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Inzynierka_Gwiazdy/machine_learning/Lib/site-packages/sklearn/decomposition/_fastica.py

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Machine learning
2023-09-20 19:46:58 +02:00
"""
Python implementation of the fast ICA algorithms.
Reference: Tables 8.3 and 8.4 page 196 in the book:
Independent Component Analysis, by Hyvarinen et al.
"""
# Authors: Pierre Lafaye de Micheaux, Stefan van der Walt, Gael Varoquaux,
# Bertrand Thirion, Alexandre Gramfort, Denis A. Engemann
# License: BSD 3 clause
import warnings
from numbers import Integral, Real
import numpy as np
from scipy import linalg
from ..base import BaseEstimator, TransformerMixin, ClassNamePrefixFeaturesOutMixin
from ..exceptions import ConvergenceWarning
from ..utils import check_array, as_float_array, check_random_state
from ..utils.validation import check_is_fitted
from ..utils._param_validation import Hidden, Interval, StrOptions
__all__ = ["fastica", "FastICA"]
def _gs_decorrelation(w, W, j):
"""
Orthonormalize w wrt the first j rows of W.
Parameters
----------
w : ndarray of shape (n,)
Array to be orthogonalized
W : ndarray of shape (p, n)
Null space definition
j : int < p
The no of (from the first) rows of Null space W wrt which w is
orthogonalized.
Notes
-----
Assumes that W is orthogonal
w changed in place
"""
w -= np.linalg.multi_dot([w, W[:j].T, W[:j]])
return w
def _sym_decorrelation(W):
"""Symmetric decorrelation
i.e. W <- (W * W.T) ^{-1/2} * W
"""
s, u = linalg.eigh(np.dot(W, W.T))
# Avoid sqrt of negative values because of rounding errors. Note that
# np.sqrt(tiny) is larger than tiny and therefore this clipping also
# prevents division by zero in the next step.
s = np.clip(s, a_min=np.finfo(W.dtype).tiny, a_max=None)
# u (resp. s) contains the eigenvectors (resp. square roots of
# the eigenvalues) of W * W.T
return np.linalg.multi_dot([u * (1.0 / np.sqrt(s)), u.T, W])
def _ica_def(X, tol, g, fun_args, max_iter, w_init):
"""Deflationary FastICA using fun approx to neg-entropy function
Used internally by FastICA.
"""
n_components = w_init.shape[0]
W = np.zeros((n_components, n_components), dtype=X.dtype)
n_iter = []
# j is the index of the extracted component
for j in range(n_components):
w = w_init[j, :].copy()
w /= np.sqrt((w**2).sum())
for i in range(max_iter):
gwtx, g_wtx = g(np.dot(w.T, X), fun_args)
w1 = (X * gwtx).mean(axis=1) - g_wtx.mean() * w
_gs_decorrelation(w1, W, j)
w1 /= np.sqrt((w1**2).sum())
lim = np.abs(np.abs((w1 * w).sum()) - 1)
w = w1
if lim < tol:
break
n_iter.append(i + 1)
W[j, :] = w
return W, max(n_iter)
def _ica_par(X, tol, g, fun_args, max_iter, w_init):
"""Parallel FastICA.
Used internally by FastICA --main loop
"""
W = _sym_decorrelation(w_init)
del w_init
p_ = float(X.shape[1])
for ii in range(max_iter):
gwtx, g_wtx = g(np.dot(W, X), fun_args)
W1 = _sym_decorrelation(np.dot(gwtx, X.T) / p_ - g_wtx[:, np.newaxis] * W)
del gwtx, g_wtx
# builtin max, abs are faster than numpy counter parts.
# np.einsum allows having the lowest memory footprint.
# It is faster than np.diag(np.dot(W1, W.T)).
lim = max(abs(abs(np.einsum("ij,ij->i", W1, W)) - 1))
W = W1
if lim < tol:
break
else:
warnings.warn(
"FastICA did not converge. Consider increasing "
"tolerance or the maximum number of iterations.",
ConvergenceWarning,
)
return W, ii + 1
# Some standard non-linear functions.
# XXX: these should be optimized, as they can be a bottleneck.
def _logcosh(x, fun_args=None):
alpha = fun_args.get("alpha", 1.0) # comment it out?
