def _fit(self, X, y, sample_weight=None, relative_penalties=None):
if self.lambda_path is not None:
n_lambda = len(self.lambda_path)
min_lambda_ratio = 1.0
else:
n_lambda = self.n_lambda
min_lambda_ratio = self.min_lambda_ratio
check_classification_targets(y)
self.classes_ = np.unique(y) # the output of np.unique is sorted
n_classes = len(self.classes_)
if n_classes < 2:
raise ValueError("Training data need to contain at least 2 "
"classes.")
# glmnet requires the labels a one-hot-encoded array of
# (n_samples, n_classes)
if n_classes == 2:
# Normally we use 1/0 for the positive and negative classes. Since
# np.unique sorts the output, the negative class will be in the 0th
# column. We want a model predicting the positive class, not the
# negative class, so we flip the columns here (the != condition).
#
# Broadcast comparison of self.classes_ to all rows of y. See the
# numpy rules on broadcasting for more info, essentially this
# "reshapes" y to (n_samples, n_classes) and self.classes_ to
# (n_samples, n_classes) and performs an element-wise comparison
# resulting in _y with shape (n_samples, n_classes).
_y = (y[:, None] != self.classes_).astype(np.float64, order='F')
else:
# multinomial case, glmnet uses the entire array so we can
# keep the original order.
_y = (y[:, None] == self.classes_).astype(np.float64, order='F')
# we need some sort of "offset" array for glmnet
# an array of shape (n_examples, n_classes)
offset = np.zeros((X.shape[0], n_classes), dtype=np.float64, order='F')
# You should have thought of that before you got here.
exclude_vars = 0
# how much each feature should be penalized relative to the others
# this may be useful to expose to the caller if there are vars that
# must be included in the final model or there is some prior knowledge
# about how important some vars are relative to others, see the glmnet
# vignette:
# http://web.stanford.edu/~hastie/glmnet/glmnet_alpha.html
if relative_penalties is None:
relative_penalties = np.ones(X.shape[1],
dtype=np.float64,
order='F')
coef_bounds = np.empty((2, X.shape[1]), dtype=np.float64, order='F')
coef_bounds[0, :] = self.lower_limits
coef_bounds[1, :] = self.upper_limits
# This is a stopping criterion (ne), add 1 to ensure the final model
# includes all features. R defaults to nx = num_features, and
# ne = num_features + 1
# Note, this will be ignored when the user specifies lambda_path.
max_features = X.shape[1] + 1
if n_classes == 2:
# binomial, tell glmnet there is only one class
# otherwise we will get a coef matrix with two dimensions
# where each pair are equal in magnitude and opposite in sign
# also since the magnitudes are constrained to sum to one, the
# returned coefficients would be one half of the proper values
n_classes = 1
# for documentation on the glmnet function lognet, see doc.py
if issparse(X):
_x = csc_matrix(X, dtype=np.float64, copy=True)
(
self.n_lambda_,
self.intercept_path_,
ca,
ia,
nin,
_, # dev0
_, # dev
self.lambda_path_,
_, # nlp
jerr) = splognet(
self.alpha,
_x.shape[0],
_x.shape[1],
n_classes,
_x.data,
_x.indptr + 1, # Fortran uses 1-based indexing
_x.indices + 1,
_y,
offset,
exclude_vars,
relative_penalties,
coef_bounds,
max_features,
max_features - 1,
min_lambda_ratio,
self.lambda_path,
self.tol,
n_lambda,
self.standardize,
self.fit_intercept,
self.max_iter,
0)
