label_models.py

#  coding=utf-8
#  Copyright 2021-present, the Recognai S.L. team.
#
#  Licensed under the Apache License, Version 2.0 (the "License");
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
#
#      http://www.apache.org/licenses/LICENSE-2.0
#
#  Unless required by applicable law or agreed to in writing, software
#  distributed under the License is distributed on an "AS IS" BASIS,
#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#  See the License for the specific language governing permissions and
#  limitations under the License.
import hashlib
import logging
from enum import Enum
from typing import Dict, List, Tuple, Union

import numpy as np

from rubrix import DatasetForTextClassification, TextClassificationRecord
from rubrix.client.datasets import Dataset
from rubrix.labeling.text_classification.weak_labels import WeakLabels, WeakMultiLabels

_LOGGER = logging.getLogger(__name__)


class TieBreakPolicy(Enum):
    """A tie break policy"""

    ABSTAIN = "abstain"
    RANDOM = "random"
    TRUE_RANDOM = "true-random"

    @classmethod
    def _missing_(cls, value):
        raise ValueError(
            f"{value} is not a valid {cls.__name__}, please select one of {list(cls._value2member_map_.keys())}"
        )


class LabelModel:
    """Abstract base class for a label model implementation.

    Args:
        weak_labels: Every label model implementation needs at least a `WeakLabels` instance.
    """

    # When we break a tie, by how much shall we increase the probability of the winner?
    _PROBABILITY_INCREASE_ON_TIE_BREAK = 0.0001

    def __init__(self, weak_labels: WeakLabels):
        self._weak_labels = weak_labels

    @property
    def weak_labels(self) -> WeakLabels:
        """The underlying `WeakLabels` object, containing the weak labels and records."""
        return self._weak_labels

    def fit(self, include_annotated_records: bool = False, *args, **kwargs):
        """Fits the label model.

        Args:
            include_annotated_records: Whether to include annotated records in the fitting.
        """
        raise NotImplementedError

    def score(self, *args, **kwargs) -> Dict:
        """Evaluates the label model."""
        raise NotImplementedError

    def predict(
        self,
        include_annotated_records: bool = False,
        prediction_agent: str = "LabelModel",
        **kwargs,
    ) -> DatasetForTextClassification:
        """Applies the label model.

        Args:
            include_annotated_records: Whether to include annotated records.
            prediction_agent: String used for the ``prediction_agent`` in the returned records.
            **kwargs: Specific to the label model implementations

        Returns:
            A dataset of records that include the predictions of the label model.
        """
        raise NotImplementedError


class MajorityVoter(LabelModel):
    """A basic label model that computes the majority vote across all rules.

    For single-label classification, it will predict the label with the most votes.
    For multi-label classification, it will predict all labels that got at least one vote by the rules.

    Args:
        weak_labels: The weak labels object.
    """

    def __init__(self, weak_labels: Union[WeakLabels, WeakMultiLabels]):
        super().__init__(weak_labels=weak_labels)

    def fit(self, *args, **kwargs):
        """Raises a NotImplementedError.

        No need to call fit on the ``MajorityVoter``!
        """
        raise NotImplementedError("No need to call fit on the 'MajorityVoter'!")

    def predict(
        self,
        include_annotated_records: bool = False,
        include_abstentions: bool = False,
        prediction_agent: str = "MajorityVoter",
        tie_break_policy: Union[TieBreakPolicy, str] = "abstain",
    ) -> DatasetForTextClassification:
        """Applies the label model.

        Args:
            include_annotated_records: Whether to include annotated records.
            include_abstentions: Whether to include records in the output, for which the label model abstained.
            prediction_agent: String used for the ``prediction_agent`` in the returned records.
            tie_break_policy: Policy to break ties (IGNORED FOR MULTI-LABEL!). You can choose among two policies:

                - `abstain`: Do not provide any prediction
                - `random`: randomly choose among tied option using deterministic hash

                The last policy can introduce quite a bit of noise, especially when the tie is among many labels,
                as is the case when all the labeling functions (rules) abstained.

        Returns:
            A dataset of records that include the predictions of the label model.
        """
        wl_matrix = self._weak_labels.matrix(
            has_annotation=None if include_annotated_records else False
        )
        records = self._weak_labels.records(
            has_annotation=None if include_annotated_records else False
        )

        if isinstance(self._weak_labels, WeakMultiLabels):
            records = self._make_multi_label_records(
                probabilities=self._compute_multi_label_probs(wl_matrix),
                records=records,
                include_abstentions=include_abstentions,
                prediction_agent=prediction_agent,
            )
        else:
            if isinstance(tie_break_policy, str):
                tie_break_policy = TieBreakPolicy(tie_break_policy)

            records = self._make_single_label_records(
                probabilities=self._compute_single_label_probs(wl_matrix),
                records=records,
                include_abstentions=include_abstentions,
                prediction_agent=prediction_agent,
                tie_break_policy=tie_break_policy,
            )

        return DatasetForTextClassification(records)

    def _compute_single_label_probs(self, wl_matrix: np.ndarray) -> np.ndarray:
        """Helper methods that computes the probabilities.

