by David Taylor, www.prooffreader.com (blog) www.dtdata.io (hire me!)
For links to more material including a slideshow explaining all this stuff in further detail, please see the front page of this GitHub repo.
This is notebook 7 of 8. The next notebook is: [08. Dimensionality reduction with PCA]
[01] [02] [03] [04] [05] [06] [07] [08]
In the previous notebook, we saw Decision Trees; now we look at an ensemble method, Random Forest.
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline
from matplotlib.colors import ListedColormap
from sklearn import neighbors
from sklearn.ensemble import RandomForestClassifier
import time
df = pd.read_csv('fruit.csv')
fruitnames = {1: 'Orange', 2: 'Pear', 3: 'Apple'}
colors = {1: '#e09028', 2: '#55aa33', 3: '#cc3333'}
fruitlist = ['Orange', 'Pear', 'Apple']
df.sort('fruit_id', inplace=True) # This is important because the factorizer assigns numbers
# based on the order the first label is encountered, e.g. if the first instance had
# fruit = 3, the y value would be 0.
df['is_train'] = np.random.uniform(0, 1, len(df)) <= .75 # randomly assign training and testing set
train, test = df[df['is_train']==True], df[df['is_train']==False]
features = ['color_id', 'elongatedness', 'weight', 'sweetness', 'acidity']
y, _ = pd.factorize(train['fruit_id'])
clf = RandomForestClassifier(n_jobs=2)
clf = clf.fit(train[features], y)
preds = clf.predict(test[features])
test_result = pd.crosstab(np.array([fruitnames[x] for x in test['fruit_id']]),
np.array([fruitnames[x+1] for x in preds]),
rownames=['actual'], colnames=['predicted'])
test_result
predicted | Apple | Orange | Pear |
---|---|---|---|
actual | |||
Apple | 15 | 0 | 0 |
Orange | 0 | 11 | 0 |
Pear | 1 | 0 | 18 |
Show feature importances
for i, score in enumerate(list(clf.feature_importances_)):
print(round(100*score, 1), features[i])
2.2 color_id 53.1 elongatedness 7.0 weight 24.8 sweetness 12.9 acidity
Show confusion matrix of 100 runs of Random Forest Classifier using all features
reps=100
features=['color_id', 'elongatedness', 'weight', 'sweetness', 'acidity']
title_suffix='with all features'
start = time.time()
for i in range(reps):
df['is_train'] = np.random.uniform(0, 1, len(df)) <= .75 # randomly assign training and testing set
train, test = df[df['is_train']==True], df[df['is_train']==False]
y, _ = pd.factorize(train['fruit_id'])
clf = RandomForestClassifier(n_jobs=2)
clf = clf.fit(train[features], y)
preds = clf.predict(test[features])
test_result = pd.crosstab(np.array([fruitnames[x] for x in test['fruit_id']]),
np.array([fruitnames[x+1] for x in preds]), rownames=['actual'], colnames=['predicted'])
if i == 0:
final_result = test_result[:]
else:
final_result += test_result
confmatrix = np.array(final_result)
correct = 0
for i in range(confmatrix.shape[0]):
correct += confmatrix[i,i]
accuracy = correct/confmatrix.sum()
print('{} runs {}\nFeatures: {}\nAccuracy: {}\ntime: {} sec'.format(reps, title_suffix, features, accuracy, int(time.time()-start)))
final_result
100 runs with all features Features: ['color_id', 'elongatedness', 'weight', 'sweetness', 'acidity'] Accuracy: 0.9856951274027715 time: 23 sec
predicted | Apple | Orange | Pear |
---|---|---|---|
actual | |||
Apple | 1184 | 31 | 21 |
Orange | 4 | 1481 | 1 |
Pear | 2 | 5 | 1745 |
Show confusion matrix of 100 runs of Random Forest Classifier using only two most important features
reps=100
features=['elongatedness','sweetness',]
title_suffix='with only 2 most important features'
import time
start = time.time()
for i in range(reps):
df['is_train'] = np.random.uniform(0, 1, len(df)) <= .75 # randomly assign training and testing set
train, test = df[df['is_train']==True], df[df['is_train']==False]
y, _ = pd.factorize(train['fruit_id'])
clf = RandomForestClassifier(n_jobs=2)
clf = clf.fit(train[features], y)
preds = clf.predict(test[features])
test_result = pd.crosstab(np.array([fruitnames[x] for x in test['fruit_id']]),
np.array([fruitnames[x+1] for x in preds]), rownames=['actual'], colnames=['predicted'])
if i == 0:
final_result = test_result[:]
else:
final_result += test_result
confmatrix = np.array(final_result)
correct = 0
for i in range(confmatrix.shape[0]):
correct += confmatrix[i,i]
accuracy = correct/confmatrix.sum()
print('{} runs {}\nFeatures: {}\nAccuracy: {}\ntime: {} sec'.format(reps, title_suffix, features, accuracy, int(time.time()-start)))
final_result
100 runs with only 2 most important features Features: ['elongatedness', 'sweetness'] Accuracy: 0.9867831541218638 time: 23 sec
predicted | Apple | Orange | Pear |
---|---|---|---|
actual | |||
Apple | 1221 | 18 | 31 |
Orange | 8 | 1481 | 0 |
Pear | 1 | 1 | 1703 |
Show confusion matrix of 100 runs of Random Forest Classifier using only two least important features
reps=100
features=['color_id','acidity',]
title_suffix='with only 2 least important features'
import time
start = time.time()
for i in range(reps):
df['is_train'] = np.random.uniform(0, 1, len(df)) <= .75 # randomly assign training and testing set
train, test = df[df['is_train']==True], df[df['is_train']==False]
y, _ = pd.factorize(train['fruit_id'])
clf = RandomForestClassifier(n_jobs=2)
clf = clf.fit(train[features], y)
preds = clf.predict(test[features])
test_result = pd.crosstab(np.array([fruitnames[x] for x in test['fruit_id']]),
np.array([fruitnames[x+1] for x in preds]), rownames=['actual'], colnames=['predicted'])
if i == 0:
final_result = test_result[:]
else:
final_result += test_result
confmatrix = np.array(final_result)
correct = 0
for i in range(confmatrix.shape[0]):
correct += confmatrix[i,i]
accuracy = correct/confmatrix.sum()
print('{} runs {}\nFeatures: {}\nAccuracy: {}\ntime: {} sec'.format(reps, title_suffix, features, accuracy, int(time.time()-start)))
final_result
100 runs with only 2 least important features Features: ['color_id', 'acidity'] Accuracy: 0.7456040191824618 time: 23 sec
predicted | Apple | Orange | Pear |
---|---|---|---|
actual | |||
Apple | 647 | 104 | 483 |
Orange | 79 | 1359 | 25 |
Pear | 353 | 70 | 1259 |