def fit(self, y):
"""
Fit label binarizer
Parameters
----------
y : array of shape [n_samples,] or [n_samples, n_classes]
Target values. The 2-d matrix should only contain 0 and 1,
represents multilabel classification.
Returns
-------
self : returns an instance of self.
"""
if y.ndim > 2:
raise ValueError("labels cannot be greater than 2 dimensions")
if y.ndim == 2:
unique_classes = rmm_cupy_ary(cp.unique, y)
if unique_classes != [0, 1]:
raise ValueError("2-d array can must be binary")
self.classes_ = rmm_cupy_ary(cp.arange, 0, y.shape[1])
else:
self.classes_ = rmm_cupy_ary(cp.unique, y).astype(y.dtype)
cp.cuda.Stream.null.synchronize()
return self
def inverse_transform(self, y, threshold=None):
"""
Transform binary labels back to original multi-class labels
Parameters
----------
y : array of shape [n_samples, n_classes]
threshold : float this value is currently ignored
Returns
-------
arr : array with original labels
"""
if has_scipy():
from scipy.sparse import isspmatrix as scipy_sparse_isspmatrix
else:
from cuml.common.import_utils import dummy_function_always_false \
as scipy_sparse_isspmatrix
# If we are already given multi-class, just return it.
if cupyx.scipy.sparse.isspmatrix(y):
y_mapped = y.tocsr().indices.astype(self._classes_.dtype)
elif scipy_sparse_isspmatrix(y):
y = y.tocsr()
y_mapped = rmm_cupy_ary(cp.array, y.indices, dtype=y.indices.dtype)
else:
y_mapped = rmm_cupy_ary(cp.argmax,
rmm_cupy_ary(cp.asarray, y, dtype=y.dtype),
axis=1).astype(y.dtype)
return invert_labels(y_mapped, self._classes_)
def fit(self, y):
"""Fit label binarizer
Parameters
----------
y : Dask.Array of shape [n_samples,] or [n_samples, n_classes]
chunked by row.
Target values. The 2-d matrix should only contain 0 and 1,
represents multilabel classification.
Returns
-------
self : returns an instance of self.
"""
# Take the unique classes and broadcast them all around the cluster.
futures = self.client.sync(_extract_partitions, y)
unique = [
self.client.submit(LabelBinarizer._func_unique_classes, f)
for w, f in futures
]
classes = self.client.compute(unique, True)
classes = rmm_cupy_ary(cp.unique,
rmm_cupy_ary(cp.stack, classes, axis=0))
self._set_internal_model(LB(**self.kwargs).fit(classes))
return self
def convert_dtype(X, to_dtype=np.float32, legacy=True):
"""
Convert X to be of dtype `dtype`
Supported float dtypes for overflow checking.
Todo: support other dtypes if needed.
"""
if isinstance(X, np.ndarray):
dtype = X.dtype
if dtype != to_dtype:
X_m = X.astype(to_dtype)
if len(X[X == np.inf]) > 0:
raise TypeError("Data type conversion resulted"
"in data loss.")
