msmbuilder.cluster.GMM¶

class msmbuilder.cluster.GMM(n_components=1, covariance_type='full', tol=0.001, reg_covar=1e-06, max_iter=100, n_init=1, init_params='kmeans', weights_init=None, means_init=None, precisions_init=None, random_state=None, warm_start=False, verbose=0, verbose_interval=10)¶

Gaussian Mixture.

Representation of a Gaussian mixture model probability distribution. This class allows to estimate the parameters of a Gaussian mixture distribution.

Read more in the User Guide.

New in version 0.18.

Parameters:

n_components : int, defaults to 1.

The number of mixture components.

covariance_type : {‘full’, ‘tied’, ‘diag’, ‘spherical’},

defaults to ‘full’.

String describing the type of covariance parameters to use. Must be one of:

'full' (each component has its own general covariance matrix),
'tied' (all components share the same general covariance matrix),
'diag' (each component has its own diagonal covariance matrix),
'spherical' (each component has its own single variance).

tol : float, defaults to 1e-3.

The convergence threshold. EM iterations will stop when the lower bound average gain is below this threshold.

reg_covar : float, defaults to 1e-6.

Non-negative regularization added to the diagonal of covariance. Allows to assure that the covariance matrices are all positive.

max_iter : int, defaults to 100.

The number of EM iterations to perform.

n_init : int, defaults to 1.

The number of initializations to perform. The best results are kept.

init_params : {‘kmeans’, ‘random’}, defaults to ‘kmeans’.

The method used to initialize the weights, the means and the precisions. Must be one of:

'kmeans' : responsibilities are initialized using kmeans.
'random' : responsibilities are initialized randomly.

weights_init : array-like, shape (n_components, ), optional

The user-provided initial weights, defaults to None. If it None, weights are initialized using the init_params method.

means_init : array-like, shape (n_components, n_features), optional

The user-provided initial means, defaults to None, If it None, means are initialized using the init_params method.

precisions_init : array-like, optional.

The user-provided initial precisions (inverse of the covariance matrices), defaults to None. If it None, precisions are initialized using the ‘init_params’ method. The shape depends on ‘covariance_type’:

(n_components,)                        if 'spherical',
(n_features, n_features)               if 'tied',
(n_components, n_features)             if 'diag',
(n_components, n_features, n_features) if 'full'

random_state : int, RandomState instance or None, optional (default=None)

If int, random_state is the seed used by the random number generator; If RandomState instance, random_state is the random number generator; If None, the random number generator is the RandomState instance used by np.random.

warm_start : bool, default to False.

If ‘warm_start’ is True, the solution of the last fitting is used as initialization for the next call of fit(). This can speed up convergence when fit is called several time on similar problems.

verbose : int, default to 0.

Enable verbose output. If 1 then it prints the current initialization and each iteration step. If greater than 1 then it prints also the log probability and the time needed for each step.

verbose_interval : int, default to 10.

Number of iteration done before the next print.

See also

BayesianGaussianMixture: Gaussian mixture model fit with a variational inference.

Attributes:

weights_ : array-like, shape (n_components,)

The weights of each mixture components.

means_ : array-like, shape (n_components, n_features)

The mean of each mixture component.

covariances_ : array-like

The covariance of each mixture component. The shape depends on covariance_type:

(n_components,)                        if 'spherical',
(n_features, n_features)               if 'tied',
(n_components, n_features)             if 'diag',
(n_components, n_features, n_features) if 'full'

precisions_ : array-like

The precision matrices for each component in the mixture. A precision matrix is the inverse of a covariance matrix. A covariance matrix is symmetric positive definite so the mixture of Gaussian can be equivalently parameterized by the precision matrices. Storing the precision matrices instead of the covariance matrices makes it more efficient to compute the log-likelihood of new samples at test time. The shape depends on covariance_type:

(n_components,)                        if 'spherical',
(n_features, n_features)               if 'tied',
(n_components, n_features)             if 'diag',
(n_components, n_features, n_features) if 'full'

precisions_cholesky_ : array-like

The cholesky decomposition of the precision matrices of each mixture component. A precision matrix is the inverse of a covariance matrix. A covariance matrix is symmetric positive definite so the mixture of Gaussian can be equivalently parameterized by the precision matrices. Storing the precision matrices instead of the covariance matrices makes it more efficient to compute the log-likelihood of new samples at test time. The shape depends on covariance_type:

(n_components,)                        if 'spherical',
(n_features, n_features)               if 'tied',
(n_components, n_features)             if 'diag',
(n_components, n_features, n_features) if 'full'

converged_ : bool

True when convergence was reached in fit(), False otherwise.

n_iter_ : int

Number of step used by the best fit of EM to reach the convergence.

lower_bound_ : float

Log-likelihood of the best fit of EM.

