`gemclus.linear`.LinearMMD¶

class gemclus.linear.LinearMMD(n_clusters=3, max_iter=1000, learning_rate=0.001, solver='adam', kernel='linear', ovo=False, batch_size=None, verbose=False, random_state=None, kernel_params=None)[source]¶

Implementation of the maximisation of the MMD GEMINI using a logistic regression as a clustering distribution \(p(y|x)\).

Parameters:

n_clustersint, default=3

The maximum number of clusters to form as well as the number of output neurons in the neural network.

max_iter: int, default=1000

Maximum number of epochs to perform gradient descent in a single run.

learning_rate: float, default=1e-3

Initial learning rate used. It controls the step-size in updating the weights.

kernel: {‘additive_chi2’, ‘chi2’, ‘cosine’,’linear’,’poly’,’polynomial’,’rbf’,’laplacian’,’sigmoid’, ‘precomputed’},

default=’linear’ The kernel to use in combination with the MMD objective. It corresponds to one value of KERNEL_PARAMS. Currently, all kernel parameters are the default ones. If the kernel is set to ‘precomputed’, then a custom kernel matrix must be passed to the argument y of fit, fit_predict and/or score.

ovo: bool, default=False

Whether to run the model using the MMD OvA (False) or the MMD OvO (True).

solver: {‘sgd’,’adam’}, default=’adam’

The solver for weight optimisation.

‘sgd’ refers to stochastic gradient descent.
‘adam’ refers to a stochastic gradient-based optimiser proposed by Kingma, Diederik and Jimmy Ba.

batch_size: int, default=None

The size of batches during gradient descent training. If set to None, the whole data will be considered.

verbose: bool, default=False

Whether to print progress messages to stdout

random_state: int, RandomState instance, default=None

Determines random number generation for weights and bias initialisation. Pass an int for reproducible results across multiple function calls.

kernel_params: dict, default=None

A dictionary of keyword arguments to pass to the chosen kernel function.

Attributes:

W_: ndarray of shape (n_features, n_clusters): The linear weights of model
b_: ndarray of shape (1, n_clusters): The biases of the model
optimiser_: `AdamOptimizer` or `SGDOptimizer`: The optimisation algorithm used for training depending on the chosen solver parameter.
labels_: ndarray of shape (n_samples): The labels that were assigned to the samples passed to the fit() method.
n_iter_: int: The number of iterations that the model took for converging.

See also

LinearModel: logistic regression trained for clustering with any GEMINI
LinearWasserstein: logistic regression trained for clustering with the Wasserstein GEMINI
RIM: logistic regression trained with a regularised mutual information

References

GEMINI - Generalised Mutual Information for Discriminative Clustering: Louis Ohl, Pierre-Alexandre Mattei, Charles Bouveyron, Warith Harchaoui, Mickaël Leclercq, Arnaud Droit, Frederic Precioso

Examples

>>> from sklearn.datasets import load_iris
>>> from gemclus.linear import LinearMMD
>>> X,y=load_iris(return_X_y=True)
>>> clf = LinearMMD(random_state=0).fit(X)
>>> clf.predict(X[:2,:])
array([0, 0])
>>> clf.predict_proba(X[:2,:]).shape
(2, 3)
>>> clf.score(X)
1.7048160115

__init__(n_clusters=3, max_iter=1000, learning_rate=0.001, solver='adam', kernel='linear', ovo=False, batch_size=None, verbose=False, random_state=None, kernel_params=None)[source]¶

fit(X, y=None)¶

Compute GEMINI clustering.

Parameters:

X{array-like, sparse matrix} of shape (n_samples, n_features): Training instances to cluster.
yndarray of shape (n_samples, n_samples), default=None: Use this parameter to give a precomputed affinity metric if the option “precomputed” was passed during construction. Otherwise, it is not used and present here for API consistency by convention.

Returns:

selfobject: Fitted estimator.

fit_predict(X, y=None)¶

Compute GEMINI clustering and returns the predicted clusters.

Parameters:

X{array-like, sparse matrix} of shape (n_samples, n_features): Training instances to cluster.
yndarray of shape (n_samples, n_samples), default=None: Use this parameter to give a precomputed affinity metric if the option “precomputed” was passed during construction. Otherwise, it is not used and present here for API consistency by convention.

Returns:

y_predndarray of shape (n_samples,): Vector containing the cluster label for each sample.

get_gemini()[source]¶

Initialise a gemclus.GEMINI instance that will be used to train the model.

Returns:

gemini: a GEMINI instance

get_metadata_routing()¶

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns:

routingMetadataRequest: A MetadataRequest encapsulating routing information.

get_params(deep=True)¶

Get parameters for this estimator.

Parameters:

deepbool, default=True: If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns:

paramsdict: Parameter names mapped to their values.

predict(X)¶

Return the cluster membership of samples. This can only be called after the model was fit to some data.

Parameters:

X{array-like, sparse matrix}, shape (n_samples, n_features): The input samples.

Returns:

yndarray of shape (n_samples,): The label for each sample is the label of the closest sample seen during fit.

predict_proba(X)¶

Probability estimates that are the output of the neural network p(y|x). The returned estimates for all classes are ordered by the label of classes.

Parameters:

X{array-like, sparse matrix} of shape (n_samples, n_features): Vector to be scored, where n_samples is the number of samples and n_features is the number of features.

Returns:

Tarray-like of shape (n_samples, n_clusters): Returns the probability of the sample for each cluster in the model.

score(X, y=None)¶

Return the value of the GEMINI evaluated on the given test data.

Parameters:

X{array-like, sparse matrix} of shape (n_samples, n_features): Test samples.
yndarray of shape (n_samples, n_samples), default=None: Use this parameter to give a precomputed affinity metric if the option “precomputed” was passed during construction. Otherwise, it is not used and present here for API consistency by convention.

Returns:

scorefloat: GEMINI evaluated on the output of self.predict(X).

set_params(**params)¶

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters:

**paramsdict: Estimator parameters.

Returns:

selfestimator instance: Estimator instance.

Examples using `gemclus.linear.LinearMMD`¶

Consensus clustering with linking constraints on sample pairs

gemclus.linear.LinearMMD¶

Examples using gemclus.linear.LinearMMD¶

`gemclus.linear`.LinearMMD¶

Examples using `gemclus.linear.LinearMMD`¶