<gh_stars>1000+
import logging
import numpy as np
from typing import Tuple
from deepchem.data import Dataset
from deepchem.trans.transformers import Transformer

logger = logging.getLogger(__name__)


class DuplicateBalancingTransformer(Transformer):
  """Balance binary or multiclass datasets by duplicating rarer class samples.

  This class balances a dataset by duplicating samples of the rarer class so
  that the sum of all example weights from all classes is the same. (Up to
  integer rounding of course). This can be useful when you're working on an
  imabalanced dataset where there are far fewer examples of some classes than
  others.

  This class differs from `BalancingTransformer` in that it actually
  duplicates rarer class samples rather than just increasing their sample
  weights. This may be more friendly for models that are numerically fragile
  and can't handle imbalanced example weights.

  Examples
  --------
  Here's an example for a binary dataset.

  >>> n_samples = 10
  >>> n_features = 3
  >>> n_tasks = 1
  >>> n_classes = 2
  >>> import deepchem as dc
  >>> import numpy as np
  >>> ids = np.arange(n_samples)
  >>> X = np.random.rand(n_samples, n_features)
  >>> y = np.random.randint(n_classes, size=(n_samples, n_tasks))
  >>> w = np.ones((n_samples, n_tasks))
  >>> dataset = dc.data.NumpyDataset(X, y, w, ids)
  >>> transformer = dc.trans.DuplicateBalancingTransformer(dataset=dataset)
  >>> dataset = transformer.transform(dataset)

  And here's a multiclass dataset example.

  >>> n_samples = 50
  >>> n_features = 3
  >>> n_tasks = 1
  >>> n_classes = 5
  >>> ids = np.arange(n_samples)
  >>> X = np.random.rand(n_samples, n_features)
  >>> y = np.random.randint(n_classes, size=(n_samples, n_tasks))
  >>> w = np.ones((n_samples, n_tasks))
  >>> dataset = dc.data.NumpyDataset(X, y, w, ids)
  >>> transformer = dc.trans.DuplicateBalancingTransformer(dataset=dataset)
  >>> dataset = transformer.transform(dataset)

  See Also
  --------
  deepchem.trans.BalancingTransformer: Balance by changing sample weights.

  Note
  ----
  This transformer is only well-defined for singletask datasets. (Since
  examples are actually duplicated, there's no meaningful way to duplicate
  across multiple tasks in a way that preserves the balance.)

  This transformer is only meaningful for classification datasets where `y`
  takes on a limited set of values. This class transforms all of `X`, `y`,
  `w`, `ids`.

  Raises
  ------
  `ValueError` if the provided dataset is multitask.
  """

  def __init__(self, dataset: Dataset):
    super(DuplicateBalancingTransformer, self).__init__(
        transform_X=True,
        transform_y=True,
        transform_w=True,
        transform_ids=True,
        dataset=dataset)

    if len(dataset.get_task_names()) > 1:
      raise ValueError(
          "This transformation is only defined for singletask datsets.")

    # Get the labels/weights
    y = dataset.y
    w = dataset.w
    # Normalize shapes
    if len(y.shape) == 1:
      y = np.reshape(y, (len(y), 1))
    if len(w.shape) == 1:
      w = np.reshape(w, (len(w), 1))
    if len(y.shape) != 2:
      raise ValueError("y must be of shape (N,) or (N, n_tasks)")
    if len(w.shape) != 2:
      raise ValueError("w must be of shape (N,) or (N, n_tasks)")
    self.classes = sorted(np.unique(y))
    # Remove labels with zero weights
    y = y[w != 0]
    class_weights = []
    # Note that we may have 0 elements of a given class since we remove those
    # labels with zero weight.
    for c in self.classes:
      # this works because y is 1D
      c_weight = np.sum(w[y == c])
      class_weights.append(c_weight)
    weight_largest = max(class_weights)
    # This is the right ratio since int(N/num_c) * num_c \approx N
    # for all classes
    duplication_ratio = [
        int(weight_largest / float(c_weight)) if c_weight > 0 else 0
        for c_weight in class_weights
    ]
    self.duplication_ratio = duplication_ratio

  def transform_array(
      self, X: np.ndarray, y: np.ndarray, w: np.ndarray,
      ids: np.ndarray) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
    """Transform the data in a set of (X, y, w, id) arrays.