Methods

`aic`(X)	Akaike information criterion for the current model on the input X.
`bic`(X)	Bayesian information criterion for the current model on the input X.
`fit`(sequences[, y])	Fit the clustering on the data
`fit_predict`(sequences[, y])	Performs clustering on X and returns cluster labels.
`fit_transform`(sequences[, y])	Alias for fit_predict
`get_params`([deep])	Get parameters for this estimator.
`partial_predict`(X[, y])	Predict the closest cluster each sample in X belongs to.
`partial_transform`(X)	Alias for partial_predict
`predict`(sequences[, y])	Predict the closest cluster each sample in each sequence in sequences belongs to.
`predict_proba`(X)	Predict posterior probability of each component given the data.
`sample`([n_samples])	Generate random samples from the fitted Gaussian distribution.
`score`(X[, y])	Compute the per-sample average log-likelihood of the given data X.
`score_samples`(X)	Compute the weighted log probabilities for each sample.
`set_params`(**params)	Set the parameters of this estimator.
`summarize`()	Return some diagnostic summary statistics about this Markov model
`transform`(sequences)	Alias for predict

__init__(n_components=1, covariance_type='full', tol=0.001, reg_covar=1e-06, max_iter=100, n_init=1, init_params='kmeans', weights_init=None, means_init=None, precisions_init=None, random_state=None, warm_start=False, verbose=0, verbose_interval=10)¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`([n_components, covariance_type, …])	Initialize self.
`aic`(X)	Akaike information criterion for the current model on the input X.
`bic`(X)	Bayesian information criterion for the current model on the input X.
`fit`(sequences[, y])	Fit the clustering on the data
`fit_predict`(sequences[, y])	Performs clustering on X and returns cluster labels.
`fit_transform`(sequences[, y])	Alias for fit_predict
`get_params`([deep])	Get parameters for this estimator.
`partial_predict`(X[, y])	Predict the closest cluster each sample in X belongs to.
`partial_transform`(X)	Alias for partial_predict
`predict`(sequences[, y])	Predict the closest cluster each sample in each sequence in sequences belongs to.
`predict_proba`(X)	Predict posterior probability of each component given the data.
`sample`([n_samples])	Generate random samples from the fitted Gaussian distribution.
`score`(X[, y])	Compute the per-sample average log-likelihood of the given data X.
`score_samples`(X)	Compute the weighted log probabilities for each sample.
`set_params`(**params)	Set the parameters of this estimator.
`summarize`()	Return some diagnostic summary statistics about this Markov model
`transform`(sequences)	Alias for predict

aic(X)¶

Akaike information criterion for the current model on the input X.

Parameters:	X : array of shape (n_samples, n_dimensions)
Returns:	aic : float The lower the better.

bic(X)¶

Bayesian information criterion for the current model on the input X.

Parameters:	X : array of shape (n_samples, n_dimensions)
Returns:	bic : float The lower the better.

fit(sequences, y=None)¶

Fit the clustering on the data

Parameters:	sequences : list of array-like, each of shape [sequence_length, n_features] A list of multivariate timeseries. Each sequence may have a different length, but they all must have the same number of features.
Returns:	self

fit_predict(sequences, y=None)¶

Performs clustering on X and returns cluster labels.

Parameters:	sequences : list of array-like, each of shape [sequence_length, n_features] A list of multivariate timeseries. Each sequence may have a different length, but they all must have the same number of features.
Returns:	Y : list of ndarray, each of shape [sequence_length, ] Cluster labels

fit_transform(sequences, y=None)¶: Alias for fit_predict

get_params(deep=True)¶

Get parameters for this estimator.

Parameters:	deep : boolean, optional If True, will return the parameters for this estimator and contained subobjects that are estimators.
Returns:	params : mapping of string to any Parameter names mapped to their values.

partial_predict(X, y=None)¶

Predict the closest cluster each sample in X belongs to.

In the vector quantization literature, cluster_centers_ is called the code book and each value returned by predict is the index of the closest code in the code book.

Parameters:	X : array-like shape=(n_samples, n_features) A single timeseries.
Returns:	Y : array, shape=(n_samples,) Index of the cluster that each sample belongs to

partial_transform(X)¶: Alias for partial_predict

predict(sequences, y=None)¶

Predict the closest cluster each sample in each sequence in sequences belongs to.

In the vector quantization literature, cluster_centers_ is called the code book and each value returned by predict is the index of the closest code in the code book.

Parameters:	sequences : list of array-like, each of shape [sequence_length, n_features] A list of multivariate timeseries. Each sequence may have a different length, but they all must have the same number of features.
Returns:	Y : list of arrays, each of shape [sequence_length,] Index of the closest center each sample belongs to.

predict_proba(X)¶

Predict posterior probability of each component given the data.

Parameters:	X : array-like, shape (n_samples, n_features) List of n_features-dimensional data points. Each row corresponds to a single data point.
Returns:	resp : array, shape (n_samples, n_components) Returns the probability each Gaussian (state) in the model given each sample.

sample(n_samples=1)¶

Generate random samples from the fitted Gaussian distribution.

Parameters:	n_samples : int, optional Number of samples to generate. Defaults to 1.
Returns:	X : array, shape (n_samples, n_features) Randomly generated sample y : array, shape (nsamples,) Component labels

score(X, y=None)¶

Compute the per-sample average log-likelihood of the given data X.

Parameters:	X : array-like, shape (n_samples, n_dimensions) List of n_features-dimensional data points. Each row corresponds to a single data point.
Returns:	log_likelihood : float Log likelihood of the Gaussian mixture given X.

score_samples(X)¶

Compute the weighted log probabilities for each sample.

Parameters:	X : array-like, shape (n_samples, n_features) List of n_features-dimensional data points. Each row corresponds to a single data point.
Returns:	log_prob : array, shape (n_samples,) Log probabilities of each data point in X.

set_params(**params)¶

Set the parameters of this estimator.

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

Returns:	self

summarize()¶: Return some diagnostic summary statistics about this Markov model

transform(sequences)¶: Alias for predict