# Source code for cleanlab.rank

```
# Copyright (C) 2017-2022 Cleanlab Inc.
# This file is part of cleanlab.
#
# cleanlab is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with cleanlab. If not, see <https://www.gnu.org/licenses/>.
"""
Methods to rank/order data by cleanlab's `label quality score`.
Except for :py:func:`order_label_issues <cleanlab.rank.order_label_issues>`, which operates only on the subset of the data identified
as potential label issues/errors, the methods in this module can be used on whichever subset
of the dataset you choose (including the entire dataset) and provide a `label quality score` for
every example. You can then do something like: ``np.argsort(label_quality_score)`` to obtain ranked
indices of individual datapoints based on their quality.
Note: multi-label classification is not supported by most methods in this module,
each example must belong to a single class, e.g. format: ``labels = np.ndarray([1,0,2,1,1,0...])``.
CAUTION: These label quality scores are computed based on `pred_probs` from your model that must be out-of-sample!
You should never provide predictions on the same examples used to train the model,
as these will be overfit and unsuitable for finding label-errors.
To obtain out-of-sample predicted probabilities for every datapoint in your dataset, you can use :ref:`cross-validation <pred_probs_cross_val>`.
Alternatively it is ok if your model was trained on a separate dataset and you are only evaluating
labels in data that was previously held-out.
"""
import numpy as np
from sklearn.metrics import log_loss
from typing import List
import warnings
from cleanlab.internal.validation import assert_valid_inputs
from cleanlab.internal.label_quality_utils import (
_subtract_confident_thresholds,
get_normalized_entropy,
)
[docs]def order_label_issues(
label_issues_mask: np.ndarray,
labels: np.ndarray,
pred_probs: np.ndarray,
*,
rank_by: str = "self_confidence",
rank_by_kwargs: dict = {},
) -> np.ndarray:
"""Sorts label issues by label quality score.
Default label quality score is "self_confidence".
Parameters
----------
label_issues_mask : np.ndarray
A boolean mask for the entire dataset where ``True`` represents a label
issue and ``False`` represents an example that is accurately labeled with
high confidence.
labels : np.ndarray
Labels in the same format expected by the :py:func:`get_label_quality_scores <cleanlab.rank.get_label_quality_scores>` function.
pred_probs : np.ndarray (shape (N, K))
Predicted-probabilities in the same format expected by the :py:func:`get_label_quality_scores <cleanlab.rank.get_label_quality_scores>` function.
rank_by : str, optional
Score by which to order label error indices (in increasing order). See
the `method` argument of :py:func:`get_label_quality_scores
<cleanlab.rank.get_label_quality_scores>`.
rank_by_kwargs : dict, optional
Optional keyword arguments to pass into :py:func:`get_label_quality_scores <cleanlab.rank.get_label_quality_scores>` function.
Accepted args include `adjust_pred_probs`.
Returns
-------
label_issues_idx : np.ndarray
Return an array of the indices of the examples with label issues,
ordered by the label-quality scoring method passed to `rank_by`.
"""
assert_valid_inputs(X=None, y=labels, pred_probs=pred_probs, multi_label=False)
# Convert bool mask to index mask
label_issues_idx = np.arange(len(labels))[label_issues_mask]
# Calculate label quality scores
label_quality_scores = get_label_quality_scores(
labels, pred_probs, method=rank_by, **rank_by_kwargs
)
# Get label quality scores for label issues
label_quality_scores_issues = label_quality_scores[label_issues_mask]
return label_issues_idx[np.argsort(label_quality_scores_issues)]
[docs]def get_label_quality_scores(
labels: np.ndarray,
pred_probs: np.ndarray,
*,
method: str = "self_confidence",
adjust_pred_probs: bool = False,
) -> np.ndarray:
"""Returns label quality scores for each datapoint.
This is a function to compute label-quality scores for classification datasets,
where lower scores indicate labels less likely to be correct.
Score is between 0 and 1.
1 - clean label (given label is likely correct).
0 - dirty label (given label is likely incorrect).
Parameters
----------
labels : np.ndarray
A discrete vector of noisy labels, i.e. some labels may be erroneous.
*Format requirements*: for dataset with K classes, labels must be in 0, 1, ..., K-1.