else: # not sparse
# some notes: glmnet requires both x and y to be float64, the two
# arrays
# may also be overwritten during the fitting process, so they need
# to be copied prior to calling lognet. The fortran wrapper will
# copy any arrays passed to a wrapped function if they are not in
# the fortran layout, to avoid making extra copies, ensure x and y
# are `F_CONTIGUOUS` prior to calling lognet.
_x = X.astype(dtype=np.float64, order='F', copy=True)
(
self.n_lambda_,
self.intercept_path_,
ca,
ia,
nin,
_, # dev0
_, # dev
self.lambda_path_,
_, # nlp
jerr) = lognet(self.alpha, n_classes, _x, _y, offset,
exclude_vars, relative_penalties, coef_bounds,
max_features, min_lambda_ratio,
self.lambda_path, self.tol, max_features - 1,
n_lambda, self.standardize, self.fit_intercept,
self.max_iter, 0)
# raises RuntimeError if self.jerr_ is nonzero
self.jerr_ = jerr
_check_glmnet_error_flag(self.jerr_)
# glmnet may not return the requested number of lambda values, so we
# need to trim the trailing zeros from the returned path so
# len(lambda_path_) is equal to n_lambda_
self.lambda_path_ = self.lambda_path_[:self.n_lambda_]
# also fix the first value of lambda
self.lambda_path_ = _fix_lambda_path(self.lambda_path_)
self.intercept_path_ = self.intercept_path_[:, :self.n_lambda_]
# also trim the compressed coefficient matrix
ca = ca[:, :, :self.n_lambda_]
# and trim the array of n_coef per lambda (may or may not be non-zero)
nin = nin[:self.n_lambda_]
# decompress the coefficients returned by glmnet, see doc.py
self.coef_path_ = lsolns(X.shape[1], ca, ia, nin)
# coef_path_ has shape (n_features, n_classes, n_lambda), we should
# match shape for scikit-learn models:
# (n_classes, n_features, n_lambda)
self.coef_path_ = np.transpose(self.coef_path_, axes=(1, 0, 2))
return self
def fit(self,
X,
y,
col_names=None,
lambdas=None,
weights=None,
rel_penalties=None,
excl_preds=None,
box_constraints=None,
offsets=None):
'''Fit a logistic or multinomial net model.
Arguments:
* X: The model matrix. A n_obs * n_preds array.
* y: The response. This method accepts the response in two
differnt configurations:
- An n_obs * n_classes array. In this case, each column in y must
be of boolean (0, 1) type indicating whether the observation is
or is not of a given class.
- An n_obs array. In this case the array must contain a discrete
number of values, and is converted into the previous form before
being passed to the model.
Optional Arguments:
* lambdas:
A user supplied list of lambdas, an elastic net will be fit for
each lambda supplied. If no array is passed, glmnet will generate
its own array of lambdas equally spaced on a logaritmic scale
between \lambda_max and \lambda_min.
* weights:
An n_obs array. Sample weights. It is an error to pass a weights
array to a logistic model.
* rel_penalties:
An n_preds array. Relative panalty weights for the covariates. If
none is passed, all covariates are penalized equally. If an array
is passed, then a zero indicates an unpenalized parameter, and a 1
a fully penalized parameter. Otherwise all covaraites recieve an
equal penalty.
* excl_preds:
An n_preds array, used to exclude covaraites from the model. To
exclude predictors, pass an array with a 1 in the first position,
then a 1 in the i+1st position excludes the ith covaraite from
model fitting. If no array is passed, all covaraites in X are
included in the model.
* box_constraints:
An array with dimension 2 * n_obs. Interval constraints on the fit
coefficients. The (0, i) entry is a lower bound on the ith
covariate, and the (1, i) entry is an upper bound. These must
satisfy lower_bound <= 0 <= upper_bound. If no array is passed,
no box constraintes are allied to the parameters.
* offsets:
A n_preds * n_classes array. Used as initial offsets for the
model fitting.
After fitting, the following attributes are set:
Private attributes:
* _n_fit_obs:
The number of rows in the model matrix X.
* _n_fit_params:
The number of columns in the model matrix X.
* _out_n_lambdas:
The number of lambdas associated with non-zero models (i.e.
models with at least one none zero parameter estiamte) after
fitting; for large enough lambda the models will become zero in
the presense of an L1 regularizer.
* _intecepts:
A one dimensional array containing the intercept estiamtes for
each value of lambda. See the intercepts (no underscore)
property for a public version.
