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cleanlab--cleanlab
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v1.0
T
Curtis G. Northcutt d2abf3459b Adhere to pep-8. add support for python v3.8
2021-04-08 22:09:55 -04:00

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# Copyright (c) 2017-2050 Curtis G. Northcutt
# This file is part of cleanlab.
#
# cleanlab is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# cleanlab is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# This agreement applies to this version and all previous versions of cleanlab.
# ## Confident Learning Utilties
#
# #### Contains ancillarly helper functions used throughout this package.
from __future__ import (
print_function, absolute_import, division, unicode_literals, with_statement
)
import numpy as np
from sklearn.utils import check_X_y
def assert_inputs_are_valid(X, s, psx=None): # pragma: no cover
"""Checks that X, s, and psx
are correctly formatted"""
if psx is not None:
if not isinstance(psx, (np.ndarray, np.generic)):
raise TypeError("psx should be a numpy array.")
if len(psx) != len(s):
raise ValueError("psx and s must have same length.")
# Check for valid probabilities.
if (psx < 0).any() or (psx > 1).any():
raise ValueError("Values in psx must be between 0 and 1.")
if not isinstance(s, (np.ndarray, np.generic)):
raise TypeError("s should be a numpy array.")
# Check that s is zero-indexed (first label is 0).
unique_classes = np.unique(s)
if all(unique_classes != np.arange(len(unique_classes))):
msg = "cleanlab requires zero-indexed labels (0,1,2,..,m-1), but in "
msg += "your case: np.unique(s) = {}".format(str(unique_classes))
raise TypeError(msg)
# Allow sparse matrices and check that they are valid format.
check_X_y(
X, s, accept_sparse=True, dtype=None, force_all_finite=False,
ensure_2d=False,
)
def remove_noise_from_class(noise_matrix, class_without_noise):
"""A helper function in the setting of PU learning.
Sets all P(s=class_without_noise|y=any_other_class) = 0
in noise_matrix for pulearning setting, where we have
generalized the positive class in PU learning to be any
class of choosing, denoted by class_without_noise.
Parameters
----------
noise_matrix : np.array of shape (K, K), K = number of classes
A conditional probablity matrix of the form P(s=k_s|y=k_y) containing
the fraction of examples in every class, labeled as every other class.
Assumes columns of noise_matrix sum to 1.
class_without_noise : int
Integer value of the class that has no noise. Traditionally,
this is 1 (positive) for PU learning."""
# Number of classes
K = len(noise_matrix)
cwn = class_without_noise
x = np.copy(noise_matrix)
# Set P( s = cwn | y != cwn) = 0 (no noise)
x[cwn, [i for i in range(K) if i != cwn]] = 0.0
# Normalize columns by increasing diagnol terms
# Ensures noise_matrix is a valid probability matrix
for i in range(K):
x[i][i] = 1 - float(np.sum(x[:, i]) - x[i][i])
return x
def clip_noise_rates(noise_matrix):
"""Clip all noise rates to proper range [0,1), but
do not modify the diagonal terms because they are not
noise rates.
ASSUMES noise_matrix columns sum to 1.
Parameters
----------
noise_matrix : np.array of shape (K, K), K = number of classes
A conditional probablity matrix containing the fraction of
examples in every class, labeled as every other class.
Diagonal terms are not noise rates, but are consistency P(s=k|y=k)
Assumes columns of noise_matrix sum to 1"""
def clip_noise_rate_range(noise_rate):
"""Clip noise rate P(s=k'|y=k) or P(y=k|s=k')
into proper range [0,1)"""
return min(max(noise_rate, 0.0), 0.9999)
# Vectorize clip_noise_rate_range for efficiency with np.arrays.
vectorized_clip = np.vectorize(clip_noise_rate_range)
# Preserve because diagonal entries are not noise rates.
diagonal = np.diagonal(noise_matrix)
# Clip all noise rates (efficiently).
noise_matrix = vectorized_clip(noise_matrix)
# Put unmodified diagonal back.
np.fill_diagonal(noise_matrix, diagonal)
# Re-normalized noise_matrix so that columns sum to one.
noise_matrix = noise_matrix / noise_matrix.sum(axis=0)
return noise_matrix
def clip_values(x, low=0.0, high=1.0, new_sum=None):
"""Clip all values in p to range [low,high].
Preserves sum of x.