x *= alpha
gx = np.tanh(x, x) # apply the tanh inplace
g_x = np.empty(x.shape[0], dtype=x.dtype)
# XXX compute in chunks to avoid extra allocation
for i, gx_i in enumerate(gx): # please don't vectorize.
g_x[i] = (alpha * (1 - gx_i**2)).mean()
return gx, g_x
def _exp(x, fun_args):
exp = np.exp(-(x**2) / 2)
gx = x * exp
g_x = (1 - x**2) * exp
return gx, g_x.mean(axis=-1)
def _cube(x, fun_args):
return x**3, (3 * x**2).mean(axis=-1)
def fastica(
X,
n_components=None,
*,
algorithm="parallel",
whiten="warn",
fun="logcosh",
fun_args=None,
max_iter=200,
tol=1e-04,
w_init=None,
whiten_solver="svd",
random_state=None,
return_X_mean=False,
compute_sources=True,
return_n_iter=False,
):
"""Perform Fast Independent Component Analysis.
The implementation is based on [1]_.
Read more in the :ref:`User Guide <ICA>`.
Parameters
----------
X : array-like of shape (n_samples, n_features)
Training vector, where `n_samples` is the number of samples and
`n_features` is the number of features.
n_components : int, default=None
Number of components to use. If None is passed, all are used.
algorithm : {'parallel', 'deflation'}, default='parallel'
Specify which algorithm to use for FastICA.
whiten : str or bool, default="warn"
Specify the whitening strategy to use.
- If 'arbitrary-variance' (default), a whitening with variance
arbitrary is used.
- If 'unit-variance', the whitening matrix is rescaled to ensure that
each recovered source has unit variance.
- If False, the data is already considered to be whitened, and no
whitening is performed.
.. deprecated:: 1.1
Starting in v1.3, `whiten='unit-variance'` will be used by default.
`whiten=True` is deprecated from 1.1 and will raise ValueError in 1.3.
Use `whiten=arbitrary-variance` instead.
fun : {'logcosh', 'exp', 'cube'} or callable, default='logcosh'
The functional form of the G function used in the
approximation to neg-entropy. Could be either 'logcosh', 'exp',
or 'cube'.
You can also provide your own function. It should return a tuple
containing the value of the function, and of its derivative, in the
point. The derivative should be averaged along its last dimension.
Example::
def my_g(x):
return x ** 3, (3 * x ** 2).mean(axis=-1)
fun_args : dict, default=None
Arguments to send to the functional form.
If empty or None and if fun='logcosh', fun_args will take value
{'alpha' : 1.0}.
max_iter : int, default=200
Maximum number of iterations to perform.
tol : float, default=1e-4
A positive scalar giving the tolerance at which the
un-mixing matrix is considered to have converged.
w_init : ndarray of shape (n_components, n_components), default=None
Initial un-mixing array. If `w_init=None`, then an array of values
drawn from a normal distribution is used.
whiten_solver : {"eigh", "svd"}, default="svd"
The solver to use for whitening.
- "svd" is more stable numerically if the problem is degenerate, and
often faster when `n_samples <= n_features`.
- "eigh" is generally more memory efficient when
`n_samples >= n_features`, and can be faster when
`n_samples >= 50 * n_features`.
.. versionadded:: 1.2
random_state : int, RandomState instance or None, default=None
Used to initialize ``w_init`` when not specified, with a
normal distribution. Pass an int, for reproducible results
across multiple function calls.
See :term:`Glossary <random_state>`.
return_X_mean : bool, default=False
If True, X_mean is returned too.
compute_sources : bool, default=True
If False, sources are not computed, but only the rotation matrix.