* _comp_coef:
The fit parameter estiamtes in a compressed form. This is a
matrix with each row giving the estimates for a single
coefficient for various values of \lambda. The order of the rows
does not correspond to the order of the coefficents as given in
the design matrix used to fit the model, this association is
given by the _p_comp_coef attribute. Only estaimtes that are
non-zero for some lambda are reported.
* _p_comp_coef:
A one dimensional integer array associating the coefficients in
_comp_coef to columns in the model matrix.
* _indices:
The same information as _p_comp_coef, but zero indexed to be
compatable with numpy arrays.
* _n_comp_coef:
The number of parameter estimates that are non-zero for some
value of lambda.
* _n_passes:
The total number of passes over the data used to fit the model.
* _error_flag:
Error flag from the fortran code.
Public Attributes:
* null_dev:
The devaince of the null (mean) model.
* exp_dev:
The devaince explained by the model.
* out_lambdas:
An array containing the lambda values associated with each fit
model.
'''
self._check_if_unfit()
self._check_y(y)
self._check_weights(weights)
# Convert to arrays is native python objects
try:
if not issparse(X):
X = np.asanyarray(X)
y = np.asanyarray(y)
except ValueError:
raise ValueError("X and y must be wither numpy arrays, or "
"convertable to numpy arrays.")
# Fortran expects an n_obs * n_classes array for y. If a one
# dimensional array is passed, we construct an appropriate widening.
# TODO: Save class names as attribute.
y = np.asanyarray(y)
if len(y.shape) == 1:
y_classes = np.unique(y)
y = np.float64(np.column_stack(y == c for c in y_classes))
self._n_classes = y.shape[1]
# Two class predictions are handled as a special case, as is usual
# with logistic models, this is signaled to fortran by passing in a
# 1 for nc (num classes).
if self._n_classes == 2:
f_n_classes = np.array([1])
else:
f_n_classes = np.array([self._n_classes])
# Grab the design info from patsy for later use, we are abbout to write
# over this object in some cases.
if hasattr(X, 'design_info'):
design_info = X.design_info
else:
design_info = None
# Make a copy if we are not able to overwrite X with its standardized
# version. Note that if X is not fortran contiguous, then it will be
# copied anyway.
if not issparse(X) and np.isfortran(X) and not self.overwrite_pred_ok:
X = X.copy(order='F')
# Make a copy if we are not able to overwrite y with its standardized
# version.
if np.isfortran(y) and not self.overwrite_targ_ok:
y = y.copy(order='F')
# Validate all the inputs:
self._validate_matrix(X)
self._validate_inputs(X, y)
self._validate_lambdas(X, y, lambdas)
self._validate_rel_penalties(X, y, rel_penalties)
self._validate_excl_preds(X, y, excl_preds)
self._validate_box_constraints(X, y, box_constraints)
self._validate_offsets(X, y, offsets)
# Setup is complete, call the wrapper
if not issparse(X):
(self._out_n_lambdas, self._intercepts, self._comp_coef,
self._p_comp_coef, self._n_comp_coef, self.null_dev, self.exp_dev,
self.out_lambdas, self._n_passes,
self._error_flag) = _glmnet.lognet(self.alpha,
f_n_classes,
X,
y,
self.offsets,
self.excl_preds,
self.rel_penalties,
self.box_constraints,
self.max_vars_all,
self.frac_lg_lambda,
self.lambdas,
self.threshold,
nlam=self.n_lambdas)
else:
X.sort_indices()
# Fortran arrays are 1 indexed.
ind_ptrs = X.indptr + 1
indices = X.indices + 1
# Call
(self._out_n_lambdas, self._intercepts, self._comp_coef,
self._p_comp_coef, self._n_comp_coef, self.null_dev, self.exp_dev,
self.out_lambdas, self._n_passes,
self._error_flag) = _glmnet.splognet(self.alpha,
X.shape[0],
X.shape[1],
f_n_classes,
X.data,
ind_ptrs,
indices,
y,
self.offsets,
self.excl_preds,
self.rel_penalties,
self.box_constraints,
self.max_vars_all,
self.frac_lg_lambda,
self.lambdas,
self.threshold,
nlam=self.n_lambdas)
self._check_errors()
