Source code for cleanlab.rank

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"""
Methods to rank examples in standard (multi-class) classification datasets by cleanlab's `label quality score`.
Except for `~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 be labeled as belonging to a single class, e.g. format: ``labels = np.ndarray([1,0,2,1,1,0...])``.
For multi-label classification, instead see :py:func:`multilabel_classification.get_label_quality_scores <cleanlab.multilabel_classification.get_label_quality_scores>`.

Note: Label quality scores are most accurate when they are computed based on out-of-sample `pred_probs` from your model.
To obtain out-of-sample predicted probabilities for every datapoint in your dataset, you can use :ref:`cross-validation <pred_probs_cross_val>`. This is encouraged to get better results.
"""

import numpy as np
from sklearn.metrics import log_loss
from typing import List, Optional
import warnings

from cleanlab.internal.validation import assert_valid_inputs
from cleanlab.internal.constants import (
    CLIPPING_LOWER_BOUND,
)  # lower-bound clipping threshold to prevents 0 in logs and division

from cleanlab.internal.label_quality_utils import (
    _subtract_confident_thresholds,
    get_normalized_entropy,
)


[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 a label quality score for each datapoint. This is a function to compute label quality scores for standard (multi-class) 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. 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. **Note**: Returned label issues are most accurate when they are computed based on out-of-sample `pred_probs` from your model. To obtain out-of-sample predicted probabilities for every datapoint in your dataset, you can use :ref:`cross-validation <pred_probs_cross_val>`. This is encouraged to get better results. 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`` Note: the actual label quality scores returned by this method may be transformed versions of the above, in order to ensure their values lie between 0-1 with lower values indicating more likely mislabeled data. Let ``C = {0, 1, ..., K-1}`` be the set of classes specified 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 (i.e. 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 """ assert_valid_inputs( X=None, y=labels, pred_probs=pred_probs, multi_label=False, allow_one_class=True ) return _compute_label_quality_scores( labels=labels, pred_probs=pred_probs, method=method, adjust_pred_probs=adjust_pred_probs )
def _compute_label_quality_scores( labels: np.ndarray, pred_probs: np.ndarray, *, method: str = "self_confidence", adjust_pred_probs: bool = False, confident_thresholds: Optional[np.ndarray] = None, ) -> np.ndarray: """Internal implementation of get_label_quality_scores that assumes inputs have already been checked and are valid. This speeds things up. Can also take in pre-computed confident_thresholds to further accelerate things. """ 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, } 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 """ ) if adjust_pred_probs: if method == "confidence_weighted_entropy": raise ValueError(f"adjust_pred_probs is not currently supported for {method}.") pred_probs = _subtract_confident_thresholds( labels=labels, pred_probs=pred_probs, confident_thresholds=confident_thresholds ) scoring_inputs = {"labels": labels, "pred_probs": pred_probs} label_quality_scores = scoring_func(**scoring_inputs) 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: Optional[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 `~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 `~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 `~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 `~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 """ # 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=CLIPPING_LOWER_BOUND, 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 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
[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 `~cleanlab.rank.get_label_quality_scores` function. pred_probs : np.ndarray (shape (N, K)) Predicted-probabilities in the same format expected by the `~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 `~cleanlab.rank.get_label_quality_scores`. rank_by_kwargs : dict, optional Optional keyword arguments to pass into `~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`. """ allow_one_class = False if isinstance(labels, np.ndarray) or all(isinstance(lab, int) for lab in labels): if set(labels) == {0}: # occurs with missing classes in multi-label settings allow_one_class = True assert_valid_inputs( X=None, y=labels, pred_probs=pred_probs, multi_label=False, allow_one_class=allow_one_class, ) # 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_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 `~cleanlab.rank.get_label_quality_scores` function. pred_probs : np.ndarray Predicted-probabilities in the same format expected by the `~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. """ # To make this work for multi-label (but it will slow down runtime), return: # np.array([np.mean(pred_probs[i, l]) for i, l in enumerate(labels)]) return pred_probs[np.arange(labels.shape[0]), labels]
[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 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 (``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. The normalized margin is simply a transformed version of the margin, to ensure values between 0-1 with lower values indicating more likely mislabeled data. Normalized margin works best 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 `~cleanlab.rank.get_label_quality_scores` function. pred_probs : np.ndarray Predicted-probabilities in the same format expected by the `~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) N, K = pred_probs.shape del_indices = np.arange(N) * K + labels max_prob_not_label = np.max( np.delete(pred_probs, del_indices, axis=None).reshape(N, K - 1), axis=-1 ) 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 defined as the normalized entropy divided by "self-confidence". The returned values are a transformed version of this score, in order to ensure values between 0-1 with lower values indicating more likely mislabeled data. Parameters ---------- labels : np.ndarray Labels in the same format expected by the `~cleanlab.rank.get_label_quality_scores` function. pred_probs : np.ndarray Predicted-probabilities in the same format expected by the `~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) self_confidence = np.clip(self_confidence, a_min=CLIPPING_LOWER_BOUND, 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=CLIPPING_LOWER_BOUND, a_max=None) label_quality_scores = np.log(label_quality_scores + 1) / clipped_scores return label_quality_scores