return X_m
elif isinstance(X, (cudf.Series, cudf.DataFrame, pd.Series, pd.DataFrame)):
return X.astype(to_dtype)
elif cuda.is_cuda_array(X):
X_m = rmm_cupy_ary(cp.asarray, X)
X_m = X_m.astype(to_dtype)
if legacy:
return cuda.as_cuda_array(X_m)
else:
return CumlArray(data=X_m)
else:
raise TypeError("Received unsupported input type: %s" % type(X))
return X
def _conv_array_to_sparse(arr):
"""
Converts an array (or cudf.DataFrame) to a sparse array
:param arr: scipy or cupy sparse matrix, cudf DataFrame,
dense numpy or cupy array
:return: cupy sparse CSR matrix
"""
if has_scipy():
from scipy.sparse import isspmatrix as scipy_sparse_isspmatrix
else:
from cuml.common.import_utils import dummy_function_always_false \
as scipy_sparse_isspmatrix
if scipy_sparse_isspmatrix(arr):
ret = \
cupyx.scipy.sparse.csr_matrix(arr.tocsr())
elif cupyx.scipy.sparse.isspmatrix(arr):
ret = arr
elif isinstance(arr, cudf.DataFrame):
ret = _conv_df_to_sparse(arr)
elif isinstance(arr, np.ndarray):
cupy_ary = rmm_cupy_ary(cp.asarray, arr, dtype=arr.dtype)
ret = cupyx.scipy.sparse.csr_matrix(cupy_ary)
elif isinstance(arr, cp.core.core.ndarray):
ret = cupyx.scipy.sparse.csr_matrix(arr)
else:
raise ValueError("Unexpected input type %s" % type(arr))
return ret
def inverse_transform(self, y, threshold=None):
"""
Invert a set of encoded labels back to original labels
Parameters
----------
y : Dask.Array of shape [n_samples, n_classes] containing encoded
labels
threshold : float This value is currently ignored
Returns
-------
arr : Dask.Array backed by CuPy arrays containing original labels
"""
parts = self.client.sync(_extract_partitions, y)
inv_func = dask.delayed(LabelBinarizer._func_inv_xform)
dtype = self.classes_.dtype
meta = rmm_cupy_ary(cp.zeros, 1, dtype=dtype)
internal_model = self._get_internal_model()
f = [
dask.array.from_delayed(inv_func(internal_model, part, threshold),
dtype=dtype,
shape=(y.shape[0], ),
meta=meta) for w, part in parts
]
ret = dask.array.stack(f, axis=0)
return ret.reshape(ret.shape[1:])
def transform(self, y):
"""
Transform and return encoded labels
Parameters
----------
y : Dask.Array of shape [n_samples,] or [n_samples, n_classes]
Returns
-------
arr : Dask.Array backed by CuPy arrays containing encoded labels
"""
parts = self.client.sync(_extract_partitions, y)
internal_model = self._get_internal_model()
xform_func = dask.delayed(LabelBinarizer._func_xform)
meta = rmm_cupy_ary(cp.zeros, 1)
if internal_model.sparse_output:
meta = cupyx.scipy.sparse.csr_matrix(meta)
f = [
dask.array.from_delayed(xform_func(internal_model, part),
meta=meta,
dtype=cp.float32,
shape=(len(y), len(self.classes_)))
for w, part in parts
]
arr = dask.array.asarray(f)
return arr.reshape(arr.shape[1:])
def label_binarize(y, classes, neg_label=0, pos_label=1, sparse_output=False):
"""
A stateless helper function to dummy encode multi-class labels.
Parameters
----------
y : array-like of size [n_samples,] or [n_samples, n_classes]
classes : the set of unique classes in the input
neg_label : integer the negative value for transformed output
pos_label : integer the positive value for transformed output
sparse_output : bool whether to return sparse array
"""
classes = rmm_cupy_ary(cp.asarray, classes, dtype=classes.dtype)
labels = rmm_cupy_ary(cp.asarray, y, dtype=y.dtype)
if not check_labels(labels, classes):
raise ValueError("Unseen classes encountered in input")
row_ind = rmm_cupy_ary(cp.arange, 0, labels.shape[0], 1, dtype=y.dtype)