# Keep some model metadata
self._n_fit_obs, self._n_fit_params = X.shape
# The indexes into the predictor array are off by one due to fortran
# convention differing from numpys, this make them indexes into the the
# numpy array.
self._indices = np.trim_zeros(self._p_comp_coef, 'b') - 1
# Create a list of column names for the fit parameters, these can be
# passed in, or attached to the matrix from patsy. If none are found
# we crate our own stupid ones.
if col_names != None:
self._col_names = col_names
elif design_info != None:
self._col_names = design_info.column_names
else:
self._col_names = [
'var_' + str(i) for i in range(self._n_fit_params)
]
def _fit(self, X, y, sample_weight=None, relative_penalties=None):
if self.lambda_path is not None:
n_lambda = len(self.lambda_path)
min_lambda_ratio = 1.0
else:
n_lambda = self.n_lambda
min_lambda_ratio = self.min_lambda_ratio
check_classification_targets(y)
self.classes_ = np.unique(y) # the output of np.unique is sorted
n_classes = len(self.classes_)
if n_classes < 2:
raise ValueError("Training data need to contain at least 2 "
"classes.")
# glmnet requires the labels a one-hot-encoded array of
# (n_samples, n_classes)
if n_classes == 2:
# Normally we use 1/0 for the positive and negative classes. Since
# np.unique sorts the output, the negative class will be in the 0th
# column. We want a model predicting the positive class, not the
# negative class, so we flip the columns here (the != condition).
#
# Broadcast comparison of self.classes_ to all rows of y. See the
# numpy rules on broadcasting for more info, essentially this
# "reshapes" y to (n_samples, n_classes) and self.classes_ to
# (n_samples, n_classes) and performs an element-wise comparison
# resulting in _y with shape (n_samples, n_classes).
_y = (y[:, None] != self.classes_).astype(np.float64, order='F')
else:
# multinomial case, glmnet uses the entire array so we can
# keep the original order.
_y = (y[:, None] == self.classes_).astype(np.float64, order='F')
# use sample weights, making sure all weights are positive
# this is inspired by the R wrapper for glmnet, in lognet.R
if sample_weight is not None:
weight_gt_0 = sample_weight > 0
sample_weight = sample_weight[weight_gt_0]
_y = _y[weight_gt_0, :]
X = X[weight_gt_0, :]
_y = _y * np.expand_dims(sample_weight, 1)
# we need some sort of "offset" array for glmnet
# an array of shape (n_examples, n_classes)
offset = np.zeros((X.shape[0], n_classes), dtype=np.float64,
order='F')
# You should have thought of that before you got here.
exclude_vars = 0
# how much each feature should be penalized relative to the others
# this may be useful to expose to the caller if there are vars that
# must be included in the final model or there is some prior knowledge
# about how important some vars are relative to others, see the glmnet
# vignette:
# http://web.stanford.edu/~hastie/glmnet/glmnet_alpha.html
if relative_penalties is None:
relative_penalties = np.ones(X.shape[1], dtype=np.float64,
order='F')
coef_bounds = np.empty((2, X.shape[1]), dtype=np.float64, order='F')
coef_bounds[0, :] = self.lower_limits
coef_bounds[1, :] = self.upper_limits
if n_classes == 2:
# binomial, tell glmnet there is only one class
# otherwise we will get a coef matrix with two dimensions
# where each pair are equal in magnitude and opposite in sign
# also since the magnitudes are constrained to sum to one, the
# returned coefficients would be one half of the proper values
n_classes = 1
# This is a stopping criterion (nx)
# R defaults to nx = num_features, and ne = num_features + 1
if self.max_features is None:
max_features = X.shape[1]
else:
max_features = self.max_features
# for documentation on the glmnet function lognet, see doc.py
if issparse(X):
_x = csc_matrix(X, dtype=np.float64, copy=True)
(self.n_lambda_,
self.intercept_path_,
ca,
ia,
nin,
_, # dev0
_, # dev
self.lambda_path_,
_, # nlp
jerr) = splognet(self.alpha,
_x.shape[0],
_x.shape[1],
n_classes,
_x.data,
_x.indptr + 1, # Fortran uses 1-based indexing
_x.indices + 1,
_y,
offset,
exclude_vars,
relative_penalties,
coef_bounds,
max_features,
X.shape[1] + 1,
min_lambda_ratio,
self.lambda_path,
self.tol,
n_lambda,
self.standardize,
self.fit_intercept,
self.max_iter,
0)