All the classes (0, 1, ..., and K-1) MUST be present in ``labels``, such that: ``len(set(labels)) == pred_probs.shape[1]``
Note: multi-label classification is not supported by this method, each example must belong to a single class, e.g. format: ``labels = np.ndarray([1,0,2,1,1,0...])``.
pred_probs : np.ndarray, optional
An array of shape ``(N, K)`` of model-predicted probabilities,
``P(label=k|x)``. Each row of this matrix corresponds
to an example `x` and contains the model-predicted probabilities that
`x` belongs to each possible class, for each of the K classes. The
columns must be ordered such that these probabilities correspond to
class 0, 1, ..., K-1.
**Caution**: `pred_probs` from your model must be out-of-sample!
You should never provide predictions on the same examples used to train the model,
as these will be overfit and unsuitable for finding label-errors.
To obtain out-of-sample predicted probabilities for every datapoint in your dataset, you can use :ref:`cross-validation <pred_probs_cross_val>`.
Alternatively it is ok if your model was trained on a separate dataset and you are only evaluating
data that was previously held-out.
method : {"self_confidence", "normalized_margin", "confidence_weighted_entropy"}, default="self_confidence"
Label quality scoring method.
Letting ``k = labels[i]`` and ``P = pred_probs[i]`` denote the given label and predicted class-probabilities
for datapoint *i*, its score can either be:
- ``'normalized_margin'``: ``P[k] - max_{k' != k}[ P[k'] ]``
- ``'self_confidence'``: ``P[k]``
- ``'confidence_weighted_entropy'``: ``entropy(P) / self_confidence``
Let ``C = {0, 1, ..., K-1}`` denote the specified set of classes for our classification task.
The normalized_margin score works better for identifying class conditional label errors,
i.e. examples for which another label in C is appropriate but the given label is not.
The self_confidence score works better for identifying alternative label issues corresponding
to bad examples that are: not from any of the classes in C, well-described by 2 or more labels in C,
or generally just out-of-distribution (ie. anomalous outliers).
adjust_pred_probs : bool, optional
Account for class imbalance in the label-quality scoring by adjusting predicted probabilities
via subtraction of class confident thresholds and renormalization.
Set this to ``True`` if you prefer to account for class-imbalance.
See `Northcutt et al., 2021 <https://jair.org/index.php/jair/article/view/12125>`_.
Returns
-------
label_quality_scores : np.ndarray
Contains one score (between 0 and 1) per example.
Lower scores indicate more likely mislabeled examples.
See Also
--------
get_self_confidence_for_each_label
get_normalized_margin_for_each_label
get_confidence_weighted_entropy_for_each_label
"""
# TODO: remove allow_missing_classes once supported
assert_valid_inputs(
X=None, y=labels, pred_probs=pred_probs, multi_label=False, allow_missing_classes=True
)
# Available scoring functions to choose from
scoring_funcs = {
"self_confidence": get_self_confidence_for_each_label,
"normalized_margin": get_normalized_margin_for_each_label,
"confidence_weighted_entropy": get_confidence_weighted_entropy_for_each_label,
}
# Select scoring function
try:
scoring_func = scoring_funcs[method]
except KeyError:
raise ValueError(
f"""
{method} is not a valid scoring method for rank_by!
Please choose a valid rank_by: self_confidence, normalized_margin, confidence_weighted_entropy
"""
)
# Adjust predicted probabilities
if adjust_pred_probs:
# Check if adjust_pred_probs is supported for the chosen method
if method == "confidence_weighted_entropy":
raise ValueError(f"adjust_pred_probs is not currently supported for {method}.")
pred_probs = _subtract_confident_thresholds(labels, pred_probs)
# Pass keyword arguments for scoring function
input = {"labels": labels, "pred_probs": pred_probs}
# Calculate scores
label_quality_scores = scoring_func(**input)
return label_quality_scores
[docs]def get_label_quality_ensemble_scores(
labels: np.ndarray,
pred_probs_list: List[np.ndarray],
*,
method: str = "self_confidence",
adjust_pred_probs: bool = False,
weight_ensemble_members_by: str = "accuracy",
custom_weights: np.ndarray = None,
log_loss_search_T_values: List[float] = [1e-4, 1e-3, 1e-2, 1e-1, 1e0, 1e1, 1e2, 2e2],
verbose: bool = True,
) -> np.ndarray:
"""Returns label quality scores based on predictions from an ensemble of models.
This is a function to compute label-quality scores for classification datasets,
where lower scores indicate labels less likely to be correct.
Ensemble scoring requires a list of pred_probs from each model in the ensemble.