col_ind, _ = make_monotonic(labels, classes, copy=True)
val = rmm_cupy_ary(cp.full, row_ind.shape[0], pos_label, dtype=y.dtype)
sp = cupyx.scipy.sparse.coo_matrix(
(val, (row_ind, col_ind)),
shape=(col_ind.shape[0], classes.shape[0]),
dtype=cp.float32)
cp.cuda.Stream.null.synchronize()
if sparse_output:
sp = sp.tocsr()
return sp
else:
arr = sp.toarray().astype(y.dtype)
arr[arr == 0] = neg_label
return arr
def _func_inv_xform(model, y, threshold):
y = rmm_cupy_ary(cp.asarray, y, dtype=y.dtype)
return model.inverse_transform(y, threshold)
def _func_xform(model, y):
xform_in = rmm_cupy_ary(cp.asarray, y, dtype=y.dtype)
return model.transform(xform_in)
def _func_unique_classes(y):
return rmm_cupy_ary(cp.unique, y)
def _unique(x):
return rmm_cupy_ary(cp.unique, x)
def _count_accurate_predictions(y_hat, y):
y_hat = rmm_cupy_ary(cp.asarray, y_hat, dtype=y_hat.dtype)
y = rmm_cupy_ary(cp.asarray, y, dtype=y.dtype)
return y.shape[0] - cp.count_nonzero(y - y_hat)
def _conv_df_to_sparse(x):
cupy_ary = rmm_cupy_ary(cp.asarray, x.to_cupy(), dtype=x.dtypes[0])
return cupyx.scipy.sparse.csr_matrix(cupy_ary)
def _conv_df_to_sparse(x):
cupy_ary = rmm_cupy_ary(cp.asarray, x.as_gpu_matrix(), dtype=x.dtypes[0])
return cp.sparse.csr_matrix(cupy_ary)
def _conv_np_to_df(x):
cupy_ary = rmm_cupy_ary(cp.asarray, x, dtype=x.dtype)
return cudf.DataFrame.from_gpu_matrix(cupy_ary)
def input_to_cuml_array(X,
order='F',
deepcopy=False,
check_dtype=False,
convert_to_dtype=False,
check_cols=False,
check_rows=False,
fail_on_order=False):
"""
Convert input X to CumlArray.
Acceptable input formats:
* cuDF Dataframe - returns a deep copy always.
* cuDF Series - returns by reference or a deep copy depending on
`deepcopy`.
* Numpy array - returns a copy in device always
* cuda array interface compliant array (like Cupy) - returns a
reference unless `deepcopy`=True.
* numba device array - returns a reference unless deepcopy=True
Parameters
----------
X : cuDF.DataFrame, cuDF.Series, numba array, NumPy array or any
cuda_array_interface compliant array like CuPy or pytorch.
order: 'F', 'C' or 'K' (default: 'F')
Whether to return a F-major ('F'), C-major ('C') array or Keep ('K')
the order of X. Used to check the order of the input. If
fail_on_order=True, the method will raise ValueError,
otherwise it will convert X to be of order `order` if needed.
deepcopy: boolean (default: False)
Set to True to always return a deep copy of X.
check_dtype: np.dtype (default: False)
Set to a np.dtype to throw an error if X is not of dtype `check_dtype`.
convert_to_dtype: np.dtype (default: False)
Set to a dtype if you want X to be converted to that dtype if it is
not that dtype already.
check_cols: int (default: False)
Set to an int `i` to check that input X has `i` columns. Set to False
(default) to not check at all.
check_rows: boolean (default: False)
Set to an int `i` to check that input X has `i` columns. Set to False
(default) to not check at all.
fail_on_order: boolean (default: False)
Set to True if you want the method to raise a ValueError if X is not
of order `order`.
Returns
-------
`cuml_array`: namedtuple('cuml_array', 'array n_rows n_cols dtype')
A new CumlArray and associated data.
"""
# dtype conversion
if convert_to_dtype:
X = convert_dtype(X, to_dtype=convert_to_dtype)
check_dtype = False
# format conversion
if (isinstance(X, cudf.Series)):
if X.null_count != 0:
raise ValueError("Error: cuDF Series has missing/null values, " +
" which are not supported by cuML.")