        Args:
            wl_matrix: The weak label matrix.

        Returns:
            A matrix of "probabilities" with nr or records x nr of labels.
            The label order matches the one from `self.weak_labels.labels`.
        """
        counts = np.column_stack(
            [
                np.count_nonzero(
                    wl_matrix == self._weak_labels.label2int[label], axis=1
                )
                for label in self._weak_labels.labels
            ]
        )
        with np.errstate(invalid="ignore"):
            probabilities = counts / counts.sum(axis=1).reshape(len(counts), -1)

        # we treat abstentions as ties among all labels (see snorkel)
        probabilities[np.isnan(probabilities)] = 1.0 / len(self._weak_labels.labels)

        return probabilities

    def _make_single_label_records(
        self,
        probabilities: np.ndarray,
        records: List[TextClassificationRecord],
        include_abstentions: bool,
        prediction_agent: str,
        tie_break_policy: TieBreakPolicy,
    ) -> List[TextClassificationRecord]:
        """Helper method to create records given predicted probabilities.

        Args:
            probabilities: The predicted probabilities.
            records: The records associated with the probabilities.
            include_abstentions: Whether to include records in the output, for which the label model abstained.
            prediction_agent: String used for the ``prediction_agent`` in the returned records.
            tie_break_policy: Policy to break ties. You can choose among two policies:

                - `abstain`: Do not provide any prediction
                - `random`: randomly choose among tied option using deterministic hash

                The last policy can introduce quite a bit of noise, especially when the tie is among many labels,
                as is the case when all the labeling functions (rules) abstained.

        Returns:
            A list of records that include the predictions of the label model.
        """
        records_with_prediction = []
        for i, prob, rec in zip(range(len(records)), probabilities, records):
            # Check if model abstains, that is if the highest probability is assigned to more than one label
            # 1.e-8 is taken from the abs tolerance of np.isclose
            equal_prob_idx = np.nonzero(np.abs(prob.max() - prob) < 1.0e-8)[0]
            tie = False
            if len(equal_prob_idx) > 1:
                tie = True

            # maybe skip record
            if not include_abstentions and (
                tie and tie_break_policy is TieBreakPolicy.ABSTAIN
            ):
                continue

            if not tie:
                pred_for_rec = [
                    (self._weak_labels.labels[idx], prob[idx])
                    for idx in np.argsort(prob)[::-1]
                ]
            # resolve ties following the tie break policy
            elif tie_break_policy is TieBreakPolicy.ABSTAIN:
                pred_for_rec = None
            elif tie_break_policy is TieBreakPolicy.RANDOM:
                random_idx = int(hashlib.sha1(f"{i}".encode()).hexdigest(), 16) % len(
                    equal_prob_idx
                )
                for idx in equal_prob_idx:
                    if idx == random_idx:
                        prob[idx] += self._PROBABILITY_INCREASE_ON_TIE_BREAK
                    else:
                        prob[idx] -= self._PROBABILITY_INCREASE_ON_TIE_BREAK / (
                            len(equal_prob_idx) - 1
                        )
                pred_for_rec = [
                    (self._weak_labels.labels[idx], prob[idx])
                    for idx in np.argsort(prob)[::-1]
                ]
            else:
                raise NotImplementedError(
                    f"The tie break policy '{tie_break_policy.value}' is not implemented for {self.__class__.__name__}!"
                )

            records_with_prediction.append(rec.copy(deep=True))
            records_with_prediction[-1].prediction = pred_for_rec
            records_with_prediction[-1].prediction_agent = prediction_agent

        return records_with_prediction

    def _compute_multi_label_probs(self, wl_matrix: np.ndarray) -> np.ndarray:
        """Helper methods that computes the probabilities.

        Args:
            wl_matrix: The weak label matrix.