For each pred_probs in list, compute label quality score.
Take the average of the scores with the chosen weighting scheme determined by `weight_ensemble_members_by`.
Score is between 0 and 1:
- 1 --- clean label (given label is likely correct).
- 0 --- dirty label (given label is likely incorrect).
Parameters
----------
labels : np.ndarray
Labels in the same format expected by the :py:func:`get_label_quality_scores <cleanlab.rank.get_label_quality_scores>` function.
pred_probs_list : List[np.ndarray]
Each element in this list should be an array of pred_probs in the same format
expected by the :py:func:`get_label_quality_scores <cleanlab.rank.get_label_quality_scores>` function.
Each element of `pred_probs_list` corresponds to the predictions from one model for all examples.
method : {"self_confidence", "normalized_margin", "confidence_weighted_entropy"}, default="self_confidence"
Label quality scoring method. See :py:func:`get_label_quality_scores <cleanlab.rank.get_label_quality_scores>`
for scenarios on when to use each method.
adjust_pred_probs : bool, optional
`adjust_pred_probs` in the same format expected by the :py:func:`get_label_quality_scores <cleanlab.rank.get_label_quality_scores>` function.
weight_ensemble_members_by : {"uniform", "accuracy", "log_loss_search", "custom"}, default="accuracy"
Weighting scheme used to aggregate scores from each model:
- "uniform": Take the simple average of scores.
- "accuracy": Take weighted average of scores, weighted by model accuracy.
- "log_loss_search": Take weighted average of scores, weighted by exp(t * -log_loss) where t is selected from log_loss_search_T_values parameter and log_loss is the log-loss between a model's pred_probs and the given labels.
- "custom": Take weighted average of scores using custom weights that the user passes to the custom_weights parameter.
custom_weights : np.ndarray, default=None
Weights used to aggregate scores from each model if weight_ensemble_members_by="custom".
Length of this array must match the number of models: len(pred_probs_list).
log_loss_search_T_values : List, default=[1e-4, 1e-3, 1e-2, 1e-1, 1e0, 1e1, 1e2, 2e2]
List of t values considered if weight_ensemble_members_by="log_loss_search".
We will choose the value of t that leads to weights which produce the best log-loss when used to form a weighted average of pred_probs from the models.
verbose : bool, default=True
Set to ``False`` to suppress all print statements.
Returns
-------
label_quality_scores : np.ndarray
Contains one score (between 0 and 1) per example.
Lower scores indicate more likely mislabeled examples.
See Also
--------
get_label_quality_scores
"""
MIN_ALLOWED = 1e-6 # lower-bound clipping threshold to prevents 0 in logs and division
# Check pred_probs_list for errors
assert isinstance(
pred_probs_list, list
), f"pred_probs_list needs to be a list. Provided pred_probs_list is a {type(pred_probs_list)}"
assert len(pred_probs_list) > 0, "pred_probs_list is empty."
if len(pred_probs_list) == 1:
warnings.warn(
"""
pred_probs_list only has one element.
Consider using get_label_quality_scores() if you only have a single array of pred_probs.
"""
)
for pred_probs in pred_probs_list:
assert_valid_inputs(X=None, y=labels, pred_probs=pred_probs, multi_label=False)
# Raise ValueError if user passed custom_weights array but did not choose weight_ensemble_members_by="custom"
if custom_weights is not None and weight_ensemble_members_by != "custom":
raise ValueError(
f"""
custom_weights provided but weight_ensemble_members_by is not "custom"!