    Parameters
    ----------
    X: np.ndarray
      Array of features
    y: np.ndarray
      Array of labels
    w: np.ndarray
      Array of weights.
    ids: np.ndarray
      Array of identifiers

    Returns
    -------
    Xtrans: np.ndarray
      Transformed array of features
    ytrans: np.ndarray
      Transformed array of labels
    wtrans: np.ndarray
      Transformed array of weights
    idtrans: np.ndarray
      Transformed array of identifiers
    """
    if not (len(y.shape) == 1 or (len(y.shape) == 2 and y.shape[1] == 1)):
      raise ValueError("y must be of shape (N,) or (N, 1)")
    if not (len(w.shape) == 1 or (len(w.shape) == 2 and w.shape[1] == 1)):
      raise ValueError("w must be of shape (N,) or (N, 1)")
    # Flattening is safe because of shape check above
    y = y.flatten()
    w = w.flatten()
    X_dups, y_dups, w_dups, ids_dups = [], [], [], []
    for i, c in enumerate(self.classes):
      duplication_ratio = self.duplication_ratio[i]
      c_inds = (y == c)
      X_c = X[c_inds]
      y_c = y[c_inds]
      w_c = w[c_inds]
      ids_c = ids[c_inds]
      X_c_dup = np.repeat(X_c, duplication_ratio, axis=0)
      y_c_dup = np.repeat(y_c, duplication_ratio, axis=0)
      w_c_dup = np.repeat(w_c, duplication_ratio, axis=0)
      ids_c_dup = np.repeat(ids_c, duplication_ratio, axis=0)
      X_dups.append(X_c_dup)
      y_dups.append(y_c_dup)
      w_dups.append(w_c_dup)
      ids_dups.append(ids_c_dup)
    Xtrans = np.concatenate(X_dups, axis=0)
    ytrans = np.concatenate(y_dups, axis=0)
    wtrans = np.concatenate(w_dups, axis=0)
    idstrans = np.concatenate(ids_dups, axis=0)
    return (Xtrans, ytrans, wtrans, idstrans)

import logging
import numpy as np
from typing import Tuple
from deepchem.data import Dataset
from deepchem.trans.transformers import Transformer

logger = logging.getLogger(__name__)


class DuplicateBalancingTransformer(Transformer):
  """Balance binary or multiclass datasets by duplicating rarer class samples.

  This class balances a dataset by duplicating samples of the rarer class so
  that the sum of all example weights from all classes is the same. (Up to
  integer rounding of course). This can be useful when you're working on an
  imabalanced dataset where there are far fewer examples of some classes than
  others.

  This class differs from `BalancingTransformer` in that it actually
  duplicates rarer class samples rather than just increasing their sample
  weights. This may be more friendly for models that are numerically fragile
  and can't handle imbalanced example weights.

  Examples
  --------
  Here's an example for a binary dataset.

  >>> n_samples = 10
  >>> n_features = 3
  >>> n_tasks = 1
  >>> n_classes = 2
  >>> import deepchem as dc
  >>> import numpy as np
  >>> ids = np.arange(n_samples)
  >>> X = np.random.rand(n_samples, n_features)
  >>> y = np.random.randint(n_classes, size=(n_samples, n_tasks))
  >>> w = np.ones((n_samples, n_tasks))
  >>> dataset = dc.data.NumpyDataset(X, y, w, ids)
  >>> transformer = dc.trans.DuplicateBalancingTransformer(dataset=dataset)
  >>> dataset = transformer.transform(dataset)

  And here's a multiclass dataset example.