This can save memory when working with big data. Defaults to True.
return_n_iter : bool, default=False
Whether or not to return the number of iterations.
Returns
-------
K : ndarray of shape (n_components, n_features) or None
If whiten is 'True', K is the pre-whitening matrix that projects data
onto the first n_components principal components. If whiten is 'False',
K is 'None'.
W : ndarray of shape (n_components, n_components)
The square matrix that unmixes the data after whitening.
The mixing matrix is the pseudo-inverse of matrix ``W K``
if K is not None, else it is the inverse of W.
S : ndarray of shape (n_samples, n_components) or None
Estimated source matrix.
X_mean : ndarray of shape (n_features,)
The mean over features. Returned only if return_X_mean is True.
n_iter : int
If the algorithm is "deflation", n_iter is the
maximum number of iterations run across all components. Else
they are just the number of iterations taken to converge. This is
returned only when return_n_iter is set to `True`.
Notes
-----
The data matrix X is considered to be a linear combination of
non-Gaussian (independent) components i.e. X = AS where columns of S
contain the independent components and A is a linear mixing
matrix. In short ICA attempts to `un-mix' the data by estimating an
un-mixing matrix W where ``S = W K X.``
While FastICA was proposed to estimate as many sources
as features, it is possible to estimate less by setting
n_components < n_features. It this case K is not a square matrix
and the estimated A is the pseudo-inverse of ``W K``.
This implementation was originally made for data of shape
[n_features, n_samples]. Now the input is transposed
before the algorithm is applied. This makes it slightly
faster for Fortran-ordered input.
References
----------
.. [1] A. Hyvarinen and E. Oja, "Fast Independent Component Analysis",
Algorithms and Applications, Neural Networks, 13(4-5), 2000,
pp. 411-430.
"""
est = FastICA(
n_components=n_components,
algorithm=algorithm,
whiten=whiten,
fun=fun,
fun_args=fun_args,
max_iter=max_iter,
tol=tol,
w_init=w_init,
whiten_solver=whiten_solver,
random_state=random_state,
)
S = est._fit_transform(X, compute_sources=compute_sources)
if est._whiten in ["unit-variance", "arbitrary-variance"]:
K = est.whitening_
X_mean = est.mean_
else:
K = None
X_mean = None
returned_values = [K, est._unmixing, S]
if return_X_mean:
returned_values.append(X_mean)
if return_n_iter:
returned_values.append(est.n_iter_)
return returned_values
class FastICA(ClassNamePrefixFeaturesOutMixin, TransformerMixin, BaseEstimator):
"""FastICA: a fast algorithm for Independent Component Analysis.
The implementation is based on [1]_.
Read more in the :ref:`User Guide <ICA>`.
Parameters
----------
n_components : int, default=None
Number of components to use. If None is passed, all are used.
algorithm : {'parallel', 'deflation'}, default='parallel'
Specify which algorithm to use for FastICA.
whiten : str or bool, default="warn"
Specify the whitening strategy to use.
- If 'arbitrary-variance' (default), a whitening with variance
arbitrary is used.
- If 'unit-variance', the whitening matrix is rescaled to ensure that
each recovered source has unit variance.
- If False, the data is already considered to be whitened, and no
whitening is performed.
.. deprecated:: 1.1
Starting in v1.3, `whiten='unit-variance'` will be used by default.
`whiten=True` is deprecated from 1.1 and will raise ValueError in 1.3.
Use `whiten=arbitrary-variance` instead.
fun : {'logcosh', 'exp', 'cube'} or callable, default='logcosh'
The functional form of the G function used in the
approximation to neg-entropy. Could be either 'logcosh', 'exp',
or 'cube'.
You can also provide your own function. It should return a tuple
containing the value of the function, and of its derivative, in the
point. The derivative should be averaged along its last dimension.
