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Adding doctests into LDA algorithm (#1621)

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* Adding doctests into <gaussian_distribution> function

* Adding doctests into <y_generator> function

* Adding doctests into <calculate_mean> function

* Adding doctests into <calculate_probabilities> function

* Adding doctests into <calculate_variance> function

* Adding doctests into <predict_y_values> function

* Adding doctests into <accuracy> function

* fixup! Format Python code with psf/black push

* Update convex_hull.py

* Update convex_hull.py
This commit is contained in:
ELNS
2019-12-09 01:45:17 +03:30
committed by Christian Clauss
parent 26b0803319
commit 43905efe29
2 changed files with 96 additions and 39 deletions
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78
machine_learning/linear_discriminant_analysis.py
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@ -45,6 +45,7 @@
from math import log
from os import name, system
from random import gauss
from random import seed
# Make a training dataset drawn from a gaussian distribution
@ -56,7 +57,15 @@ def gaussian_distribution(mean: float, std_dev: float, instance_count: int) -> l
:param instance_count: instance number of class
:return: a list containing generated values based-on given mean, std_dev and
instance_count
>>> gaussian_distribution(5.0, 1.0, 20) # doctest: +NORMALIZE_WHITESPACE
[6.288184753155463, 6.4494456086997705, 5.066335808938262, 4.235456349028368,
3.9078267848958586, 5.031334516831717, 3.977896829989127, 3.56317055489747,
5.199311976483754, 5.133374604658605, 5.546468300338232, 4.086029056264687,
5.005005283626573, 4.935258239627312, 3.494170998739258, 5.537997178661033,
5.320711100998849, 7.3891120432406865, 5.202969177309964, 4.855297691835079]
"""
seed(1)
return [gauss(mean, std_dev) for _ in range(instance_count)]
@ -67,6 +76,14 @@ def y_generator(class_count: int, instance_count: list) -> list:
:param class_count: Number of classes(data groupings) in dataset
:param instance_count: number of instances in class
:return: corresponding values for data groupings in dataset
>>> y_generator(1, [10])
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
>>> y_generator(2, [5, 10])
[0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
>>> y_generator(4, [10, 5, 15, 20]) # doctest: +NORMALIZE_WHITESPACE
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3]
"""
return [k for k in range(class_count) for _ in range(instance_count[k])]
@ -79,6 +96,10 @@ def calculate_mean(instance_count: int, items: list) -> float:
:param instance_count: Number of instances in class
:param items: items that related to specific class(data grouping)
:return: calculated actual mean of considered class
>>> items = gaussian_distribution(5.0, 1.0, 20)
>>> calculate_mean(len(items), items)
5.011267842911003
"""
# the sum of all items divided by number of instances
return sum(items) / instance_count
@ -91,6 +112,11 @@ def calculate_probabilities(instance_count: int, total_count: int) -> float:
:param instance_count: number of instances in class
:param total_count: the number of all instances
:return: value of probability for considered class
>>> calculate_probabilities(20, 60)
0.3333333333333333
>>> calculate_probabilities(30, 100)
0.3
"""
# number of instances in specific class divided by number of all instances
return instance_count / total_count
@ -104,6 +130,12 @@ def calculate_variance(items: list, means: list, total_count: int) -> float:
:param means: a list containing real mean values of each class
:param total_count: the number of all instances
:return: calculated variance for considered dataset
>>> items = gaussian_distribution(5.0, 1.0, 20)
>>> means = [5.011267842911003]
>>> total_count = 20
>>> calculate_variance([items], means, total_count)
0.9618530973487491
"""
squared_diff = [] # An empty list to store all squared differences
# iterate over number of elements in items
@ -129,6 +161,36 @@ def predict_y_values(
:param variance: calculated value of variance by calculate_variance function
:param probabilities: a list containing all probabilities of classes
:return: a list containing predicted Y values
>>> x_items = [[6.288184753155463, 6.4494456086997705, 5.066335808938262,
... 4.235456349028368, 3.9078267848958586, 5.031334516831717,
... 3.977896829989127, 3.56317055489747, 5.199311976483754,
... 5.133374604658605, 5.546468300338232, 4.086029056264687,
... 5.005005283626573, 4.935258239627312, 3.494170998739258,
... 5.537997178661033, 5.320711100998849, 7.3891120432406865,
... 5.202969177309964, 4.855297691835079], [11.288184753155463,
... 11.44944560869977, 10.066335808938263, 9.235456349028368,
... 8.907826784895859, 10.031334516831716, 8.977896829989128,
... 8.56317055489747, 10.199311976483754, 10.133374604658606,
... 10.546468300338232, 9.086029056264687, 10.005005283626572,
... 9.935258239627313, 8.494170998739259, 10.537997178661033,
... 10.320711100998848, 12.389112043240686, 10.202969177309964,
... 9.85529769183508], [16.288184753155463, 16.449445608699772,
... 15.066335808938263, 14.235456349028368, 13.907826784895859,
... 15.031334516831716, 13.977896829989128, 13.56317055489747,
... 15.199311976483754, 15.133374604658606, 15.546468300338232,
... 14.086029056264687, 15.005005283626572, 14.935258239627313,
... 13.494170998739259, 15.537997178661033, 15.320711100998848,
... 17.389112043240686, 15.202969177309964, 14.85529769183508]]
>>> means = [5.011267842911003, 10.011267842911003, 15.011267842911002]
>>> variance = 0.9618530973487494
>>> probabilities = [0.3333333333333333, 0.3333333333333333, 0.3333333333333333]
>>> predict_y_values(x_items, means, variance, probabilities) # doctest: +NORMALIZE_WHITESPACE
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2]
"""
# An empty list to store generated discriminant values of all items in dataset for
# each class
@ -148,7 +210,7 @@ def predict_y_values(
)
# appending discriminant values of each item to 'results' list
results.append(temp)
print("Generated Discriminants: \n", results)
return [l.index(max(l)) for l in results]
@ -161,6 +223,20 @@ def accuracy(actual_y: list, predicted_y: list) -> float:
:param predicted_y: a list containing predicted Y values generated by
'predict_y_values' function
:return: percentage of accuracy
>>> actual_y = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1,
... 1, 1 ,1 ,1 ,1 ,1 ,1]
>>> predicted_y = [0, 0, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0,
... 0, 0, 1, 1, 1, 0, 1, 1, 1]
>>> accuracy(actual_y, predicted_y)
50.0
>>> actual_y = [0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1,
... 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]
>>> predicted_y = [0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1,
... 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]
>>> accuracy(actual_y, predicted_y)
100.0
"""
# iterate over one element of each list at a time (zip mode)
# prediction is correct if actual Y value equals to predicted Y value