# converting pandas to numpy before sending it to CumlArray
if isinstance(X, pd.DataFrame) or isinstance(X, pd.Series):
# pandas doesn't support custom order in to_numpy
X = cp.asarray(X.to_numpy(copy=False), order=order)
if isinstance(X, cudf.DataFrame):
if order == 'K':
X_m = CumlArray(data=X.as_gpu_matrix(order='F'))
else:
X_m = CumlArray(data=X.as_gpu_matrix(order=order))
elif isinstance(X, CumlArray):
X_m = X
elif hasattr(X, "__array_interface__") or \
hasattr(X, "__cuda_array_interface__"):
X_m = CumlArray(data=X)
if deepcopy:
X_m = copy.deepcopy(X_m)
else:
msg = "X matrix format " + str(X.__class__) + " not supported"
raise TypeError(msg)
if check_dtype:
if not isinstance(check_dtype, list):
check_dtype = [check_dtype]
check_dtype = [np.dtype(dtype) for dtype in check_dtype]
if X_m.dtype not in check_dtype:
type_str = X_m.dtype
del X_m
raise TypeError("Expected input to be of type in " +
str(check_dtype) + " but got " + str(type_str))
# Checks based on parameters
n_rows = X_m.shape[0]
if len(X_m.shape) > 1:
n_cols = X_m.shape[1]
else:
n_cols = 1
if n_cols == 1 or n_rows == 1:
order = 'K'
if check_cols:
if n_cols != check_cols:
raise ValueError("Expected " + str(check_cols) +
" columns but got " + str(n_cols) + " columns.")
if check_rows:
if n_rows != check_rows:
raise ValueError("Expected " + str(check_rows) + " rows but got " +
str(n_rows) + " rows.")
if order != 'K' and X_m.order != order:
if fail_on_order:
raise ValueError("Expected " + order_to_str(order) +
" major order, but got the opposite.")
else:
warnings.warn("Expected " + order_to_str(order) + " major order, "
"but got the opposite. Converting data, this will "
"result in additional memory utilization.")
X_m = rmm_cupy_ary(cp.array, X_m, copy=False, order=order)
X_m = CumlArray(data=X_m)
return cuml_array(array=X_m, n_rows=n_rows, n_cols=n_cols, dtype=X_m.dtype)
def to_sparse_dask_array(cudf_or_array, client=None):
"""
Converts an array or cuDF to a sparse Dask array backed by sparse CuPy.
CSR matrices. Unfortunately, due to current limitations in Dask, there is
no direct path to convert a cupy.sparse.spmatrix into a CuPy backed
dask.Array without copying to host.
NOTE: Until https://github.com/cupy/cupy/issues/2655 and
https://github.com/dask/dask/issues/5604 are implemented, compute()
will not be able to be called on a Dask.array that is backed with
sparse CuPy arrays because they lack the necessary functionality
to be stacked into a single array. The array returned from this
utility will, however, still be able to be passed into functions
that can make use of sparse CuPy-backed Dask.Array (eg. Distributed
Naive Bayes).
Relevant cuML issue: https://github.com/rapidsai/cuml/issues/1387
Parameters
----------
cudf_or_array : cuDF Dataframe, array-like sparse / dense array, or
Dask DataFrame/Array
client : dask.distributed.Client (optional) Dask client
dtype : output dtype
Returns
-------
dask_array : dask.Array backed by cupy.sparse.csr_matrix
"""
client = default_client() if client is None else client
# Makes sure the MatDescriptor workaround for CuPy sparse arrays
# is loaded (since Dask lazy-loaded serialization in cuML is only
# executed when object from the cuML package needs serialization.
# This can go away once the MatDescriptor pickling bug is fixed
# in CuPy.
# Ref: https://github.com/cupy/cupy/issues/3061
from cuml.comm import serialize # NOQA
shape = cudf_or_array.shape
meta = cupyx.scipy.sparse.csr_matrix(rmm_cupy_ary(cp.zeros, 1))
ret = cudf_or_array
# If we have a Dask array, convert it to a Dask DataFrame
if isinstance(ret, dask.array.Array):