"""
)
# This weighting scheme performs search of t in log_loss_search_T_values for "best" log loss
if weight_ensemble_members_by == "log_loss_search":
# Initialize variables for log loss search
pred_probs_avg_log_loss_weighted = None
neg_log_loss_weights = None
best_eval_log_loss = float("inf")
for t in log_loss_search_T_values:
neg_log_loss_list = []
# pred_probs for each model
for pred_probs in pred_probs_list:
pred_probs_clipped = np.clip(
pred_probs, a_min=MIN_ALLOWED, a_max=None
) # lower-bound clipping threshold to prevents 0 in logs when calculating log loss
pred_probs_clipped /= pred_probs_clipped.sum(axis=1)[:, np.newaxis] # renormalize
neg_log_loss = np.exp(-t * log_loss(labels, pred_probs_clipped))
neg_log_loss_list.append(neg_log_loss)
# weights using negative log loss
neg_log_loss_weights_temp = np.array(neg_log_loss_list) / sum(neg_log_loss_list)
# weighted average using negative log loss
pred_probs_avg_log_loss_weighted_temp = sum(
[neg_log_loss_weights_temp[i] * p for i, p in enumerate(pred_probs_list)]
)
# evaluate log loss with this weighted average pred_probs
eval_log_loss = log_loss(labels, pred_probs_avg_log_loss_weighted_temp)
# check if eval_log_loss is the best so far (lower the better)
if best_eval_log_loss > eval_log_loss:
best_eval_log_loss = eval_log_loss
pred_probs_avg_log_loss_weighted = pred_probs_avg_log_loss_weighted_temp
neg_log_loss_weights = neg_log_loss_weights_temp.copy()
# Generate scores for each model's pred_probs
scores_list = []
accuracy_list = []
for pred_probs in pred_probs_list:
# Calculate scores and accuracy
scores = get_label_quality_scores(
labels=labels,
pred_probs=pred_probs,
method=method,
adjust_pred_probs=adjust_pred_probs,
)
scores_list.append(scores)
# Only compute if weighting by accuracy
if weight_ensemble_members_by == "accuracy":
accuracy = (pred_probs.argmax(axis=1) == labels).mean()
accuracy_list.append(accuracy)
if verbose:
print(f"Weighting scheme for ensemble: {weight_ensemble_members_by}")
# Transform list of scores into an array of shape (N, M) where M is the number of models in the ensemble
scores_ensemble = np.vstack(scores_list).T
# Aggregate scores with chosen weighting scheme
if weight_ensemble_members_by == "uniform":
label_quality_scores = scores_ensemble.mean(axis=1) # Uniform weights (simple average)
elif weight_ensemble_members_by == "accuracy":
weights = np.array(accuracy_list) / sum(accuracy_list) # Weight by relative accuracy
if verbose:
print("Ensemble members will be weighted by their relative accuracy")
for i, acc in enumerate(accuracy_list):
print(f" Model {i} accuracy : {acc}")
print(f" Model {i} weight : {weights[i]}")
# Aggregate scores with weighted average
label_quality_scores = (scores_ensemble * weights).sum(axis=1)
elif weight_ensemble_members_by == "log_loss_search":
assert neg_log_loss_weights is not None
weights = neg_log_loss_weights # Weight by exp(t * -log_loss) where t is found by searching through log_loss_search_T_values
if verbose:
print(
"Ensemble members will be weighted by log-loss between their predicted probabilities and given labels"
)
for i, weight in enumerate(weights):
print(f" Model {i} weight : {weight}")
# Aggregate scores with weighted average
label_quality_scores = (scores_ensemble * weights).sum(axis=1)
elif weight_ensemble_members_by == "custom":
# Check custom_weights for errors
assert (
custom_weights is not None
), "custom_weights is None! Please pass a valid custom_weights."
assert len(custom_weights) == len(
pred_probs_list
), "Length of custom_weights array must match the number of models: len(pred_probs_list)."
# Aggregate scores with custom weights
label_quality_scores = (scores_ensemble * custom_weights).sum(axis=1)
else:
raise ValueError(
f"""
{weight_ensemble_members_by} is not a valid weighting method for weight_ensemble_members_by!
Please choose a valid weight_ensemble_members_by: uniform, accuracy, custom
"""
)
return label_quality_scores
[docs]def get_self_confidence_for_each_label(
labels: np.ndarray,
pred_probs: np.ndarray,
) -> np.ndarray:
"""Returns the self-confidence label-quality score for each datapoint.
This is a function to compute label-quality scores for classification datasets,
where lower scores indicate labels less likely to be correct.
The self-confidence is the classifier's predicted probability that an example belongs to
its given class label.
Self-confidence can work better than normalized-margin for detecting label errors due to out-of-distribution (OOD) or weird examples
vs. label errors in which labels for random examples have been replaced by other classes.
Parameters
----------
labels : np.ndarray
Labels in the same format expected by the :py:func:`get_label_quality_scores <cleanlab.rank.get_label_quality_scores>` function.
pred_probs : np.ndarray
Predicted-probabilities in the same format expected by the :py:func:`get_label_quality_scores <cleanlab.rank.get_label_quality_scores>` function.
Returns
-------
label_quality_scores : np.ndarray
Contains one score (between 0 and 1) per example.