        Returns:
            A matrix of "probabilities" with nr or records x nr of labels.
            The label order matches the one from `self.weak_labels.labels`.
        """
        # turn abstentions (-1) into 0
        counts = np.where(wl_matrix == -1, 0, wl_matrix).sum(axis=1)
        # binary probability, predict all labels with at least one vote
        probabilities = np.where(counts > 0, 1, 0).astype(np.float16)

        all_rules_abstained = wl_matrix.sum(axis=1).sum(axis=1) == (
            -1 * self._weak_labels.cardinality * len(self._weak_labels.rules)
        )
        probabilities[all_rules_abstained] = [np.nan] * len(self._weak_labels.labels)

        # more "nuanced probability", not sure if useful though
        # with np.errstate(invalid="ignore"):
        #     probabilities = counts / counts.sum(axis=1).reshape(len(counts), -1)

        return probabilities

    def _make_multi_label_records(
        self,
        probabilities: np.ndarray,
        records: List[TextClassificationRecord],
        include_abstentions: bool,
        prediction_agent: str,
    ) -> List[TextClassificationRecord]:
        """Helper method to create records given predicted probabilities.

        Args:
            probabilities: The predicted probabilities.
            records: The records associated with the probabilities.
            include_abstentions: Whether to include records in the output, for which the label model abstained.
            prediction_agent: String used for the ``prediction_agent`` in the returned records.

        Returns:
            A list of records that include the predictions of the label model.
        """
        records_with_prediction = []
        for prob, rec in zip(probabilities, records):
            all_abstained = np.isnan(prob).all()
            # maybe skip record
            if not include_abstentions and all_abstained:
                continue

            pred_for_rec = None
            if not all_abstained:
                pred_for_rec = [
                    (self._weak_labels.labels[i], prob[i])
                    for i in np.argsort(prob)[::-1]
                ]

            records_with_prediction.append(rec.copy(deep=True))
            records_with_prediction[-1].prediction = pred_for_rec
            records_with_prediction[-1].prediction_agent = prediction_agent

        return records_with_prediction

    def score(
        self,
        tie_break_policy: Union[TieBreakPolicy, str] = "abstain",
        output_str: bool = False,
    ) -> Union[Dict[str, float], str]:
        """Returns some scores/metrics of the label model with respect to the annotated records.

        The metrics are:

        - accuracy
        - micro/macro averages for precision, recall and f1
        - precision, recall, f1 and support for each label

        For more details about the metrics, check out the
        `sklearn docs <https://scikit-learn.org/stable/modules/generated/sklearn.metrics.precision_recall_fscore_support.html#sklearn-metrics-precision-recall-fscore-support>`__.

        .. note:: Metrics are only calculated over non-abstained predictions!

        Args:
            tie_break_policy: Policy to break ties (IGNORED FOR MULTI-LABEL). You can choose among two policies:

                - `abstain`: Do not provide any prediction
                - `random`: randomly choose among tied option using deterministic hash

                The last policy can introduce quite a bit of noise, especially when the tie is among many labels,
                as is the case when all the labeling functions (rules) abstained.
            output_str: If True, return output as nicely formatted string.

        Returns:
            The scores/metrics in a dictionary or as a nicely formatted str.

        Raises:
            MissingAnnotationError: If the ``weak_labels`` do not contain annotated records.
        """
        try:
            import sklearn
        except ModuleNotFoundError:
            raise ModuleNotFoundError(
                "'sklearn' must be installed to compute the metrics! "
                "You can install 'sklearn' with the command: `pip install scikit-learn`"
            )
        from sklearn.metrics import classification_report

        wl_matrix = self._weak_labels.matrix(has_annotation=True)

        if isinstance(self._weak_labels, WeakMultiLabels):
            probabilities = self._compute_multi_label_probs(wl_matrix)

            annotation, prediction = self._score_multi_label(probabilities)
            target_names = self._weak_labels.labels
        else:
            if isinstance(tie_break_policy, str):
                tie_break_policy = TieBreakPolicy(tie_break_policy)

            probabilities = self._compute_single_label_probs(wl_matrix)

            annotation, prediction = self._score_single_label(
                probabilities, tie_break_policy
            )
            target_names = self._weak_labels.labels[: annotation.max() + 1]

        return classification_report(
            annotation,
            prediction,
            target_names=target_names,
            output_dict=not output_str,
        )

    def _score_single_label(
        self, probabilities: np.ndarray, tie_break_policy: TieBreakPolicy
    ) -> Tuple[np.ndarray, np.ndarray]:
        """Helper method to compute scores for single-label classifications.

        Args:
            probabilities: The probabilities.
            tie_break_policy: Policy to break ties. You can choose among two policies:

                - `abstain`: Exclude from scores.
                - `random`: randomly choose among tied option using deterministic hash.

                The last policy can introduce quite a bit of noise, especially when the tie is among many labels,
                as is the case when all the labeling functions (rules) abstained.

