Python naive_bayes.GaussianNB类代码示例

def selectKBest(previous_result, data):
	# remove 'restricted_stock_deferred' and 'director_fees'
	previous_result.pop(4)
	previous_result.pop(4)

	result = []
	_k = 10
	for k in range(0,_k):
		feature_list = ['poi']
		for n in range(0,k+1):
			feature_list.append(previous_result[n][0])

		data = featureFormat(my_dataset, feature_list, sort_keys = True, remove_all_zeroes = False)
		labels, features = targetFeatureSplit(data)
		features = [abs(x) for x in features]
		from sklearn.cross_validation import StratifiedShuffleSplit
		cv = StratifiedShuffleSplit(labels, 1000, random_state = 42)
		features_train = []
		features_test  = []
		labels_train   = []
		labels_test    = []
		for train_idx, test_idx in cv:
			for ii in train_idx:
				features_train.append( features[ii] )
				labels_train.append( labels[ii] )
			for jj in test_idx:
				features_test.append( features[jj] )
				labels_test.append( labels[jj] )
		from sklearn.naive_bayes import GaussianNB
		clf = GaussianNB()
		clf.fit(features_train, labels_train)
		predictions = clf.predict(features_test)
		score = score_func(labels_test,predictions)
		result.append((k+1,score[0],score[1],score[2]))
	return result

def test_gnb_sample_weight():
    """Test whether sample weights are properly used in GNB. """
    # Sample weights all being 1 should not change results
    sw = np.ones(6)
    clf = GaussianNB().fit(X, y)
    clf_sw = GaussianNB().fit(X, y, sw)

    assert_array_almost_equal(clf.theta_, clf_sw.theta_)
    assert_array_almost_equal(clf.sigma_, clf_sw.sigma_)

    # Fitting twice with half sample-weights should result
    # in same result as fitting once with full weights
    sw = rng.rand(y.shape[0])
    clf1 = GaussianNB().fit(X, y, sample_weight=sw)
    clf2 = GaussianNB().partial_fit(X, y, classes=[1, 2], sample_weight=sw / 2)
    clf2.partial_fit(X, y, sample_weight=sw / 2)

    assert_array_almost_equal(clf1.theta_, clf2.theta_)
    assert_array_almost_equal(clf1.sigma_, clf2.sigma_)

    # Check that duplicate entries and correspondingly increased sample
    # weights yield the same result
    ind = rng.randint(0, X.shape[0], 20)
    sample_weight = np.bincount(ind, minlength=X.shape[0])

    clf_dupl = GaussianNB().fit(X[ind], y[ind])
    clf_sw = GaussianNB().fit(X, y, sample_weight)

    assert_array_almost_equal(clf_dupl.theta_, clf_sw.theta_)
    assert_array_almost_equal(clf_dupl.sigma_, clf_sw.sigma_)

	def scikitNBClassfier(self):
		dataMat, labels = self.loadProcessedData()
		bayesian = Bayesian()
		myVocabList = bayesian.createVocabList(dataMat)
		## 建立bag of words 矩阵
		trainMat = []
		for postinDoc in dataMat:
			trainMat.append(bayesian.setOfWords2Vec(myVocabList, postinDoc))

		from sklearn.naive_bayes import GaussianNB

		gnb = GaussianNB()
		X = array(trainMat)
		y = labels

		testText = "美国军队的军舰今天访问了巴西港口城市，并首次展示了核潜艇攻击能力，飞机，监听。他们表演了足球。"
		testEntry = self.testEntryProcess(testText)

		bayesian = Bayesian()
		thisDoc = array(bayesian.setOfWords2Vec(myVocabList, testEntry))
		## 拟合并预测
		y_pred = gnb.fit(X, y).predict(thisDoc)
		clabels = ['军事', '体育']
		y_pred = gnb.fit(X, y).predict(X)
		print("Number of mislabeled points : %d" % (labels != y_pred).sum())

def categorize(train_data,test_data,train_class,n_features):
    #cf= ExtraTreesClassifier()
    #cf.fit(train_data,train_class)
    #print (cf.feature_importances_)
    