Lower scores indicate more likely mislabeled examples.
"""
# np.mean is used so that this works for multi-labels (list of lists)
label_quality_scores = np.array([np.mean(pred_probs[i, l]) for i, l in enumerate(labels)])
return label_quality_scores
[docs]def get_normalized_margin_for_each_label(
labels: np.ndarray,
pred_probs: np.ndarray,
) -> np.ndarray:
"""Returns the "normalized margin" label-quality score for each datapoint.
This is a function to compute label-quality scores for classification datasets,
where lower scores indicate labels less likely to be correct.
Letting k denote the given label for a datapoint, the normalized margin is
``(p(label = k) - max(p(label != k)))``, i.e. the probability
of the given label minus the probability of the argmax label that is not
the given label (``normalized_margin = prob_label - max_prob_not_label``).
This gives you an idea of how likely an example is BOTH its given label AND not another label,
and therefore, scores its likelihood of being a good label or a label error.
Normalized margin works better for finding class conditional label errors where
there is another label in the set of classes that is clearly better than the given label.
Parameters
----------
labels : np.ndarray
Labels in the same format expected by the :py:func:`get_label_quality_scores <cleanlab.rank.get_label_quality_scores>` function.
pred_probs : np.ndarray
Predicted-probabilities in the same format expected by the :py:func:`get_label_quality_scores <cleanlab.rank.get_label_quality_scores>` function.
Returns
-------
label_quality_scores : np.ndarray
Contains one score (between 0 and 1) per example.
Lower scores indicate more likely mislabeled examples.
"""
self_confidence = get_self_confidence_for_each_label(labels, pred_probs)
max_prob_not_label = np.array(
[max(np.delete(pred_probs[i], l, -1)) for i, l in enumerate(labels)]
)
label_quality_scores = (self_confidence - max_prob_not_label + 1) / 2
return label_quality_scores
[docs]def get_confidence_weighted_entropy_for_each_label(
labels: np.ndarray, pred_probs: np.ndarray
) -> np.ndarray:
"""Returns the "confidence weighted entropy" label-quality score for each datapoint.
This is a function to compute label-quality scores for classification datasets,
where lower scores indicate labels less likely to be correct.
"confidence weighted entropy" is the normalized entropy divided by "self-confidence".
Parameters
----------
labels : np.ndarray
Labels in the same format expected by the :py:func:`get_label_quality_scores <cleanlab.rank.get_label_quality_scores>` function.
pred_probs : np.ndarray
Predicted-probabilities in the same format expected by the :py:func:`get_label_quality_scores <cleanlab.rank.get_label_quality_scores>` function.
Returns
-------
label_quality_scores : np.ndarray
Contains one score (between 0 and 1) per example.
Lower scores indicate more likely mislabeled examples.
"""
MIN_ALLOWED = 1e-6 # lower-bound clipping threshold to prevents 0 in logs and division
self_confidence = get_self_confidence_for_each_label(labels, pred_probs)
self_confidence = np.clip(self_confidence, a_min=MIN_ALLOWED, a_max=None)
# Divide entropy by self confidence
label_quality_scores = get_normalized_entropy(pred_probs) / self_confidence
# Rescale
clipped_scores = np.clip(label_quality_scores, a_min=MIN_ALLOWED, a_max=None)
label_quality_scores = np.log(label_quality_scores + 1) / clipped_scores
return label_quality_scores
[docs]def find_top_issues(quality_scores: np.ndarray, *, top: int = 10) -> np.ndarray:
"""Returns the sorted indices of the `top` issues in `quality_scores`, ordered from smallest to largest quality score
(i.e., from most to least likely to be an issue). For example, the first value returned is the index corresponding
to the smallest value in `quality_scores` (most likely to be an issue). The second value in the returned array is
the index corresponding to the second smallest value in `quality-scores` (second-most likely to be an issue), and so forth.
This method assumes that `quality_scores` shares an index with some dataset such that the indices returned by this method
map to the examples in that dataset.
Parameters
----------
quality_scores :
Array of shape ``(N,)``, where N is the number of examples, containing one quality score for each example in the dataset.
top :
The number of indices to return.
Returns
-------
top_issue_indices :
Indices of top examples most likely to suffer from an issue (ranked by issue severity)."""
if top is None or top > len(quality_scores):
top = len(quality_scores)
top_outlier_indices = quality_scores.argsort()[:top]
return top_outlier_indices
```