Example::
def my_g(x):
return x ** 3, (3 * x ** 2).mean(axis=-1)
fun_args : dict, default=None
Arguments to send to the functional form.
If empty or None and if fun='logcosh', fun_args will take value
{'alpha' : 1.0}.
max_iter : int, default=200
Maximum number of iterations during fit.
tol : float, default=1e-4
A positive scalar giving the tolerance at which the
un-mixing matrix is considered to have converged.
w_init : array-like of shape (n_components, n_components), default=None
Initial un-mixing array. If `w_init=None`, then an array of values
drawn from a normal distribution is used.
whiten_solver : {"eigh", "svd"}, default="svd"
The solver to use for whitening.
- "svd" is more stable numerically if the problem is degenerate, and
often faster when `n_samples <= n_features`.
- "eigh" is generally more memory efficient when
`n_samples >= n_features`, and can be faster when
`n_samples >= 50 * n_features`.
.. versionadded:: 1.2
random_state : int, RandomState instance or None, default=None
Used to initialize ``w_init`` when not specified, with a
normal distribution. Pass an int, for reproducible results
across multiple function calls.
See :term:`Glossary <random_state>`.
Attributes
----------
components_ : ndarray of shape (n_components, n_features)
The linear operator to apply to the data to get the independent
sources. This is equal to the unmixing matrix when ``whiten`` is
False, and equal to ``np.dot(unmixing_matrix, self.whitening_)`` when
``whiten`` is True.
mixing_ : ndarray of shape (n_features, n_components)
The pseudo-inverse of ``components_``. It is the linear operator
that maps independent sources to the data.
mean_ : ndarray of shape(n_features,)
The mean over features. Only set if `self.whiten` is True.
n_features_in_ : int
Number of features seen during :term:`fit`.
.. versionadded:: 0.24
feature_names_in_ : ndarray of shape (`n_features_in_`,)
Names of features seen during :term:`fit`. Defined only when `X`
has feature names that are all strings.
.. versionadded:: 1.0
n_iter_ : int
If the algorithm is "deflation", n_iter is the
maximum number of iterations run across all components. Else
they are just the number of iterations taken to converge.
whitening_ : ndarray of shape (n_components, n_features)
Only set if whiten is 'True'. This is the pre-whitening matrix
that projects data onto the first `n_components` principal components.
See Also
--------
PCA : Principal component analysis (PCA).
IncrementalPCA : Incremental principal components analysis (IPCA).
KernelPCA : Kernel Principal component analysis (KPCA).
MiniBatchSparsePCA : Mini-batch Sparse Principal Components Analysis.
SparsePCA : Sparse Principal Components Analysis (SparsePCA).
References
----------
.. [1] A. Hyvarinen and E. Oja, Independent Component Analysis:
Algorithms and Applications, Neural Networks, 13(4-5), 2000,
pp. 411-430.
Examples
--------
>>> from sklearn.datasets import load_digits
>>> from sklearn.decomposition import FastICA
>>> X, _ = load_digits(return_X_y=True)
>>> transformer = FastICA(n_components=7,
... random_state=0,
... whiten='unit-variance')
>>> X_transformed = transformer.fit_transform(X)
>>> X_transformed.shape
(1797, 7)
"""
_parameter_constraints: dict = {
"n_components": [Interval(Integral, 1, None, closed="left"), None],
"algorithm": [StrOptions({"parallel", "deflation"})],
"whiten": [
Hidden(StrOptions({"warn"})),
StrOptions({"arbitrary-variance", "unit-variance"}),
"boolean",
],
"fun": [StrOptions({"logcosh", "exp", "cube"}), callable],
"fun_args": [dict, None],
"max_iter": [Interval(Integral, 1, None, closed="left")],
"tol": [Interval(Real, 0.0, None, closed="left")],
"w_init": ["array-like", None],
"whiten_solver": [StrOptions({"eigh", "svd"})],
"random_state": ["random_state"],
}
def __init__(
self,
n_components=None,
*,
algorithm="parallel",
whiten="warn",
fun="logcosh",
fun_args=None,
max_iter=200,
tol=1e-4,
w_init=None,
whiten_solver="svd",
random_state=None,
):
super().__init__()
self.n_components = n_components
self.algorithm = algorithm
self.whiten = whiten
self.fun = fun
self.fun_args = fun_args
self.max_iter = max_iter
self.tol = tol
self.w_init = w_init
self.whiten_solver = whiten_solver
self.random_state = random_state
def _fit_transform(self, X, compute_sources=False):
"""Fit the model.