    #lsvmcf = sklearn.svm.LinearSVC(penalty='l2', loss='l2', dual=True, tol=0.0001, C=100.0)  
    model = LogisticRegression()
    lgr = LogisticRegression(C=100.0,penalty='l1')    
    #knn = KNeighborsClassifier(n_neighbors=5, weights='uniform', algorithm='auto', leaf_size=10, p=2, metric='minkowski', metric_params=None)
    svmlcf = sklearn.svm.SVC(C=1000.0, kernel='linear', degree=1, gamma=0.01,  probability=True)#2
    svmcf = sklearn.svm.SVC(C=1000.0, kernel='rbf', degree=1, gamma=0.01,  probability=True)#2
    cf = DecisionTreeClassifier() 
    dct = DecisionTreeClassifier(criterion='gini', splitter='best',  min_samples_split=7, min_samples_leaf=4)
    rf = RandomForestClassifier(n_estimators=10, criterion='gini',  min_samples_split=7, min_samples_leaf=4, max_features='auto')
    gnb = GaussianNB()  #1
    adbst = sklearn.ensemble.AdaBoostClassifier(base_estimator=rf, n_estimators=5, learning_rate=1.0, algorithm='SAMME.R', random_state=True)

    #ch2 = SelectKBest(chi2, k=n_features)
    #train_data = ch2.fit_transform(train_data, train_class)
    #test_data = ch2.transform(test_data)

    #rfe = RFE(svmlcf,n_features)
    #rfe = rfe.fit(train_data, train_class)
    gnb.fit(train_data,train_class)
    return gnb.predict(test_data)

def performNB(trainingScores, trainingResults, testScores):
	print "->Gaussian NB"
	X = []
	for currMark in trainingScores:
		pass
	for idx in range(0, len(trainingScores[currMark])):
		X.append([])

	for currMark in trainingScores:
		if "Asym" in currMark:
			continue
		print currMark, 
		for idx in range(0, len(trainingScores[currMark])):
			X[idx].append(trainingScores[currMark][idx])

	X_test = []
	for idx in range(0, len(testScores[currMark])):
		X_test.append([])

	for currMark in trainingScores:
		if "Asym" in currMark:
			continue
		for idx in range(0, len(testScores[currMark])):
			X_test[idx].append(testScores[currMark][idx])
	gnb = GaussianNB()
	gnb.fit(X, np.array(trainingResults))
	y_pred = gnb.predict_proba(X_test)[:, 1]
	print "->Gaussian NB"
	return y_pred

def NBAccuracy(features_train, labels_train, features_test, labels_test):
    """ compute the accuracy of your Naive Bayes classifier """
    ### import the sklearn module for GaussianNB
    from sklearn.naive_bayes import GaussianNB

    ### create classifier
    clf = GaussianNB()

    t0 = time()
    ### fit the classifier on the training features and labels
    clf.fit(features_train, labels_train)
    print "training time:", round(time()-t0, 3), "s"

    ### use the trained classifier to predict labels for the test features
    import numpy as np
    t1 = time()
    pred = clf.predict(features_test)
    print "predicting time:", round(time()-t1, 3), "s"

    ### calculate and return the accuracy on the test data
    ### this is slightly different than the example,
    ### where we just print the accuracy
    ### you might need to import an sklearn module
    accuracy = clf.score(features_test, labels_test)
    return accuracy

def classify(features_train, labels_train):
    clf = GaussianNB()
    clf.fit(features_train, labels_train)
    ### import the sklearn module for GaussianNB
    ### create classifier
    ### fit the classifier on the training features and labels
    return clf

def naive_bayes(features, labels):
    classifier = GaussianNB()
    classifier.fit(features, labels)
    scores = cross_validation.cross_val_score(
        classifier, features, labels, cv=10, score_func=metrics.precision_recall_fscore_support
    )
    print_table("Naive Bayes", numpy.around(numpy.mean(scores, axis=0), 2))

def test_gnb_prior():
    # Test whether class priors are properly set.
    clf = GaussianNB().fit(X, y)
    assert_array_almost_equal(np.array([3, 3]) / 6.0, clf.class_prior_, 8)
    clf.fit(X1, y1)
    # Check that the class priors sum to 1
    assert_array_almost_equal(clf.class_prior_.sum(), 1)

def nb_names():
	#generate list of tuple names
	engine = create_engine('sqlite:///names.db')
	DBSession = sessionmaker(bind=engine)
	session = DBSession()
	db_names = names.Names.getAllNames(session)
	names_list = [(x,'name') for x in db_names]
	words_list = generate_words()
	sample_names = [names_list[i] for i in sorted(random.sample(xrange(len(names_list)), len(words_list)))]

	data = sample_names + words_list
	shuffled_data = np.random.permutation(data)
	strings = []
	classification = []
	for item in shuffled_data:
		strings.append([item[0]])
		classification.append(str(item[1]))