        Returns:
            A tuple of the annotation and prediction array.
        """
        # 1.e-8 is taken from the abs tolerance of np.isclose
        is_max = (
            np.abs(probabilities.max(axis=1, keepdims=True) - probabilities) < 1.0e-8
        )
        is_tie = is_max.sum(axis=1) > 1

        prediction = np.argmax(is_max, axis=1)
        # we need to transform the indexes!
        annotation = np.array(
            [
                self._weak_labels.labels.index(self._weak_labels.int2label[i])
                for i in self._weak_labels.annotation()
            ],
            dtype=np.short,
        )

        if not is_tie.any():
            pass
        # resolve ties
        elif tie_break_policy is TieBreakPolicy.ABSTAIN:
            prediction, annotation = prediction[~is_tie], annotation[~is_tie]
        elif tie_break_policy is TieBreakPolicy.RANDOM:
            for i in np.nonzero(is_tie)[0]:
                equal_prob_idx = np.nonzero(is_max[i])[0]
                random_idx = int(hashlib.sha1(f"{i}".encode()).hexdigest(), 16) % len(
                    equal_prob_idx
                )
                prediction[i] = equal_prob_idx[random_idx]
        else:
            raise NotImplementedError(
                f"The tie break policy '{tie_break_policy.value}' is not implemented for MajorityVoter!"
            )

        return annotation, prediction

    def _score_multi_label(
        self, probabilities: np.ndarray
    ) -> Tuple[np.ndarray, np.ndarray]:
        """Helper method to compute scores for multi-label classifications.

        Args:
            probabilities: The probabilities.

        Returns:
            A tuple of the annotation and prediction array.
        """
        prediction = np.where(probabilities > 0.5, 1, 0)

        is_abstain = np.isnan(probabilities).all(axis=1)

        prediction, annotation = (
            prediction[~is_abstain],
            self._weak_labels.annotation()[~is_abstain],
        )

        return annotation, prediction


class Snorkel(LabelModel):
    """The label model by `Snorkel <https://github.com/snorkel-team/snorkel/>`__.

    .. note:: It is not suited for multi-label classification and does not support it!

    Args:
        weak_labels: A `WeakLabels` object containing the weak labels and records.
        verbose: Whether to show print statements
        device: What device to place the model on ('cpu' or 'cuda:0', for example).
            Passed on to the `torch.Tensor.to()` calls.

    Examples:
        >>> from rubrix.labeling.text_classification import WeakLabels
        >>> weak_labels = WeakLabels(dataset="my_dataset")
        >>> label_model = Snorkel(weak_labels)
        >>> label_model.fit()
        >>> records = label_model.predict()
    """

    def __init__(
        self, weak_labels: WeakLabels, verbose: bool = True, device: str = "cpu"
    ):
        try:
            import snorkel
        except ModuleNotFoundError:
            raise ModuleNotFoundError(
                "'snorkel' must be installed to use the `Snorkel` label model! "
                "You can install 'snorkel' with the command: `pip install snorkel`"
            )
        else:
            from snorkel.labeling.model import LabelModel as SnorkelLabelModel

        super().__init__(weak_labels)

        # Check if we need to remap the weak labels to int mapping
        # Snorkel expects the abstain id to be -1 and the rest of the labels to be sequential
        if self._weak_labels.label2int[None] != -1 or sorted(
            self._weak_labels.int2label
        ) != list(range(-1, self._weak_labels.cardinality)):
            self._need_remap = True
            self._weaklabelsInt2snorkelInt = {
                self._weak_labels.label2int[label]: i
                for i, label in enumerate([None] + self._weak_labels.labels, -1)
            }
        else:
            self._need_remap = False
            self._weaklabelsInt2snorkelInt = {
                i: i for i in range(-1, self._weak_labels.cardinality)
            }

        self._snorkelInt2weaklabelsInt = {
            val: key for key, val in self._weaklabelsInt2snorkelInt.items()
        }

        # instantiate Snorkel's label model
        self._model = SnorkelLabelModel(
            cardinality=self._weak_labels.cardinality,
            verbose=verbose,
            device=device,
        )

    def fit(self, include_annotated_records: bool = False, **kwargs):
        """Fits the label model.

        Args:
            include_annotated_records: Whether to include annotated records in the fitting.
            **kwargs: Additional kwargs are passed on to Snorkel's
                `fit method <https://snorkel.readthedocs.io/en/latest/packages/_autosummary/labeling/snorkel.labeling.model.label_model.LabelModel.html#snorkel.labeling.model.label_model.LabelModel.fit>`__.
                They must not contain ``L_train``, the label matrix is provided automatically.
        """
        if "L_train" in kwargs:
            raise ValueError(
                "Your kwargs must not contain 'L_train', it is provided automatically."
            )

        l_train = self._weak_labels.matrix(
            has_annotation=None if include_annotated_records else False
        )
        if self._need_remap:
            l_train = self._copy_and_remap(l_train)

        self._model.fit(L_train=l_train, **kwargs)

    def _copy_and_remap(self, matrix_or_array: np.ndarray):
        """Helper function to copy and remap the weak label matrix or annotation array to be compatible with snorkel.