else: # not sparse
# some notes: glmnet requires both x and y to be float64, the two
# arrays
# may also be overwritten during the fitting process, so they need
# to be copied prior to calling lognet. The fortran wrapper will
# copy any arrays passed to a wrapped function if they are not in
# the fortran layout, to avoid making extra copies, ensure x and y
# are `F_CONTIGUOUS` prior to calling lognet.
_x = X.astype(dtype=np.float64, order='F', copy=True)
(self.n_lambda_,
self.intercept_path_,
ca,
ia,
nin,
_, # dev0
_, # dev
self.lambda_path_,
_, # nlp
jerr) = lognet(self.alpha,
n_classes,
_x,
_y,
offset,
exclude_vars,
relative_penalties,
coef_bounds,
X.shape[1] + 1,
min_lambda_ratio,
self.lambda_path,
self.tol,
max_features,
n_lambda,
self.standardize,
self.fit_intercept,
self.max_iter,
0)
# raises RuntimeError if self.jerr_ is nonzero
self.jerr_ = jerr
_check_error_flag(self.jerr_)
# glmnet may not return the requested number of lambda values, so we
# need to trim the trailing zeros from the returned path so
# len(lambda_path_) is equal to n_lambda_
self.lambda_path_ = self.lambda_path_[:self.n_lambda_]
# also fix the first value of lambda
self.lambda_path_ = _fix_lambda_path(self.lambda_path_)
self.intercept_path_ = self.intercept_path_[:, :self.n_lambda_]
# also trim the compressed coefficient matrix
ca = ca[:, :, :self.n_lambda_]
# and trim the array of n_coef per lambda (may or may not be non-zero)
nin = nin[:self.n_lambda_]
# decompress the coefficients returned by glmnet, see doc.py
self.coef_path_ = lsolns(X.shape[1], ca, ia, nin)
# coef_path_ has shape (n_features, n_classes, n_lambda), we should
# match shape for scikit-learn models:
# (n_classes, n_features, n_lambda)
self.coef_path_ = np.transpose(self.coef_path_, axes=(1, 0, 2))
return self
def fit(self, X, y, col_names=None,
lambdas=None, weights=None, rel_penalties=None,
excl_preds=None, box_constraints=None, offsets=None,
normalize=True,include_intercept=True):
'''Fit a logistic or multinomial net model.
Arguments:
* X: The model matrix. A n_obs * n_preds array.
* y: The response. This method accepts the response in two
differnt configurations:
- An n_obs * n_classes array. In this case, each column in y must
be of boolean (0, 1) type indicating whether the observation is
or is not of a given class.
- An n_obs array. In this case the array must contain a discrete
number of values, and is converted into the previous form before
being passed to the model.
Optional Arguments:
* lambdas:
A user supplied list of lambdas, an elastic net will be fit for
each lambda supplied. If no array is passed, glmnet will generate
its own array of lambdas equally spaced on a logaritmic scale
between \lambda_max and \lambda_min.
* weights:
An n_obs array. Sample weights. It is an error to pass a weights
array to a logistic model.
* rel_penalties:
An n_preds array. Relative panalty weights for the covariates. If
none is passed, all covariates are penalized equally. If an array
is passed, then a zero indicates an unpenalized parameter, and a 1
a fully penalized parameter. Otherwise all covaraites recieve an
equal penalty.
