[ML L2 - N19] Naive Bayes GaussianNB

ClassifyNB.py:

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

prep_terrain_data.py

#!/usr/bin/python
import random


def makeTerrainData(n_points=1000):
###############################################################################
### make the toy dataset
    random.seed(42)
    grade = [random.random() for ii in range(0,n_points)]
    bumpy = [random.random() for ii in range(0,n_points)]
    error = [random.random() for ii in range(0,n_points)]
    y = [round(grade[ii]*bumpy[ii]+0.3+0.1*error[ii]) for ii in range(0,n_points)]
    for ii in range(0, len(y)):
        if grade[ii]>0.8 or bumpy[ii]>0.8:
            y[ii] = 1.0

### split into train/test sets
    X = [[gg, ss] for gg, ss in zip(grade, bumpy)]
    split = int(0.75*n_points)
    X_train = X[0:split]
    X_test  = X[split:]
    y_train = y[0:split]
    y_test  = y[split:]

    grade_sig = [X_train[ii][0] for ii in range(0, len(X_train)) if y_train[ii]==0]
    bumpy_sig = [X_train[ii][1] for ii in range(0, len(X_train)) if y_train[ii]==0]
    grade_bkg = [X_train[ii][0] for ii in range(0, len(X_train)) if y_train[ii]==1]
    bumpy_bkg = [X_train[ii][1] for ii in range(0, len(X_train)) if y_train[ii]==1]

#    training_data = {"fast":{"grade":grade_sig, "bumpiness":bumpy_sig}
#            , "slow":{"grade":grade_bkg, "bumpiness":bumpy_bkg}}


    grade_sig = [X_test[ii][0] for ii in range(0, len(X_test)) if y_test[ii]==0]
    bumpy_sig = [X_test[ii][1] for ii in range(0, len(X_test)) if y_test[ii]==0]
    grade_bkg = [X_test[ii][0] for ii in range(0, len(X_test)) if y_test[ii]==1]
    bumpy_bkg = [X_test[ii][1] for ii in range(0, len(X_test)) if y_test[ii]==1]

    test_data = {"fast":{"grade":grade_sig, "bumpiness":bumpy_sig}
            , "slow":{"grade":grade_bkg, "bumpiness":bumpy_bkg}}

    return X_train, y_train, X_test, y_test
#    return training_data, test_data

　　

class_vis.py

#!/usr/bin/python

#from udacityplots import *
import warnings
warnings.filterwarnings("ignore")

import matplotlib 
matplotlib.use('agg')

import matplotlib.pyplot as plt
import pylab as pl
import numpy as np

#import numpy as np
#import matplotlib.pyplot as plt
#plt.ioff()

def prettyPicture(clf, X_test, y_test):
    x_min = 0.0; x_max = 1.0
    y_min = 0.0; y_max = 1.0

    # Plot the decision boundary. For that, we will assign a color to each
    # point in the mesh [x_min, m_max]x[y_min, y_max].
    h = .01  # step size in the mesh
    xx, yy = np.meshgrid(np.arange(x_min, x_max, h), np.arange(y_min, y_max, h))
    Z = clf.predict(np.c_[xx.ravel(), yy.ravel()])

    # Put the result into a color plot
    Z = Z.reshape(xx.shape)
    plt.xlim(xx.min(), xx.max())
    plt.ylim(yy.min(), yy.max())

    plt.pcolormesh(xx, yy, Z, cmap=pl.cm.seismic)

    # Plot also the test points
    grade_sig = [X_test[ii][0] for ii in range(0, len(X_test)) if y_test[ii]==0]
    bumpy_sig = [X_test[ii][1] for ii in range(0, len(X_test)) if y_test[ii]==0]
    grade_bkg = [X_test[ii][0] for ii in range(0, len(X_test)) if y_test[ii]==1]
    bumpy_bkg = [X_test[ii][1] for ii in range(0, len(X_test)) if y_test[ii]==1]

    plt.scatter(grade_sig, bumpy_sig, color = "b", label="fast")
    plt.scatter(grade_bkg, bumpy_bkg, color = "r", label="slow")
    plt.legend()
    plt.xlabel("bumpiness")
    plt.ylabel("grade")

    plt.savefig("test.png")
    
import base64
import json
import subprocess

def output_image(name, format, bytes):
    image_start = "BEGIN_IMAGE_f9825uweof8jw9fj4r8"
    image_end = "END_IMAGE_0238jfw08fjsiufhw8frs"
    data = {}
    data['name'] = name
    data['format'] = format
    data['bytes'] = base64.encodestring(bytes)
    print image_start+json.dumps(data)+image_end

　　

studentMain.py

#!/usr/bin/python

""" Complete the code in ClassifyNB.py with the sklearn
    Naive Bayes classifier to classify the terrain data.
    
    The objective of this exercise is to recreate the decision 
    boundary found in the lesson video, and make a plot that
    visually shows the decision boundary """


from prep_terrain_data import makeTerrainData
from class_vis import prettyPicture, output_image
from ClassifyNB import classify

import numpy as np
import pylab as pl


features_train, labels_train, features_test, labels_test = makeTerrainData()

### the training data (features_train, labels_train) have both "fast" and "slow" points mixed
### in together--separate them so we can give them different colors in the scatterplot,
### and visually identify them
grade_fast = [features_train[ii][0] for ii in range(0, len(features_train)) if labels_train[ii]==0]
bumpy_fast = [features_train[ii][1] for ii in range(0, len(features_train)) if labels_train[ii]==0]
grade_slow = [features_train[ii][0] for ii in range(0, len(features_train)) if labels_train[ii]==1]
bumpy_slow = [features_train[ii][1] for ii in range(0, len(features_train)) if labels_train[ii]==1]


# You will need to complete this function imported from the ClassifyNB script.
# Be sure to change to that code tab to complete this quiz.
clf = classify(features_train, labels_train)



### draw the decision boundary with the text points overlaid
prettyPicture(clf, features_test, labels_test)
output_image("test.png", "png", open("test.png", "rb").read())

　　

 

Calculating NB Accuracy

def NBAccuracy(features_train, labels_train, features_test, labels_test):
    from sklearn.naive_bayes import GaussianNB
    clf = GaussianNB()
    clf.fit(features_train, labels_train)
    pred = clf.predict(features_test)
    accuracy = clf.score(features_test, labels_test)
    return accuracy