        Snorkel expects the abstain id to be -1 and the rest of the labels to be sequential.

        Args:
            matrix_or_array: The original weak label matrix or annotation array

        Returns:
            A copy of the weak label matrix, remapped to match snorkel's requirements.
        """
        matrix_or_array = matrix_or_array.copy()

        # save masks for swapping
        label_masks = {}

        # compute masks
        for idx in self._weaklabelsInt2snorkelInt:
            label_masks[idx] = matrix_or_array == idx

        # swap integers
        for idx in self._weaklabelsInt2snorkelInt:
            matrix_or_array[label_masks[idx]] = self._weaklabelsInt2snorkelInt[idx]

        return matrix_or_array

    def predict(
        self,
        include_annotated_records: bool = False,
        include_abstentions: bool = False,
        prediction_agent: str = "Snorkel",
        tie_break_policy: Union[TieBreakPolicy, str] = "abstain",
    ) -> DatasetForTextClassification:
        """Returns a list of records that contain the predictions of the label model

        Args:
            include_annotated_records: Whether to include annotated records.
            include_abstentions: Whether to include records in the output, for which the label model abstained.
            prediction_agent: String used for the ``prediction_agent`` in the returned records.
            tie_break_policy: Policy to break ties. You can choose among three policies:

                - `abstain`: Do not provide any prediction
                - `random`: randomly choose among tied option using deterministic hash
                - `true-random`: randomly choose among the tied options. NOTE: repeated runs may have slightly different results due to differences in broken ties

                The last two policies can introduce quite a bit of noise, especially when the tie is among many labels,
                as is the case when all the labeling functions (rules) abstained.

        Returns:
            A dataset of records that include the predictions of the label model.
        """
        if isinstance(tie_break_policy, str):
            tie_break_policy = TieBreakPolicy(tie_break_policy)

        l_pred = self._weak_labels.matrix(
            has_annotation=None if include_annotated_records else False
        )
        if self._need_remap:
            l_pred = self._copy_and_remap(l_pred)

        # get predictions and probabilities
        predictions, probabilities = self._model.predict(
            L=l_pred,
            return_probs=True,
            tie_break_policy=tie_break_policy.value,
        )

        # add predictions to records
        records_with_prediction = []
        for rec, pred, prob in zip(
            self._weak_labels.records(
                has_annotation=None if include_annotated_records else False
            ),
            predictions,
            probabilities,
        ):
            if not include_abstentions and pred == -1:
                continue

            records_with_prediction.append(rec.copy(deep=True))

            # set predictions to None if model abstained
            pred_for_rec = None
            if pred != -1:
                # If we have a tie, increase a bit the probability of the random winner (see tie_break_policy)
                # 1.e-8 is taken from the abs tolerance of np.isclose
                equal_prob_idx = np.nonzero(np.abs(prob.max() - prob) < 1.0e-8)[0]
                if len(equal_prob_idx) > 1:
                    for idx in equal_prob_idx:
                        if idx == pred:
                            prob[idx] += self._PROBABILITY_INCREASE_ON_TIE_BREAK
                        else:
                            prob[idx] -= self._PROBABILITY_INCREASE_ON_TIE_BREAK / (
                                len(equal_prob_idx) - 1
                            )

                pred_for_rec = [
                    (
                        self._weak_labels.int2label[
                            self._snorkelInt2weaklabelsInt[snorkel_idx]
                        ],
                        prob[snorkel_idx],
                    )
                    for snorkel_idx in np.argsort(prob)[::-1]
                ]

            records_with_prediction[-1].prediction = pred_for_rec
            records_with_prediction[-1].prediction_agent = prediction_agent

        return DatasetForTextClassification(records_with_prediction)

    def score(
        self,
        tie_break_policy: Union[TieBreakPolicy, str] = "abstain",
        output_str: bool = False,
    ) -> Union[Dict[str, float], str]:
        """Returns some scores/metrics of the label model with respect to the annotated records.

        The metrics are:

        - accuracy
        - micro/macro averages for precision, recall and f1
        - precision, recall, f1 and support for each label

        For more details about the metrics, check out the
        `sklearn docs <https://scikit-learn.org/stable/modules/generated/sklearn.metrics.precision_recall_fscore_support.html#sklearn-metrics-precision-recall-fscore-support>`__.

        .. note:: Metrics are only calculated over non-abstained predictions!