# At the time of developing this, using map_blocks will not work
# to convert a Dask.Array to CuPy sparse arrays underneath.
def _conv_np_to_df(x):
cupy_ary = rmm_cupy_ary(cp.asarray, x, dtype=x.dtype)
return cudf.DataFrame.from_gpu_matrix(cupy_ary)
parts = client.sync(_extract_partitions, ret)
futures = [
client.submit(_conv_np_to_df, part, workers=[w], pure=False)
for w, part in parts
]
ret = df_to_dask_cudf(futures)
# If we have a Dask Dataframe, use `map_partitions` to convert it
# to a Sparse Cupy-backed Dask Array. This will also convert the dense
# Dask array above to a Sparse Cupy-backed Dask Array, since we cannot
# use map_blocks on the array, but we can use `map_partitions` on the
# Dataframe.
if isinstance(ret, dask.dataframe.DataFrame):
ret = ret.map_partitions(_conv_df_to_sparse,
meta=dask.array.from_array(meta))
# This will also handle the input of dask.array.Array
return ret
else:
ret = _conv_array_to_sparse(ret)
# Push to worker
final_result = client.scatter(ret)
return dask.array.from_delayed(final_result, shape=shape, meta=meta)
def train_test_split(X,
y,
test_size: Union[float, int] = None,
train_size: Union[float, int] = None,
shuffle: bool = True,
random_state: Union[int, cp.random.RandomState,
np.random.RandomState] = None,
seed: Union[int, cp.random.RandomState,
np.random.RandomState] = None):
"""
Partitions device data into four collated objects, mimicking
Scikit-learn's `train_test_split`
Parameters
----------
X : cudf.DataFrame or cuda_array_interface compliant device array
Data to split, has shape (n_samples, n_features)
y : str, cudf.Series or cuda_array_interface compliant device array
Set of labels for the data, either a series of shape (n_samples) or
the string label of a column in X (if it is a cuDF DataFrame)
containing the labels
train_size : float or int, optional
If float, represents the proportion [0, 1] of the data
to be assigned to the training set. If an int, represents the number
of instances to be assigned to the training set. Defaults to 0.8
shuffle : bool, optional
Whether or not to shuffle inputs before splitting
random_state : int, CuPy RandomState or NumPy RandomState optional
If shuffle is true, seeds the generator. Unseeded by default
seed: random_state : int, CuPy RandomState or NumPy RandomState optional
Deprecated in favor of `random_state`.
If shuffle is true, seeds the generator. Unseeded by default
Examples
--------
.. code-block:: python
import cudf
from cuml.preprocessing.model_selection import train_test_split
# Generate some sample data
df = cudf.DataFrame({'x': range(10),
'y': [0, 1] * 5})
print(f'Original data: {df.shape[0]} elements')
# Suppose we want an 80/20 split
X_train, X_test, y_train, y_test = train_test_split(df, 'y',
train_size=0.8)
print(f'X_train: {X_train.shape[0]} elements')
print(f'X_test: {X_test.shape[0]} elements')
print(f'y_train: {y_train.shape[0]} elements')
print(f'y_test: {y_test.shape[0]} elements')
# Alternatively, if our labels are stored separately
labels = df['y']
df = df.drop(['y'])
# we can also do
X_train, X_test, y_train, y_test = train_test_split(df, labels,
train_size=0.8)
Output:
.. code-block:: python
Original data: 10 elements
X_train: 8 elements
X_test: 2 elements
y_train: 8 elements
y_test: 2 elements
Returns
-------
X_train, X_test, y_train, y_test : cudf.DataFrame
Partitioned dataframes. If `y` was provided as a column name, the
column was dropped from the `X`s
"""
if isinstance(y, str):
# Use the column with name `str` as y
if isinstance(X, cudf.DataFrame):
name = y
y = X[name]
X = X.drop(name)
else:
raise TypeError("X needs to be a cuDF Dataframe when y is a \
string")
# todo: this check will be replaced with upcoming improvements
# to input_utils with PR #1379
if not cuda.is_cuda_array(X) and not isinstance(X, cudf.DataFrame) \
and isinstance(y, cudf.Series):
raise TypeError("X needs to be either a cuDF DataFrame, Series or \
a cuda_array_interface compliant array.")