Parameters
----------
X : array-like of shape (n_samples, n_features)
Training data, where `n_samples` is the number of samples
and `n_features` is the number of features.
compute_sources : bool, default=False
If False, sources are not computes but only the rotation matrix.
This can save memory when working with big data. Defaults to False.
Returns
-------
S : ndarray of shape (n_samples, n_components) or None
Sources matrix. `None` if `compute_sources` is `False`.
"""
self._whiten = self.whiten
if self._whiten == "warn":
warnings.warn(
"Starting in v1.3, whiten='unit-variance' will be used by default.",
FutureWarning,
)
self._whiten = "arbitrary-variance"
if self._whiten is True:
warnings.warn(
"Starting in v1.3, whiten=True should be specified as "
"whiten='arbitrary-variance' (its current behaviour). This "
"behavior is deprecated in 1.1 and will raise ValueError in 1.3.",
FutureWarning,
stacklevel=2,
)
self._whiten = "arbitrary-variance"
XT = self._validate_data(
X, copy=self._whiten, dtype=[np.float64, np.float32], ensure_min_samples=2
).T
fun_args = {} if self.fun_args is None else self.fun_args
random_state = check_random_state(self.random_state)
alpha = fun_args.get("alpha", 1.0)
if not 1 <= alpha <= 2:
raise ValueError("alpha must be in [1,2]")
if self.fun == "logcosh":
g = _logcosh
elif self.fun == "exp":
g = _exp
elif self.fun == "cube":
g = _cube
elif callable(self.fun):
def g(x, fun_args):
return self.fun(x, **fun_args)
n_features, n_samples = XT.shape
n_components = self.n_components
if not self._whiten and n_components is not None:
n_components = None
warnings.warn("Ignoring n_components with whiten=False.")
if n_components is None:
n_components = min(n_samples, n_features)
if n_components > min(n_samples, n_features):
n_components = min(n_samples, n_features)
warnings.warn(
"n_components is too large: it will be set to %s" % n_components
)
if self._whiten:
# Centering the features of X
X_mean = XT.mean(axis=-1)
XT -= X_mean[:, np.newaxis]
# Whitening and preprocessing by PCA
if self.whiten_solver == "eigh":
# Faster when num_samples >> n_features
d, u = linalg.eigh(XT.dot(X))
sort_indices = np.argsort(d)[::-1]
eps = np.finfo(d.dtype).eps
degenerate_idx = d < eps
if np.any(degenerate_idx):
warnings.warn(
"There are some small singular values, using "
"whiten_solver = 'svd' might lead to more "
"accurate results."