Parameters
----------
x : np.array
An array / list of values to be clipped.
low : float
values in x greater than 'low' are clipped to this value
high : float
values in x greater than 'high' are clipped to this value
new_sum : float
normalizes x after clipping to sum to new_sum
Returns
-------
x : np.array
A list of clipped values, summing to the same sum as x."""
def clip_range(a, low=low, high=high):
"""Clip a into range [low,high]"""
return min(max(a, low), high)
# Vectorize clip_range for efficiency with np.arrays.
vectorized_clip = np.vectorize(clip_range)
# Store previous sum
prev_sum = sum(x) if new_sum is None else new_sum
# Clip all values (efficiently).
x = vectorized_clip(x)
# Re-normalized values to sum to previous sum.
x = x * prev_sum / float(sum(x))
return x
def value_counts(x):
"""Returns an np.array of shape (K, 1), with the
value counts for every unique item in the labels list/array,
where K is the number of unique entries in labels.
Why this matters? Here is an example:
x = [np.random.randint(0,100) for i in range(100000)]
%timeit np.bincount(x)
--Result: 100 loops, best of 3: 3.9 ms per loop
%timeit np.unique(x, return_counts=True)[1]
--Result: 100 loops, best of 3: 7.47 ms per loop
Parameters
----------
x : list or np.array (one dimensional)
A list of discrete objects, like lists or strings, for
example, class labels 'y' when training a classifier.
e.g. ["dog","dog","cat"] or [1,2,0,1,1,0,2]"""
try:
return x.value_counts()
except:
if type(x[0]) is int and (np.array(x) >= 0).all():
return np.bincount(x)
else:
return np.unique(x, return_counts=True)[1]
def round_preserving_sum(iterable):
"""Rounds an iterable of floats while retaining the original summed value.
Function parameters should be documented in the ``Args`` section. The name
of each parameter is required. The type and description of each parameter
is optional, but should be included if not obvious.
The while loop in this code was adapted from:
https://github.com/cgdeboer/iteround
Parameters
-----------
iterable : list<float> or np.array<float>
An iterable of floats
Returns
-------
iterable : list<int> or np.array<int>
The iterable rounded to int, preserving sum."""
floats = np.asarray(iterable, dtype=float)
ints = floats.round()
orig_sum = np.sum(floats).round()
int_sum = np.sum(ints).round()
# Adjust the integers so that they sum to orig_sum
while abs(int_sum - orig_sum) > 1e-6:
diff = np.round(orig_sum - int_sum)
increment = -1 if int(diff < 0.) else 1
changes = min(int(abs(diff)), len(iterable))
# Orders indices by difference. Increments # of changes.
indices = np.argsort(floats - ints)[::-increment][:changes]
for i in indices:
ints[i] = ints[i] + increment
int_sum = np.sum(ints).round()
return ints.astype(int)
def round_preserving_row_totals(confident_joint):
"""Rounds confident_joint cj to type int
while preserving the totals of reach row.
Assumes that cj is a 2D np.array of type float.
Parameters:
confident_joint : 2D np.array<float> of shape (K, K)
See compute_confident_joint docstring for details.
Returns:
confident_joint : 2D np.array<int> of shape (K,K)
Rounded to int while preserving row totals."""
return np.apply_along_axis(
func1d=round_preserving_sum,
axis=1,
arr=confident_joint,
).astype(int)
def int2onehot(labels):
"""Convert list of lists to a onehot matrix for multi-labels
Parameters
----------
labels: list of lists of integers
e.g. [[0,1], [3], [1,2,3], [1], [2]]
All integers from 0,1,...,K-1 must be represented."""
from sklearn.preprocessing import MultiLabelBinarizer
mlb = MultiLabelBinarizer()
return mlb.fit_transform(labels)
def onehot2int(onehot_matrix):
"""Convert a onehot matrix for multi-labels to a list of lists of ints
Parameters
----------
onehot_matrix: 2D np.array of 0s and 1s
A one hot encoded matrix representation of multi-labels.
Returns
-------
labels: list of lists of integers
e.g. [[0,1], [3], [1,2,3], [1], [2]]
All integers from 0,1,...,K-1 must be represented."""
return [list(np.where(row == 1)[0]) for row in onehot_matrix]
def estimate_pu_f1(s, prob_s_eq_1):
"""Computes Claesen's estimate of f1 in the pulearning setting.
Parameters
----------
s : iterable (list or np.array)
Binary label (whether each element is labeled or not) in pu learning.
prob_s_eq_1 : iterable (list or np.array)
The probability, for each example, whether it is s==1 P(s==1|x)
Output (float)
------
Claesen's estimate for f1 in the pulearning setting."""
pred = np.asarray(prob_s_eq_1) >= 0.5
true_positives = sum((np.asarray(s) == 1) & (np.asarray(pred) == 1))
all_positives = sum(s)
recall = true_positives / float(all_positives)
frac_positive = sum(pred) / float(len(s))
return recall ** 2 / (2.0 * frac_positive) if frac_positive != 0 else np.nan
def confusion_matrix(true, pred):
"""Implements a confusion matrix for true labels
and predicted labels. true and pred MUST BE the same length
and have the same distinct set of class labels represtented.