	X = np.array(strings)
	Y = np.array(classification)

	print X,Y
	clf = GaussianNB()
	clf.fit(X, Y)

class CruiseAlgorithm(object):
	# cruise algorithm is used to classify the cruise phase vs noncruise phase, it uses the differential change in data stream as the input matrix
	def __init__(self, testing=False):
		self.core = GaussianNB()
		self.scaler = RobustScaler()
		self.X_prev = None
		self.testing = testing
	def fit(self,X,Y): # Y should be the label of cruise or not
		X = self.prepare(X)
		self.core.fit(X,Y.ravel())
	def predict(self, X):
		if self.testing:
			X_t = self.prepare(X)
		else:
			if self.X_prev:
				X_t = X - self.X_prev
			else:
				X_t = X
			self.X_prev = X

		print repr(X_t)
		prediction_result = self.core.predict(X_t)
		return np.asmatrix(prediction_result)

	def prepare(self,X):
		a = np.zeros((X.shape[0],X.shape[1]))
		for i in xrange(X.shape[0]-1):
			a[i+1,:] = X[i+1] - X[i]
		return a

def trainNB():
    

    featureVector = []
    classVector = []
    temp= []
    headerLine = True


    #training
    train = open(r'C:\Python34\alchemyapi_python\TrainingDataDummy.csv')

    for line in train:
        if(headerLine):
            headerLine = False
        else:
            temp = line.split(",")
            x = [float(temp[i]) for i in activeFeatureIndex]
            #print(x)
            featureVector.append(x)
            #temp = [int(x) for x in line.split(",")[-1].rstrip("\n")]
            classVector.append(int(line.split(",")[-1].rstrip("\n")))

        
    fVector = np.array(featureVector)
    cVector = np.array(classVector)
    #print(classVector)
    print(fVector.shape)
    print(cVector.shape)

    clf = GaussianNB()
    clf.fit(fVector,cVector)
    train.close()

    return clf

def univariateFeatureSelection(f_list, my_dataset):
	result = []
	for feature in f_list:
		# Replace 'NaN' with 0
		for name in my_dataset:
			data_point = my_dataset[name]
			if not data_point[feature]:
				data_point[feature] = 0
			elif data_point[feature] == 'NaN':
				data_point[feature] =0

		data = featureFormat(my_dataset, ['poi',feature], sort_keys = True, remove_all_zeroes = False)
		labels, features = targetFeatureSplit(data)
		features = [abs(x) for x in features]
		from sklearn.cross_validation import StratifiedShuffleSplit
		cv = StratifiedShuffleSplit(labels, 1000, random_state = 42)
		features_train = []
		features_test  = []
		labels_train   = []
		labels_test    = []
		for train_idx, test_idx in cv:
			for ii in train_idx:
				features_train.append( features[ii] )
				labels_train.append( labels[ii] )
			for jj in test_idx:
				features_test.append( features[jj] )
				labels_test.append( labels[jj] )
		from sklearn.naive_bayes import GaussianNB
		clf = GaussianNB()
		clf.fit(features_train, labels_train)
		predictions = clf.predict(features_test)
		score = score_func(labels_test,predictions)
		result.append((feature,score[0],score[1],score[2]))
	result = sorted(result, reverse=True, key=lambda x: x[3])
	return result

def NBAccuracy(features_train, labels_train, features_test, labels_test):
	#Import sklearn modules for GaussianNB
	from sklearn.naive_bayes import GaussianNB
	from sklearn.metrics import accuracy_score
	
	#Create classifer
	classifer = GaussianNB();
	
	#Timing fit algorithm
	t0 = time();
	
	#Fit classier on the training features
	classifer.fit(features_train, labels_train);
	
	print "Training Time: ", round(time() - t0, 3), "s";
	
	GaussianNB();
	
	#Timing prediction algorithm
	t0=time();
	
	#Use trained classifer to predict labels for test features
	pred = classifer.predict(features_test);
	
	print "Prediction Time: ", round(time() - t0, 3), "s";
	
	#Calculate accuracy from features_test with answer in labels_test
	
	accuracy = accuracy_score(pred, labels_test);
	
	return accuracy;

class GaussianNBClassifier:

	def __init__(self):
		"""
		This is the constructor responsible for initializing the classifier
		"""
		self.outputHeader = "#gnb"
		self.clf = None

	def buildModel(self):
		"""
		This builds the model of the Gaussian NB classifier
		"""
		self.clf =  GaussianNB()

	def trainGaussianNB(self,X, Y):
		"""
		Training the Gaussian NB Classifier
		"""
		self.clf.fit(X, Y)

	def validateGaussianNB(self,X, Y):
		"""
		Validate the Gaussian NB Classifier
		"""
		YPred = self.clf.predict(X)
		print accuracy_score(Y, YPred)

	def testGaussianNB(self,X, Y):
		"""
		Test the Gaussian NB Classifier
		"""
		YPred = self.clf.predict(X)
		print accuracy_score(Y, YPred)