`simpleml.models.classifiers.sklearn.gaussian_process`

Wrapper module around sklearn.gaussian_process

Module Contents

Classes

`SklearnGaussianProcessClassifier`	No different than base model. Here just to maintain the pattern
`WrappedSklearnGaussianProcessClassifier`	Gaussian process classification (GPC) based on Laplace approximation.

Attributes

__author__

simpleml.models.classifiers.sklearn.gaussian_process.__author__ = Elisha Yadgaran[source]

class simpleml.models.classifiers.sklearn.gaussian_process.SklearnGaussianProcessClassifier(has_external_files=True, external_model_kwargs=None, params=None, fitted=False, pipeline_id=None, **kwargs)[source]

Bases: simpleml.models.classifiers.sklearn.base_sklearn_classifier.SklearnClassifier

No different than base model. Here just to maintain the pattern Generic Base -> Library Base -> Domain Base -> Individual Models (ex: [Library]Model -> SklearnModel -> SklearnClassifier -> SklearnLogisticRegression)

Need to explicitly separate passthrough kwargs to external models since most do not support arbitrary **kwargs in the constructors

Two supported patterns - full initialization in constructor or stepwise configured before fit and save

Parameters

has_external_files (bool) –
external_model_kwargs (Optional[Dict[str, Any]]) –
params (Optional[Dict[str, Any]]) –
fitted (bool) –
pipeline_id (Optional[Union[str, uuid.uuid4]]) –

_create_external_model(self, **kwargs)[source]

Abstract method for each subclass to implement

should return the desired model object

class simpleml.models.classifiers.sklearn.gaussian_process.WrappedSklearnGaussianProcessClassifier(kernel=None, *, optimizer='fmin_l_bfgs_b', n_restarts_optimizer=0, max_iter_predict=100, warm_start=False, copy_X_train=True, random_state=None, multi_class='one_vs_rest', n_jobs=None)[source]

Bases: sklearn.gaussian_process.GaussianProcessClassifier, simpleml.models.classifiers.external_models.ClassificationExternalModelMixin

Gaussian process classification (GPC) based on Laplace approximation.

The implementation is based on Algorithm 3.1, 3.2, and 5.1 of Gaussian Processes for Machine Learning (GPML) by Rasmussen and Williams.

Internally, the Laplace approximation is used for approximating the non-Gaussian posterior by a Gaussian.

Currently, the implementation is restricted to using the logistic link function. For multi-class classification, several binary one-versus rest classifiers are fitted. Note that this class thus does not implement a true multi-class Laplace approximation.

Read more in the User Guide.

New in version 0.18.

kernelkernel instance, default=None

The kernel specifying the covariance function of the GP. If None is passed, the kernel “1.0 * RBF(1.0)” is used as default. Note that the kernel’s hyperparameters are optimized during fitting.

optimizer‘fmin_l_bfgs_b’ or callable, default=’fmin_l_bfgs_b’

Can either be one of the internally supported optimizers for optimizing the kernel’s parameters, specified by a string, or an externally defined optimizer passed as a callable. If a callable is passed, it must have the signature:

def optimizer(obj_func, initial_theta, bounds):
    # * 'obj_func' is the objective function to be maximized, which
    #   takes the hyperparameters theta as parameter and an
    #   optional flag eval_gradient, which determines if the
    #   gradient is returned additionally to the function value
    # * 'initial_theta': the initial value for theta, which can be
    #   used by local optimizers
    # * 'bounds': the bounds on the values of theta
    ....
    # Returned are the best found hyperparameters theta and
    # the corresponding value of the target function.
    return theta_opt, func_min

Per default, the ‘L-BFGS-B’ algorithm from scipy.optimize.minimize is used. If None is passed, the kernel’s parameters are kept fixed. Available internal optimizers are:

'fmin_l_bfgs_b'

n_restarts_optimizerint, default=0

The number of restarts of the optimizer for finding the kernel’s parameters which maximize the log-marginal likelihood. The first run of the optimizer is performed from the kernel’s initial parameters, the remaining ones (if any) from thetas sampled log-uniform randomly from the space of allowed theta-values. If greater than 0, all bounds must be finite. Note that n_restarts_optimizer=0 implies that one run is performed.

max_iter_predictint, default=100

The maximum number of iterations in Newton’s method for approximating the posterior during predict. Smaller values will reduce computation time at the cost of worse results.

warm_startbool, default=False

If warm-starts are enabled, the solution of the last Newton iteration on the Laplace approximation of the posterior mode is used as initialization for the next call of _posterior_mode(). This can speed up convergence when _posterior_mode is called several times on similar problems as in hyperparameter optimization. See the Glossary.

copy_X_trainbool, default=True

If True, a persistent copy of the training data is stored in the object. Otherwise, just a reference to the training data is stored, which might cause predictions to change if the data is modified externally.

random_stateint, RandomState instance or None, default=None

Determines random number generation used to initialize the centers. Pass an int for reproducible results across multiple function calls. See Glossary.

multi_class{‘one_vs_rest’, ‘one_vs_one’}, default=’one_vs_rest’

Specifies how multi-class classification problems are handled. Supported are ‘one_vs_rest’ and ‘one_vs_one’. In ‘one_vs_rest’, one binary Gaussian process classifier is fitted for each class, which is trained to separate this class from the rest. In ‘one_vs_one’, one binary Gaussian process classifier is fitted for each pair of classes, which is trained to separate these two classes. The predictions of these binary predictors are combined into multi-class predictions. Note that ‘one_vs_one’ does not support predicting probability estimates.

n_jobsint, default=None

The number of jobs to use for the computation: the specified multiclass problems are computed in parallel. None means 1 unless in a joblib.parallel_backend context. -1 means using all processors. See Glossary for more details.

base_estimator_Estimator instance: The estimator instance that defines the likelihood function using the observed data.
kernel_kernel instance: The kernel used for prediction. In case of binary classification, the structure of the kernel is the same as the one passed as parameter but with optimized hyperparameters. In case of multi-class classification, a CompoundKernel is returned which consists of the different kernels used in the one-versus-rest classifiers.
log_marginal_likelihood_value_float: The log-marginal-likelihood of self.kernel_.theta
classesarray-like of shape (n_classes,): Unique class labels.
n_classes_int: The number of classes in the training data
n_features_in_int: Number of features seen during fit.

New in version 0.24.
feature_names_in_ndarray of shape (n_features_in_,): Names of features seen during fit. Defined only when X has feature names that are all strings.

New in version 1.0.

GaussianProcessRegressor : Gaussian process regression (GPR).

>>> from sklearn.datasets import load_iris
>>> from sklearn.gaussian_process import GaussianProcessClassifier
>>> from sklearn.gaussian_process.kernels import RBF
>>> X, y = load_iris(return_X_y=True)
>>> kernel = 1.0 * RBF(1.0)
>>> gpc = GaussianProcessClassifier(kernel=kernel,
...         random_state=0).fit(X, y)
>>> gpc.score(X, y)
0.9866...
>>> gpc.predict_proba(X[:2,:])
array([[0.83548752, 0.03228706, 0.13222543],
       [0.79064206, 0.06525643, 0.14410151]])

simpleml.models.classifiers.sklearn.gaussian_process

Module Contents

Classes

Attributes

`simpleml.models.classifiers.sklearn.gaussian_process`