* excl_preds:
An n_preds array, used to exclude covaraites from the model. To
exclude predictors, pass an array with a 1 in the first position,
then a 1 in the i+1st position excludes the ith covaraite from
model fitting. If no array is passed, all covaraites in X are
included in the model.
* box_constraints:
An array with dimension 2 * n_obs. Interval constraints on the fit
coefficients. The (0, i) entry is a lower bound on the ith
covariate, and the (1, i) entry is an upper bound. These must
satisfy lower_bound <= 0 <= upper_bound. If no array is passed,
no box constraintes are allied to the parameters.
* offsets:
A n_preds * n_classes array. Used as initial offsets for the
model fitting.
After fitting, the following attributes are set:
Private attributes:
* _n_fit_obs:
The number of rows in the model matrix X.
* _n_fit_params:
The number of columns in the model matrix X.
* _out_n_lambdas:
The number of lambdas associated with non-zero models (i.e.
models with at least one none zero parameter estiamte) after
fitting; for large enough lambda the models will become zero in
the presense of an L1 regularizer.
* _intecepts:
A one dimensional array containing the intercept estiamtes for
each value of lambda. See the intercepts (no underscore)
property for a public version.
* _comp_coef:
The fit parameter estiamtes in a compressed form. This is a
matrix with each row giving the estimates for a single
coefficient for various values of \lambda. The order of the rows
does not correspond to the order of the coefficents as given in
the design matrix used to fit the model, this association is
given by the _p_comp_coef attribute. Only estaimtes that are
non-zero for some lambda are reported.
* _p_comp_coef:
A one dimensional integer array associating the coefficients in
_comp_coef to columns in the model matrix.
* _indices:
The same information as _p_comp_coef, but zero indexed to be
compatable with numpy arrays.
* _n_comp_coef:
The number of parameter estimates that are non-zero for some
value of lambda.
* _n_passes:
The total number of passes over the data used to fit the model.
* _error_flag:
Error flag from the fortran code.
Public Attributes:
* null_dev:
The devaince of the null (mean) model.
* exp_dev:
The devaince explained by the model.
* out_lambdas:
An array containing the lambda values associated with each fit
model.
'''
self._check_if_unfit()
self._check_y(y)
self._check_weights(weights)
# Convert to arrays is native python objects
try:
if not issparse(X):
X = np.asanyarray(X)
y = np.asanyarray(y)
except ValueError:
raise ValueError("X and y must be wither numpy arrays, or "
"convertable to numpy arrays."
)
# Fortran expects an n_obs * n_classes array for y. If a one
# dimensional array is passed, we construct an appropriate widening.
# TODO: Save class names as attribute.
y = np.asanyarray(y)
if len(y.shape) == 1:
y_classes = np.unique(y)
y = np.float64(np.column_stack(y == c for c in y_classes))
self._n_classes = y.shape[1]
# Two class predictions are handled as a special case, as is usual
# with logistic models, this is signaled to fortran by passing in a
# 1 for nc (num classes).
if self._n_classes == 2:
f_n_classes = np.array([1])
else:
f_n_classes = np.array([self._n_classes])
# Grab the design info from patsy for later use, we are abbout to write
# over this object in some cases.
if hasattr(X, 'design_info'):
design_info = X.design_info
else:
design_info = None
# Make a copy if we are not able to overwrite X with its standardized
# version. Note that if X is not fortran contiguous, then it will be
# copied anyway.
if not issparse(X) and np.isfortran(X) and not self.overwrite_pred_ok:
X = X.copy(order='F')