Results are identical (and similar computation time) to:
"sklearn.metrics.confusion_matrix"
However, this function avoids the dependency on sklearn.
Parameters
----------
y : np.array 1d
Contains labels.
Assumes s and y contains the same distinct set of labels.
s : np.array 1d
Contains labels.
Assumes s and y contains the same distinct set of labels.
Returns
-------
confusion_matrix : np.array (2D)
matrix of confusion counts with true on rows and pred on columns."""
assert (len(true) == len(pred))
true_classes = np.unique(true)
pred_classes = np.unique(pred)
K_true = len(true_classes) # Number of classes in true
K_pred = len(pred_classes) # Number of classes in pred
map_true = dict(zip(true_classes, range(K_true)))
map_pred = dict(zip(pred_classes, range(K_pred)))
result = np.zeros((K_true, K_pred))
for i in range(len(true)):
result[map_true[true[i]]][map_pred[pred[i]]] += 1
return result
def print_square_matrix(
matrix,
left_name='s',
top_name='y',
title=' A square matrix',
short_title='s,y',
round_places=2,
):
"""Pretty prints a matrix.
Parameters
----------
matrix : np.array
the matrix to be printed
left_name : str
the name of the variable on the left of the matrix
top_name : str
the name of the variable on the top of the matrix
title : str
Prints this string above the printed square matrix.
short_title : str
A short title (6 characters or less) like P(s|y) or P(s,y).
round_places : int
Number of decimals to show for each matrix value."""
short_title = short_title[:6]
K = len(matrix) # Number of classes
# Make sure matrix is 2d array
if len(np.shape(matrix)) == 1:
matrix = np.array([matrix])
print()
print(title, 'of shape', matrix.shape)
print(" " + short_title + "".join(['\t' + top_name + '=' + str(i) for i in range(K)]))
print('\t---' * K)
for i in range(K):
entry = "\t".join([str(z) for z in list(matrix.round(round_places)[i, :])])
print(left_name + "=" + str(i) + " |\t" + entry)
print("\tTrace(matrix) =", np.round(np.trace(matrix), round_places))
print()
def print_noise_matrix(noise_matrix, round_places=2):
"""Pretty prints the noise matrix."""
print_square_matrix(
noise_matrix,
title=' Noise Matrix (aka Noisy Channel) P(s|y)',
short_title='p(s|y)',
round_places=round_places,
)
def print_inverse_noise_matrix(inverse_noise_matrix, round_places=2):
"""Pretty prints the inverse noise matrix."""
print_square_matrix(
inverse_noise_matrix,
left_name='y',
top_name='s',
title=' Inverse Noise Matrix P(y|s)',
short_title='p(y|s)',
round_places=round_places,
)
def print_joint_matrix(joint_matrix, round_places=2):
"""Pretty prints the joint label noise matrix."""
print_square_matrix(
joint_matrix,
title=' Joint Label Noise Distribution Matrix P(s,y)',
short_title='p(s,y)',
round_places=round_places,
)
def _python_version_is_compatible(
warning_str="pyTorch supports Python version 2.7, 3.5, 3.6, 3.7, 3.8",
warning_already_issued=False,
list_of_compatible_versions=[2.7, 3.5, 3.6, 3.7, 3.8],
):
"""Helper function for VersionWarning class that issues
a warning (if a warning has not already been issued),
whenever the python version is not in the
list_of_compatible_versions.
"""
import sys
v = sys.version_info[0] + 0.1 * sys.version_info[1]
if v in list_of_compatible_versions:
return True
elif not warning_already_issued:
import warnings
warning = '''
{}
cleanlab supports Python versions 2.7, 3.4, 3.5, 3.6.
You are using Python version {}.
You'll need to use a version compatible with both.'''.format(warning_str, v)
warnings.warn(warning)
warning_already_issued = True
return False
class VersionWarning(object):
"""Functor that calls _python_version_is_compatible
and manages the state of the bool variable
warning_already_issued to make sure the same warning
is never displayed multiple times. """
def __init__(self, warning_str, list_of_compatible_versions):
self.warning_str = warning_str
self.warning_already_issued = False
self.list_of_compatible_versions = list_of_compatible_versions
def is_compatible(self):
compatible = _python_version_is_compatible(
self.warning_str,
self.warning_already_issued,
self.list_of_compatible_versions,
)
if not compatible:
self.warning_already_issued = True
return compatible
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