropy so that it is able to work together with the softmax. And use the metric categorical_accuracy.
seed = 7
numpy.random.seed(seed)
dataframe = read_csv("glass.csv", header=None)
dataset = dataframe.values
X = dataset[:,0:10].astype(float)
Y = dataset[:,10]
encoder = LabelEncoder()
encoder.fit(Y)
from keras.utils import to_categorical
encoded_Y = to_categorical(encoder.transform(Y))
def create_baseline():
model = Sequential()
model.add(Dense(10, input_dim=10, init='normal', activation='relu'))
model.add(Dense(encoded_Y.shape[1], init='normal', activation='softmax'))
model.compile(loss='categorical_crossentropy', optimizer='adam', metrics=['categorical_accuracy'])
model_json = model.to_json()
with open("glass.json", "w") as json_file:
json_file.write(model_json)
model.save_weights('glass.h5')
return model
model = create_baseline()
model.fit(X, encoded_Y, epochs=1000, batch_size=100)
The number of neurons does not depend on the backend you use.
But if it is true that you will never have the same results. That's
because there are enough stochastic processes within a network:
initialization, dropout (if you use), batch order, etc.
What is known is that expanding the number of neurons per dense
makes the model more complex and therefore has more potential to
represent your problem but is more difficult to learn and more
expensive both in time and in calculations. That way you always have
to look for a balance.
At the moment there is no clear evidence that it is better:
expand the number of neurons per layer.
add more layers.
There are models that use one architecture and others the other.
Using this architecture you get the following result:
Epoch 1000/1000
214/214 [==============================] - 0s 17us/step - loss: 0.0777 - categorical_accuracy: 0.9953
Using this architecture you get the following result:
I am new to Machine Learning. I am working on document classification.
For that I am trying to train SVM on a subset of "20 newsgroup" dataset.
I am using scikit learn for this.
link: SVM - Scikit Learn
As a training set I have taken 3 categories of news and 40 documents in each category.
For each document, I have done the following so far:
tokenization
removing stop words (i.e. 'the','on','in' etc.)
lemmatization (stemming words) (i.e. 'runs','running','ran' = 'run')
calculating tf-idf score for the remaining words
(labels[ ]:list containing category labels for each document)
(final_list[ ]: list containing list of words and their tf-idf scores for each documents. i.e.
final_list=[
[['run',0.16544],['ground',0.1224]...]
[['disk',0.9677],['pc',0.8888]....]
.....
.....
])
As other classifiers, SVC, NuSVC, and LinearSVC take as input two arrays:
an array X of size [n_samples, n_features] holding the training samples,
and an array y of class labels (strings or integers), size [n_samples]:
Sample code from Scikit Learn webpage:(for numeric data)
>>> from sklearn import svm
>>> X = [[0, 0], [1, 1]]
>>> y = [0, 1]
>>> clf = svm.SVC()
>>> clf.fit(X, y)
SVC(C=1.0, cache_size=200, class_weight=None, coef0=0.0,
decision_function_shape=None, degree=3, gamma='auto', kernel='rbf',
max_iter=-1, probability=False, random_state=None, shrinking=True,
tol=0.001, verbose=False)
After being fitted, the model can then be used to predict new values:
>>> clf.predict([[2., 2.]])
array([1])
Now when I am using the following lines:
>>> from sklearn import svm
>>> clf = svm.SVC()
>>> clf.fit(final_list, labels)
it is giving,
ValueError: setting an array element with a sequence.
I am not sure what parameters to pass to svm function for my problem statement.
In order to split my data into train and test data separately, I'm using
sklearn.cross_validation.train_test_split function.
When I supply my data and labels as list of lists to this function, it returns train and test data in two separate lists.
I want to get the indices of the train and test data elements from the original data list.
Can anyone help me out with this?
Thanks in advance
You can supply the index vector as an additional argument. Using the example from sklearn:
import numpy as np
from sklearn.cross_validation import train_test_split
X, y,indices = (0.1*np.arange(10)).reshape((5, 2)),range(10,15),range(5)
X_train, X_test, y_train, y_test,indices_train,indices_test = train_test_split(X, y,indices, test_size=0.33, random_state=42)
indices_train,indices_test
#([2, 0, 3], [1, 4])
Try the below solutions (depending on whether you have imbalance):
NUM_ROWS = train.shape[0]
TEST_SIZE = 0.3
indices = np.arange(NUM_ROWS)
# usual train-val split
train_idx, val_idx = train_test_split(indices, test_size=TEST_SIZE, train_size=None)
# stratified train-val split as per Response's proportion (if imbalance)
strat_train_idx, strat_val_idx = train_test_split(indices, test_size=TEST_SIZE, stratify=y)
I'm getting the following warning repeatedly when using GridsearchCV in Sklearn
"DataConversionWarning: Copying input dataframe for slicing."
I tried running some of the models separately outside of Gridsearch and didn't get any warnings. It also didn't prevent Gridsearch from finding a model.
I have 2 Questions:
1) What does this error mean?
2) What are the implications for my output, if any?
The relevant parts of the code are below:
df = pd.read_csv(os.path.join(filepath, "Modeling_Set.csv")) #loads main data
keep_vars = pd.read_csv(os.path.join(filepath, "keep_vars.csv")) #loads a list of variables to keep from a CSV list
model_vars = keep_vars[keep_vars['keep']==1]['name'] #creates a list of vars to keep
modeling_df = df[model_vars] #creates the df with only keep vars
model_feature_vars = model_vars[:-1]
#Splits test and train data
X_train, X_test, y_train, y_test = train_test_split(modeling_df[model_feature_vars], modeling_df['Segment'], test_size=0.30, random_state=42)
#sets up models
#Range of parameters for gridsearch with decision trees
max_depth = range(2,20,2)
min_samples_split = range(2,10,2)
features = range(2, len(X_train.columns))
#set up for decision trees with gridsearch
parametersDT ={'feature_selection__k':features,
'feature_selection__score_func':(chi2, f_classif),
'classification__criterion':('gini','entropy'),
'classification__max_depth':max_depth,
'classification__min_samples_split':min_samples_split}
DT_with_K_Best = Pipeline([
('feature_selection', SelectKBest()),
('classification', DecisionTreeClassifier())
])
clf_DT = GridSearchCV(DT_with_K_Best, parametersDT, cv=10, verbose=2, scoring='f1_weighted', n_jobs = -2)
clf_DT.fit(X_train,y_train)
As far as I can tell it only means that the DataFrame you're using is copied before being fed to the model.
This shouldn't affect the training results. It's only an efficiency problem, unrelated to the performance of the classifier.