if not cuda.is_cuda_array(y) and not isinstance(y, cudf.DataFrame) \
and isinstance(y, cudf.Series):
raise TypeError("y needs to be either a cuDF DataFrame, Series or \
a cuda_array_interface compliant array.")
if X.shape[0] != y.shape[0]:
raise ValueError("X and y must have the same first dimension"
"(found {} and {})".format(X.shape[0], y.shape[0]))
if isinstance(train_size, float):
if not 0 <= train_size <= 1:
raise ValueError("proportion train_size should be between"
"0 and 1 (found {})".format(train_size))
if isinstance(train_size, int):
if not 0 <= train_size <= X.shape[0]:
raise ValueError(
"Number of instances train_size should be between 0 and the"
"first dimension of X (found {})".format(train_size))
if isinstance(test_size, float):
if not 0 <= test_size <= 1:
raise ValueError("proportion test_size should be between"
"0 and 1 (found {})".format(train_size))
if isinstance(test_size, int):
if not 0 <= test_size <= X.shape[0]:
raise ValueError(
"Number of instances test_size should be between 0 and the"
"first dimension of X (found {})".format(test_size))
x_numba = False
y_numba = False
if seed is not None:
if random_state is None:
warnings.warn("Parameter 'seed' is deprecated, please use \
'random_state' instead.")
random_state = seed
else:
warnings.warn("Both 'seed' and 'random_state' parameters were \
set, using 'random_state' since 'seed' is \
deprecated. ")
if shuffle:
if random_state is None or isinstance(random_state, int):
idxs = rmm_cupy_ary(cp.arange, X.shape[0])
random_state = cp.random.RandomState(seed=random_state)
elif isinstance(random_state, cp.random.RandomState):
idxs = rmm_cupy_ary(cp.arange, X.shape[0])
elif isinstance(random_state, np.random.RandomState):
idxs = np.arange(X.shape[0])
else:
raise TypeError("`random_state` must be an int, NumPy RandomState \
or CuPy RandomState.")
random_state.shuffle(idxs)
if isinstance(X, cudf.DataFrame) or isinstance(X, cudf.Series):
X = X.iloc[idxs].reset_index(drop=True)
elif cuda.is_cuda_array(X):
# numba (and therefore rmm device_array) does not support
# fancy indexing
if cuda.devicearray.is_cuda_ndarray(X):
x_numba = True
X = cp.asarray(X)[idxs]
if isinstance(y, cudf.DataFrame) or isinstance(y, cudf.Series):
y = y.iloc[idxs]
elif cuda.is_cuda_array(y):
if cuda.devicearray.is_cuda_ndarray(y):
y_numba = True
y = cp.asarray(y)[idxs]
# Determining sizes of splits
if isinstance(train_size, float):
train_size = int(X.shape[0] * train_size)
if test_size is None:
if train_size is None:
train_size = int(X.shape[0] * 0.75)
test_size = X.shape[0] - train_size
if isinstance(test_size, float):
test_size = int(X.shape[0] * test_size)
if train_size is None:
train_size = X.shape[0] - test_size
elif isinstance(test_size, int):
if train_size is None:
train_size = X.shape[0] - test_size
if cuda.is_cuda_array(X) or isinstance(X, cp.sparse.csr_matrix):
X_train = X[0:train_size]
y_train = y[0:train_size]
elif isinstance(X, cudf.DataFrame):
X_train = X.iloc[0:train_size]
y_train = y.iloc[0:train_size]
if cuda.is_cuda_array(y) or isinstance(X, cp.sparse.csr_matrix):
X_test = X[-1 * test_size:]
y_test = y[-1 * test_size:]
elif isinstance(y, cudf.DataFrame):
X_test = X.iloc[-1 * test_size:]
y_test = y.iloc[-1 * test_size:]
if x_numba:
X_train = cuda.as_cuda_array(X_train)
X_test = cuda.as_cuda_array(X_test)
if y_numba:
y_train = cuda.as_cuda_array(y_train)
y_test = cuda.as_cuda_array(y_test)
return X_train, X_test, y_train, y_test