        Args:
            tie_break_policy: Policy to break ties. You can choose among three policies:

                - `abstain`: Do not provide any prediction
                - `random`: randomly choose among tied option using deterministic hash
                - `true-random`: randomly choose among the tied options. NOTE: repeated runs may have slightly different results due to differences in broken ties

                The last two policies can introduce quite a bit of noise, especially when the tie is among many labels,
                as is the case when all the labeling functions (rules) abstained.
            output_str: If True, return output as nicely formatted string.

        Returns:
            The scores/metrics in a dictionary or as a nicely formatted str.

        Raises:
            MissingAnnotationError: If the ``weak_labels`` do not contain annotated records.
        """
        from sklearn.metrics import classification_report

        if isinstance(tie_break_policy, str):
            tie_break_policy = TieBreakPolicy(tie_break_policy)

        if self._weak_labels.annotation().size == 0:
            raise MissingAnnotationError(
                "You need annotated records to compute scores/metrics for your label model."
            )

        l_pred = self._weak_labels.matrix(has_annotation=True)
        if self._need_remap:
            l_pred = self._copy_and_remap(l_pred)

        # get predictions and probabilities
        predictions, probabilities = self._model.predict(
            L=l_pred,
            return_probs=True,
            tie_break_policy=tie_break_policy.value,
        )

        # metrics are only calculated for non-abstained data points
        idx = predictions != -1

        annotation = self._weak_labels.annotation()[idx]
        if self._need_remap:
            annotation = self._copy_and_remap(annotation)

        return classification_report(
            annotation,
            predictions[idx],
            target_names=self._weak_labels.labels[: annotation.max() + 1],
            output_dict=not output_str,
        )


class FlyingSquid(LabelModel):
    """The label model by `FlyingSquid <https://github.com/HazyResearch/flyingsquid>`__.

    .. note:: It is not suited for multi-label classification and does not support it!

    Args:
        weak_labels: A `WeakLabels` object containing the weak labels and records.
        **kwargs: Passed on to the init of the FlyingSquid's
            `LabelModel <https://github.com/HazyResearch/flyingsquid/blob/master/flyingsquid/label_model.py#L18>`__.

    Examples:
        >>> from rubrix.labeling.text_classification import WeakLabels
        >>> weak_labels = WeakLabels(dataset="my_dataset")
        >>> label_model = FlyingSquid(weak_labels)
        >>> label_model.fit()
        >>> records = label_model.predict()
    """

    def __init__(self, weak_labels: WeakLabels, **kwargs):
        try:
            import flyingsquid
            import pgmpy
        except ModuleNotFoundError:
            raise ModuleNotFoundError(
                "'flyingsquid' must be installed to use the `FlyingSquid` label model! "
                "You can install 'flyingsquid' with the command: `pip install pgmpy flyingsquid`"
            )
        else:
            from flyingsquid.label_model import LabelModel as FlyingSquidLabelModel

            self._FlyingSquidLabelModel = FlyingSquidLabelModel

        super().__init__(weak_labels)

        if len(self._weak_labels.rules) < 3:
            raise TooFewRulesError(
                "The FlyingSquid label model needs at least three (independent) rules!"
            )

        if "m" in kwargs:
            raise ValueError(
                "Your kwargs must not contain 'm', it is provided automatically."
            )

        self._init_kwargs = kwargs
        self._models: List[FlyingSquidLabelModel] = []

    def fit(self, include_annotated_records: bool = False, **kwargs):
        """Fits the label model.

        Args:
            include_annotated_records: Whether to include annotated records in the fitting.
            **kwargs: Passed on to the FlyingSquid's
                `LabelModel.fit() <https://github.com/HazyResearch/flyingsquid/blob/master/flyingsquid/label_model.py#L320>`__
                method.
        """
        wl_matrix = self._weak_labels.matrix(
            has_annotation=None if include_annotated_records else False
        )

        models = []
        # create a label model for each label (except for binary classification)
        # much of the implementation is taken from wrench:
        # https://github.com/JieyuZ2/wrench/blob/main/wrench/labelmodel/flyingsquid.py
        # If binary, we only need one model
        for i in range(
            1 if self._weak_labels.cardinality == 2 else self._weak_labels.cardinality
        ):
            model = self._FlyingSquidLabelModel(
                m=len(self._weak_labels.rules), **self._init_kwargs
            )
            wl_matrix_i = self._copy_and_transform_wl_matrix(wl_matrix, i)
            model.fit(L_train=wl_matrix_i, **kwargs)
            models.append(model)

        self._models = models

    def _copy_and_transform_wl_matrix(self, weak_label_matrix: np.ndarray, i: int):
        """Helper function to copy and transform the weak label matrix with respect to a target label.