# Make a copy if we are not able to overwrite y with its standardized
# version.
if np.isfortran(y) and not self.overwrite_targ_ok:
y = y.copy(order='F')
# Validate all the inputs:
self._validate_matrix(X)
self._validate_inputs(X, y)
self._validate_lambdas(X, y, lambdas)
self._validate_rel_penalties(X, y, rel_penalties)
self._validate_excl_preds(X, y, excl_preds)
self._validate_box_constraints(X, y, box_constraints)
self._validate_offsets(X, y, offsets)
normalize = int(normalize) # probably not necessary
include_intercept = int(include_intercept) # probably not necessary
# Setup is complete, call the wrapper
if not issparse(X):
(self._out_n_lambdas,
self._intercepts,
self._comp_coef,
self._p_comp_coef,
self._n_comp_coef,
self.null_dev,
self.exp_dev,
self.out_lambdas,
self._n_passes,
self._error_flag) = _glmnet.lognet(
self.alpha,
f_n_classes,
X,
y,
self.offsets,
self.excl_preds,
self.rel_penalties,
self.box_constraints,
self.max_vars_all,
self.frac_lg_lambda,
self.lambdas,
self.threshold,
nlam=self.n_lambdas,
isd= normalize,
intr=include_intercept
)
else:
X.sort_indices()
# Fortran arrays are 1 indexed.
ind_ptrs = X.indptr + 1
indices = X.indices + 1
# Call
(self._out_n_lambdas,
self._intercepts,
self._comp_coef,
self._p_comp_coef,
self._n_comp_coef,
self.null_dev,
self.exp_dev,
self.out_lambdas,
self._n_passes,
self._error_flag) = _glmnet.splognet(
self.alpha,
X.shape[0],
X.shape[1],
f_n_classes,
X.data,
ind_ptrs,
indices,
y,
self.offsets,
self.excl_preds,
self.rel_penalties,
self.box_constraints,
self.max_vars_all,
self.frac_lg_lambda,
self.lambdas,
self.threshold,
nlam=self.n_lambdas,
isd= normalize,
intr=include_intercept
)
self._check_errors()
# Keep some model metadata
self._n_fit_obs, self._n_fit_params = X.shape
# The indexes into the predictor array are off by one due to fortran
# convention differing from numpys, this make them indexes into the the
# numpy array.
self._indices = np.trim_zeros(self._p_comp_coef, 'b') - 1
# Create a list of column names for the fit parameters, these can be
# passed in, or attached to the matrix from patsy. If none are found
# we crate our own stupid ones.
if col_names != None:
self._col_names = col_names
elif design_info != None:
self._col_names = design_info.column_names
else:
self._col_names = [
'var_' + str(i) for i in range(self._n_fit_params)
]
def fit(self, X, y,
lambdas=None, weights=None, rel_penalties=None,
excl_preds=None, box_constraints=None, offsets=None):
'''Fit a logistic or multinomial net model.
Arguments:
* X: The predictors. A n_obs * n_preds array.
* y: The response. This method accepts the predictors in two
differnt configurations:
- An n_obs * n_classes array. In this case, each column in y must
be a boolean flag indicating whether the observation is or is not
of this class.
- An n_obs array. In this case the array must contain a discrete
number of values, and is converted into the previous form before
being passed to the model.
Optional Arguments:
* lambdas: A user supplied list of lambdas, an elastic net will be
fit for each lambda supplied. If no array is passed, glmnet
will generate its own array of lambdas.
* weights: An n_obs array. Observation weights.
* rel_penalties: An n_preds array. Relative panalty weights for the
covariates. If none is passed, all covariates are penalized
equally. If an array is passed, then a zero indicates an
unpenalized parameter, and a 1 a fully penalized parameter.
* excl_preds: An n_preds array, used to exclude covaraites from
the model. To exclude predictors, pass an array with a 1 in the
first position, then a 1 in the i+1st position excludes the ith
covaraite from model fitting.
* box_constraints: An array with dimension 2 * n_obs. Interval
constraints on the fit coefficients. The (0, i) entry
is a lower bound on the ith covariate, and the (1, i) entry is
an upper bound.
* offsets: A n_preds * n_classes array. Used as initial offsets for
the model fitting.
After fitting, the following attributes are set:
Private attributes:
* _out_n_lambdas: The number of fit lambdas associated with non-zero
models; for large enough lambdas the models will become zero in the
presense of an L1 regularizer.