)
d[degenerate_idx] = eps # For numerical issues
np.sqrt(d, out=d)
d, u = d[sort_indices], u[:, sort_indices]
elif self.whiten_solver == "svd":
u, d = linalg.svd(XT, full_matrices=False, check_finite=False)[:2]
# Give consistent eigenvectors for both svd solvers
u *= np.sign(u[0])
K = (u / d).T[:n_components] # see (6.33) p.140
del u, d
X1 = np.dot(K, XT)
# see (13.6) p.267 Here X1 is white and data
# in X has been projected onto a subspace by PCA
X1 *= np.sqrt(n_samples)
else:
# X must be casted to floats to avoid typing issues with numpy
# 2.0 and the line below
X1 = as_float_array(XT, copy=False) # copy has been taken care of
w_init = self.w_init
if w_init is None:
w_init = np.asarray(
random_state.normal(size=(n_components, n_components)), dtype=X1.dtype
)
else:
w_init = np.asarray(w_init)
if w_init.shape != (n_components, n_components):
raise ValueError(
"w_init has invalid shape -- should be %(shape)s"
% {"shape": (n_components, n_components)}
)
kwargs = {
"tol": self.tol,
"g": g,
"fun_args": fun_args,
"max_iter": self.max_iter,
"w_init": w_init,
}
if self.algorithm == "parallel":
W, n_iter = _ica_par(X1, **kwargs)
elif self.algorithm == "deflation":
W, n_iter = _ica_def(X1, **kwargs)
del X1
self.n_iter_ = n_iter
if compute_sources:
if self._whiten:
S = np.linalg.multi_dot([W, K, XT]).T
else:
S = np.dot(W, XT).T
else:
S = None
if self._whiten:
if self._whiten == "unit-variance":
if not compute_sources:
S = np.linalg.multi_dot([W, K, XT]).T
S_std = np.std(S, axis=0, keepdims=True)
S /= S_std
W /= S_std.T
self.components_ = np.dot(W, K)
self.mean_ = X_mean
self.whitening_ = K
else:
self.components_ = W
self.mixing_ = linalg.pinv(self.components_, check_finite=False)
self._unmixing = W
return S
def fit_transform(self, X, y=None):
"""Fit the model and recover the sources from X.
Parameters
----------
X : array-like of shape (n_samples, n_features)
Training data, where `n_samples` is the number of samples
and `n_features` is the number of features.
y : Ignored
Not used, present for API consistency by convention.
Returns
-------
X_new : ndarray of shape (n_samples, n_components)
Estimated sources obtained by transforming the data with the
estimated unmixing matrix.
"""
self._validate_params()
return self._fit_transform(X, compute_sources=True)
def fit(self, X, y=None):
"""Fit the model to X.
Parameters
----------
X : array-like of shape (n_samples, n_features)
Training data, where `n_samples` is the number of samples
and `n_features` is the number of features.
y : Ignored
Not used, present for API consistency by convention.
Returns
-------
self : object
Returns the instance itself.
"""
self._validate_params()
self._fit_transform(X, compute_sources=False)
return self
def transform(self, X, copy=True):
"""Recover the sources from X (apply the unmixing matrix).
Parameters
----------
X : array-like of shape (n_samples, n_features)
Data to transform, where `n_samples` is the number of samples
and `n_features` is the number of features.
copy : bool, default=True
If False, data passed to fit can be overwritten. Defaults to True.
Returns
-------
X_new : ndarray of shape (n_samples, n_components)
Estimated sources obtained by transforming the data with the
estimated unmixing matrix.
"""
check_is_fitted(self)
X = self._validate_data(
X, copy=(copy and self._whiten), dtype=[np.float64, np.float32], reset=False
)
if self._whiten:
X -= self.mean_
return np.dot(X, self.components_.T)
def inverse_transform(self, X, copy=True):
"""Transform the sources back to the mixed data (apply mixing matrix).
Parameters
----------
X : array-like of shape (n_samples, n_components)
Sources, where `n_samples` is the number of samples
and `n_components` is the number of components.
copy : bool, default=True
If False, data passed to fit are overwritten. Defaults to True.
Returns
-------
X_new : ndarray of shape (n_samples, n_features)
Reconstructed data obtained with the mixing matrix.
"""
check_is_fitted(self)
X = check_array(X, copy=(copy and self._whiten), dtype=[np.float64, np.float32])
X = np.dot(X, self.mixing_.T)
if self._whiten:
X += self.mean_
return X
@property
def _n_features_out(self):
"""Number of transformed output features."""
return self.components_.shape[0]
def _more_tags(self):
return {"preserves_dtype": [np.float32, np.float64]}
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