  >>> n_samples = 50
  >>> n_features = 3
  >>> n_tasks = 1
  >>> n_classes = 5
  >>> ids = np.arange(n_samples)
  >>> X = np.random.rand(n_samples, n_features)
  >>> y = np.random.randint(n_classes, size=(n_samples, n_tasks))
  >>> w = np.ones((n_samples, n_tasks))
  >>> dataset = dc.data.NumpyDataset(X, y, w, ids)
  >>> transformer = dc.trans.DuplicateBalancingTransformer(dataset=dataset)
  >>> dataset = transformer.transform(dataset)

  See Also
  --------
  deepchem.trans.BalancingTransformer: Balance by changing sample weights.

  Note
  ----
  This transformer is only well-defined for singletask datasets. (Since
  examples are actually duplicated, there's no meaningful way to duplicate
  across multiple tasks in a way that preserves the balance.)

  This transformer is only meaningful for classification datasets where `y`
  takes on a limited set of values. This class transforms all of `X`, `y`,
  `w`, `ids`.

  Raises
  ------
  `ValueError` if the provided dataset is multitask.
  """

  def __init__(self, dataset: Dataset):
    super(DuplicateBalancingTransformer, self).__init__(
        transform_X=True,
        transform_y=True,
        transform_w=True,
        transform_ids=True,
        dataset=dataset)

    if len(dataset.get_task_names()) > 1:
      raise ValueError(
          "This transformation is only defined for singletask datsets.")

    # Get the labels/weights
    y = dataset.y
    w = dataset.w
    # Normalize shapes
    if len(y.shape) == 1:
      y = np.reshape(y, (len(y), 1))
    if len(w.shape) == 1:
      w = np.reshape(w, (len(w), 1))
    if len(y.shape) != 2:
      raise ValueError("y must be of shape (N,) or (N, n_tasks)")
    if len(w.shape) != 2:
      raise ValueError("w must be of shape (N,) or (N, n_tasks)")
    self.classes = sorted(np.unique(y))
    # Remove labels with zero weights
    y = y[w != 0]
    class_weights = []
    # Note that we may have 0 elements of a given class since we remove those
    # labels with zero weight.
    for c in self.classes:
      # this works because y is 1D
      c_weight = np.sum(w[y == c])
      class_weights.append(c_weight)
    weight_largest = max(class_weights)
    # This is the right ratio since int(N/num_c) * num_c \approx N
    # for all classes
    duplication_ratio = [
        int(weight_largest / float(c_weight)) if c_weight > 0 else 0
        for c_weight in class_weights
    ]
    self.duplication_ratio = duplication_ratio

  def transform_array(
      self, X: np.ndarray, y: np.ndarray, w: np.ndarray,
      ids: np.ndarray) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
    """Transform the data in a set of (X, y, w, id) arrays.

    Parameters
    ----------
    X: np.ndarray
      Array of features
    y: np.ndarray
      Array of labels
    w: np.ndarray
      Array of weights.
    ids: np.ndarray
      Array of identifiers