         FlyingSquid expects the matrix to contain -1, 0 and 1, which are mapped the following way:

        - target label: -1
        - abstain label: 0
        - other label: 1

        Args:
            weak_label_matrix: The original weak label matrix
            i: Index of the target label

        Returns:
            A copy of the weak label matrix, transformed with respect to the target label.
        """
        wl_matrix_i = weak_label_matrix.copy()

        target_mask = (
            wl_matrix_i == self._weak_labels.label2int[self._weak_labels.labels[i]]
        )
        abstain_mask = wl_matrix_i == self._weak_labels.label2int[None]
        other_mask = (~target_mask) & (~abstain_mask)

        wl_matrix_i[target_mask] = -1
        wl_matrix_i[abstain_mask] = 0
        wl_matrix_i[other_mask] = 1

        return wl_matrix_i

    def predict(
        self,
        include_annotated_records: bool = False,
        include_abstentions: bool = False,
        prediction_agent: str = "FlyingSquid",
        verbose: bool = True,
        tie_break_policy: Union[TieBreakPolicy, str] = "abstain",
    ) -> DatasetForTextClassification:
        """Applies the label model.

        Args:
            include_annotated_records: Whether to include annotated records.
            include_abstentions: Whether to include records in the output, for which the label model abstained.
            prediction_agent: String used for the ``prediction_agent`` in the returned records.
            verbose: If True, print out messages of the progress to stderr.
            tie_break_policy: Policy to break ties. You can choose among two policies:

                - `abstain`: Do not provide any prediction
                - `random`: randomly choose among tied option using deterministic hash

                The last policy can introduce quite a bit of noise, especially when the tie is among many labels,
                as is the case when all the labeling functions (rules) abstained.

        Returns:
            A dataset of records that include the predictions of the label model.

        Raises:
            NotFittedError: If the label model was still not fitted.
        """
        if isinstance(tie_break_policy, str):
            tie_break_policy = TieBreakPolicy(tie_break_policy)

        wl_matrix = self._weak_labels.matrix(
            has_annotation=None if include_annotated_records else False
        )
        probabilities = self._predict(wl_matrix, verbose)

        # add predictions to records
        records_with_prediction = []
        for i, prob, rec in zip(
            range(len(probabilities)),
            probabilities,
            self._weak_labels.records(
                has_annotation=None if include_annotated_records else False
            ),
        ):
            # Check if model abstains, that is if the highest probability is assigned to more than one label
            # 1.e-8 is taken from the abs tolerance of np.isclose
            equal_prob_idx = np.nonzero(np.abs(prob.max() - prob) < 1.0e-8)[0]
            tie = False
            if len(equal_prob_idx) > 1:
                tie = True

            # maybe skip record
            if not include_abstentions and (
                tie and tie_break_policy is TieBreakPolicy.ABSTAIN
            ):
                continue

            if not tie:
                pred_for_rec = [
                    (self._weak_labels.labels[i], prob[i])
                    for i in np.argsort(prob)[::-1]
                ]
            # resolve ties following the tie break policy
            elif tie_break_policy is TieBreakPolicy.ABSTAIN:
                pred_for_rec = None
            elif tie_break_policy is TieBreakPolicy.RANDOM:
                random_idx = int(hashlib.sha1(f"{i}".encode()).hexdigest(), 16) % len(
                    equal_prob_idx
                )
                for idx in equal_prob_idx:
                    if idx == random_idx:
                        prob[idx] += self._PROBABILITY_INCREASE_ON_TIE_BREAK
                    else:
                        prob[idx] -= self._PROBABILITY_INCREASE_ON_TIE_BREAK / (
                            len(equal_prob_idx) - 1
                        )
                pred_for_rec = [
                    (self._weak_labels.labels[i], prob[i])
                    for i in np.argsort(prob)[::-1]
                ]
            else:
                raise NotImplementedError(
                    f"The tie break policy '{tie_break_policy.value}' is not implemented for FlyingSquid!"
                )

            records_with_prediction.append(rec.copy(deep=True))
            records_with_prediction[-1].prediction = pred_for_rec
            records_with_prediction[-1].prediction_agent = prediction_agent

        return DatasetForTextClassification(records_with_prediction)

    def _predict(self, weak_label_matrix: np.ndarray, verbose: bool) -> np.ndarray:
        """Helper function that calls the ``predict_proba`` method of FlyingSquid's label model.

        Much of the implementation is taken from wrench:
        https://github.com/JieyuZ2/wrench/blob/main/wrench/labelmodel/flyingsquid.py

        Args:
            weak_label_matrix: The weak label matrix.
            verbose: If True, print out messages of the progress to stderr.