* _comp_coef: The fit coefficients in a compressed form. Only
coefficients that are non-zero for some lambda are reported, and the
associated between these parameters and the predictors are given by
the _p_comp_coef attribute.
* _p_comp_coef: An array associating the coefficients in _comp_coef to
columns in the predictor array.
* _indicies: The same information as _p_comp_coef, but zero indexed to
be compatable with numpy arrays.
* _n_comp_coef: The number of coefficients that are non-zero for some
value of lambda.
* _n_passes: The total number of passes over the data used to fit the
model.
* _error_flag: Error flag from the fortran code.
Public Attributes:
* null_dev: The devaince of the null model.
* exp_dev: The devaince explained by the model.
* out_lambdas: An array containing the lambda values associated with
each fit model.
'''
if weights is not None:
raise ValueError("LogisticNet cannot be fit with weights.")
# Convert to arrays is native python objects
try:
if not issparse(X):
X = np.asanyarray(X)
y = np.asanyarray(y)
except ValueError:
raise ValueError("X and y must be wither numpy arrays, or "
"convertable to numpy arrays."
)
# Fortran expects an n_obs * n_classes array for y. If a one
# dimensional array is passed, we construct an appropriate widening.
y = np.asanyarray(y)
if len(y.shape) == 1:
self.logistic = True
y_classes = np.unique(y)
y = np.float64(np.column_stack(y == c for c in y_classes))
else:
self.logistic = False
# Count the number of classes in y.
y_level_count = y.shape[1]
# Two class predictions are handled as a special case, as is usual
# with logistic models
if y_level_count == 2:
self.y_level_count = np.array([1])
else:
self.y_level_count = np.array([y_level_count])
# Make a copy if we are not able to overwrite X with its standardized
# version. Note that if X is not fortran contiguous, then it will be
# copied anyway.
if not issparse(X) and np.isfortran(X) and not self.overwrite_pred_ok:
X = X.copy(order='F')
# The target array will usually be overwritten with its standardized
# version, if this is not ok, we should copy.
if np.isfortran(y) and not self.overwrite_targ_ok:
y = y.copy(order='F')
# Validate all the inputs:
self._validate_matrix(X)
self._validate_inputs(X, y)
self._validate_lambdas(X, y, lambdas)
self._validate_weights(X, y, weights)
self._validate_rel_penalties(X, y, rel_penalties)
self._validate_excl_preds(X, y, excl_preds)
self._validate_box_constraints(X, y, box_constraints)
self._validate_offsets(X, y, offsets)
# Setup is complete, call the wrapper
if not issparse(X):
(self._out_n_lambdas,
self._intercepts,
self._comp_coef,
self._p_comp_coef,
self._n_comp_coef,
self.null_dev,
self.exp_dev,
self.out_lambdas,
self._n_passes,
self._error_flag) = _glmnet.lognet(
self.alpha,
self.y_level_count,
X,
y,
self.offsets,
self.excl_preds,
self.rel_penalties,
self.box_constraints,
self.max_vars_all,
self.frac_lg_lambda,
self.lambdas,
self.threshold,
nlam=self.n_lambdas
)
else:
ind_ptrs = X.indptr + 1
indices = X.indices + 1
(self._out_n_lambdas,
self._intercepts,
self._comp_coef,
self._p_comp_coef,
self._n_comp_coef,
self.null_dev,
self.exp_dev,
self.out_lambdas,
self._n_passes,
self._error_flag) = _glmnet.splognet(
self.alpha,
X.shape[0],
X.shape[1],
self.y_level_count,
X.data,
ind_ptrs,
indices,
y,
self.offsets,
self.excl_preds,
self.rel_penalties,
self.box_constraints,
self.max_vars_all,
self.frac_lg_lambda,
self.lambdas,
self.threshold,
nlam=self.n_lambdas
)
self._check_errors()
# Keep some model metadata
self._n_fit_obs, self._n_fit_params = X.shape
# The indexes into the predictor array are off by one due to fortran
# convention, fix it up.
self._indicies = np.trim_zeros(self._p_comp_coef, 'b') - 1