    Returns
    -------
    Xtrans: np.ndarray
      Transformed array of features
    ytrans: np.ndarray
      Transformed array of labels
    wtrans: np.ndarray
      Transformed array of weights
    idtrans: np.ndarray
      Transformed array of identifiers
    """
    if not (len(y.shape) == 1 or (len(y.shape) == 2 and y.shape[1] == 1)):
      raise ValueError("y must be of shape (N,) or (N, 1)")
    if not (len(w.shape) == 1 or (len(w.shape) == 2 and w.shape[1] == 1)):
      raise ValueError("w must be of shape (N,) or (N, 1)")
    # Flattening is safe because of shape check above
    y = y.flatten()
    w = w.flatten()
    X_dups, y_dups, w_dups, ids_dups = [], [], [], []
    for i, c in enumerate(self.classes):
      duplication_ratio = self.duplication_ratio[i]
      c_inds = (y == c)
      X_c = X[c_inds]
      y_c = y[c_inds]
      w_c = w[c_inds]
      ids_c = ids[c_inds]
      X_c_dup = np.repeat(X_c, duplication_ratio, axis=0)
      y_c_dup = np.repeat(y_c, duplication_ratio, axis=0)
      w_c_dup = np.repeat(w_c, duplication_ratio, axis=0)
      ids_c_dup = np.repeat(ids_c, duplication_ratio, axis=0)
      X_dups.append(X_c_dup)
      y_dups.append(y_c_dup)
      w_dups.append(w_c_dup)
      ids_dups.append(ids_c_dup)
    Xtrans = np.concatenate(X_dups, axis=0)
    ytrans = np.concatenate(y_dups, axis=0)
    wtrans = np.concatenate(w_dups, axis=0)
    idstrans = np.concatenate(ids_dups, axis=0)
    return (Xtrans, ytrans, wtrans, idstrans)
Balance binary or multiclass datasets by duplicating rarer class samples.    This class balances a dataset by duplicating samples of the rarer class so   that the sum of all example weights from all classes is the same. (Up to   integer rounding of course). This can be useful when you're working on an   imabalanced dataset where there are far fewer examples of some classes than   others.    This class differs from `BalancingTransformer` in that it actually   duplicates rarer class samples rather than just increasing their sample   weights. This may be more friendly for models that are numerically fragile   and can't handle imbalanced example weights.    Examples   --------   Here's an example for a binary dataset.    >>> n_samples = 10   >>> n_features = 3   >>> n_tasks = 1   >>> n_classes = 2   >>> import deepchem as dc   >>> import numpy as np   >>> ids = np.arange(n_samples)   >>> X = np.random.rand(n_samples, n_features)   >>> y = np.random.randint(n_classes, size=(n_samples, n_tasks))   >>> w = np.ones((n_samples, n_tasks))   >>> dataset = dc.data.NumpyDataset(X, y, w, ids)   >>> transformer = dc.trans.DuplicateBalancingTransformer(dataset=dataset)   >>> dataset = transformer.transform(dataset)    And here's a multiclass dataset example.    >>> n_samples = 50   >>> n_features = 3   >>> n_tasks = 1   >>> n_classes = 5   >>> ids = np.arange(n_samples)   >>> X = np.random.rand(n_samples, n_features)   >>> y = np.random.randint(n_classes, size=(n_samples, n_tasks))   >>> w = np.ones((n_samples, n_tasks))   >>> dataset = dc.data.NumpyDataset(X, y, w, ids)   >>> transformer = dc.trans.DuplicateBalancingTransformer(dataset=dataset)   >>> dataset = transformer.transform(dataset)    See Also   --------   deepchem.trans.BalancingTransformer: Balance by changing sample weights.    Note   ----   This transformer is only well-defined for singletask datasets. (Since   examples are actually duplicated, there's no meaningful way to duplicate   across multiple tasks in a way that preserves the balance.)    This transformer is only meaningful for classification datasets where `y`   takes on a limited set of values. This class transforms all of `X`, `y`,   `w`, `ids`.    Raises   ------   `ValueError` if the provided dataset is multitask. # Get the labels/weights # Normalize shapes # Remove labels with zero weights # Note that we may have 0 elements of a given class since we remove those # labels with zero weight. # this works because y is 1D # This is the right ratio since int(N/num_c) * num_c \approx N # for all classes Transform the data in a set of (X, y, w, id) arrays.      Parameters     ----------     X: np.ndarray       Array of features     y: np.ndarray       Array of labels     w: np.ndarray       Array of weights.     ids: np.ndarray       Array of identifiers      Returns     -------     Xtrans: np.ndarray       Transformed array of features     ytrans: np.ndarray       Transformed array of labels     wtrans: np.ndarray       Transformed array of weights     idtrans: np.ndarray       Transformed array of identifiers # Flattening is safe because of shape check above