        Returns:
            A matrix containing the probability for each label and record.

        Raises:
            NotFittedError: If the label model was still not fitted.
        """
        if not self._models:
            raise NotFittedError(
                "This FlyingSquid instance is not fitted yet. Call `fit` before using this model."
            )
        # create predictions for each label
        if self._weak_labels.cardinality > 2:
            probas = np.zeros((len(weak_label_matrix), self._weak_labels.cardinality))
            for i in range(self._weak_labels.cardinality):
                wl_matrix_i = self._copy_and_transform_wl_matrix(weak_label_matrix, i)
                probas[:, i] = self._models[i].predict_proba(
                    L_matrix=wl_matrix_i, verbose=verbose
                )[:, 0]
            probas = np.nan_to_num(probas, nan=-np.inf)  # handle NaN
            probas = np.exp(probas) / np.sum(np.exp(probas), axis=1, keepdims=True)
        # if binary, we only have one model
        else:
            wl_matrix_i = self._copy_and_transform_wl_matrix(weak_label_matrix, 0)
            probas = self._models[0].predict_proba(
                L_matrix=wl_matrix_i, verbose=verbose
            )

        return probas

    def score(
        self,
        tie_break_policy: Union[TieBreakPolicy, str] = "abstain",
        verbose: bool = False,
        output_str: bool = False,
    ) -> Union[Dict[str, float], str]:
        """Returns some scores/metrics of the label model with respect to the annotated records.

        The metrics are:

        - accuracy
        - micro/macro averages for precision, recall and f1
        - precision, recall, f1 and support for each label

        For more details about the metrics, check out the
        `sklearn docs <https://scikit-learn.org/stable/modules/generated/sklearn.metrics.precision_recall_fscore_support.html#sklearn-metrics-precision-recall-fscore-support>`__.

        .. note:: Metrics are only calculated over non-abstained predictions!

        Args:
            tie_break_policy: Policy to break ties. You can choose among two policies:

                - `abstain`: Do not provide any prediction
                - `random`: randomly choose among tied option using deterministic hash

                The last policy can introduce quite a bit of noise, especially when the tie is among many labels,
                as is the case when all the labeling functions (rules) abstained.
            verbose: If True, print out messages of the progress to stderr.
            output_str: If True, return output as nicely formatted string.

        Returns:
            The scores/metrics in a dictionary or as a nicely formatted str.

        Raises:
            NotFittedError: If the label model was still not fitted.
            MissingAnnotationError: If the ``weak_labels`` do not contain annotated records.
        """
        try:
            import sklearn
        except ModuleNotFoundError:
            raise ModuleNotFoundError(
                "'sklearn' must be installed to compute the metrics! "
                "You can install 'sklearn' with the command: `pip install scikit-learn`"
            )
        from sklearn.metrics import classification_report

        if isinstance(tie_break_policy, str):
            tie_break_policy = TieBreakPolicy(tie_break_policy)

        wl_matrix = self._weak_labels.matrix(has_annotation=True)
        probabilities = self._predict(wl_matrix, verbose)

        # 1.e-8 is taken from the abs tolerance of np.isclose
        is_max = (
            np.abs(probabilities.max(axis=1, keepdims=True) - probabilities) < 1.0e-8
        )
        is_tie = is_max.sum(axis=1) > 1

        prediction = np.argmax(is_max, axis=1)
        # we need to transform the indexes!
        annotation = np.array(
            [
                self._weak_labels.labels.index(self._weak_labels.int2label[i])
                for i in self._weak_labels.annotation()
            ],
            dtype=np.short,
        )

        if not is_tie.any():
            pass
        # resolve ties
        elif tie_break_policy is TieBreakPolicy.ABSTAIN:
            prediction, annotation = prediction[~is_tie], annotation[~is_tie]
        elif tie_break_policy is TieBreakPolicy.RANDOM:
            for i in np.nonzero(is_tie)[0]:
                equal_prob_idx = np.nonzero(is_max[i])[0]
                random_idx = int(hashlib.sha1(f"{i}".encode()).hexdigest(), 16) % len(
                    equal_prob_idx
                )
                prediction[i] = equal_prob_idx[random_idx]
        else:
            raise NotImplementedError(
                f"The tie break policy '{tie_break_policy.value}' is not implemented for FlyingSquid!"
            )

        return classification_report(
            annotation,
            prediction,
            target_names=self._weak_labels.labels[: annotation.max() + 1],
            output_dict=not output_str,
        )


class LabelModelError(Exception):
    pass


class MissingAnnotationError(LabelModelError):
    pass


class TooFewRulesError(LabelModelError):
    pass


class NotFittedError(LabelModelError):
    pass