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class sklearn.cluster.bicluster.SpectralBiclustering(n_clusters=3, method='bistochastic', n_components=6, n_best=3, svd_method='randomized', n_svd_vecs=None, mini_batch=False, init='k-means++', n_init=10, n_jobs=1, random_state=None)
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Spectral biclustering (Kluger, 2003).
Partitions rows and columns under the assumption that the data has an underlying checkerboard structure. For instance, if there are two row partitions and three column partitions, each row will belong to three biclusters, and each column will belong to two biclusters. The outer product of the corresponding row and column label vectors gives this checkerboard structure.
Read more in the User Guide.
Parameters: n_clusters : integer or tuple (n_row_clusters, n_column_clusters)
The number of row and column clusters in the checkerboard structure.
method : string, optional, default: ?bistochastic?
Method of normalizing and converting singular vectors into biclusters. May be one of ?scale?, ?bistochastic?, or ?log?. The authors recommend using ?log?. If the data is sparse, however, log normalization will not work, which is why the default is ?bistochastic?. CAUTION: if
method=?log?
, the data must not be sparse.n_components : integer, optional, default: 6
Number of singular vectors to check.
n_best : integer, optional, default: 3
Number of best singular vectors to which to project the data for clustering.
svd_method : string, optional, default: ?randomized?
Selects the algorithm for finding singular vectors. May be ?randomized? or ?arpack?. If ?randomized?, uses
sklearn.utils.extmath.randomized_svd
, which may be faster for large matrices. If ?arpack?, usessklearn.utils.arpack.svds
, which is more accurate, but possibly slower in some cases.n_svd_vecs : int, optional, default: None
Number of vectors to use in calculating the SVD. Corresponds to
ncv
whensvd_method=arpack
andn_oversamples
whensvd_method
is ?randomized`.mini_batch : bool, optional, default: False
Whether to use mini-batch k-means, which is faster but may get different results.
init : {?k-means++?, ?random? or an ndarray}
Method for initialization of k-means algorithm; defaults to ?k-means++?.
n_init : int, optional, default: 10
Number of random initializations that are tried with the k-means algorithm.
If mini-batch k-means is used, the best initialization is chosen and the algorithm runs once. Otherwise, the algorithm is run for each initialization and the best solution chosen.
n_jobs : int, optional, default: 1
The number of jobs to use for the computation. This works by breaking down the pairwise matrix into n_jobs even slices and computing them in parallel.
If -1 all CPUs are used. If 1 is given, no parallel computing code is used at all, which is useful for debugging. For n_jobs below -1, (n_cpus + 1 + n_jobs) are used. Thus for n_jobs = -2, all CPUs but one are used.
random_state : int seed, RandomState instance, or None (default)
A pseudo random number generator used by the K-Means initialization.
Attributes: rows_ : array-like, shape (n_row_clusters, n_rows)
Results of the clustering.
rows[i, r]
is True if clusteri
contains rowr
. Available only after callingfit
.columns_ : array-like, shape (n_column_clusters, n_columns)
Results of the clustering, like
rows
.row_labels_ : array-like, shape (n_rows,)
Row partition labels.
column_labels_ : array-like, shape (n_cols,)
Column partition labels.
References
- Kluger, Yuval, et. al., 2003. Spectral biclustering of microarray data: coclustering genes and conditions.
Methods
fit
(X)Creates a biclustering for X. get_indices
(i)Row and column indices of the i?th bicluster. get_params
([deep])Get parameters for this estimator. get_shape
(i)Shape of the i?th bicluster. get_submatrix
(i, data)Returns the submatrix corresponding to bicluster i
.set_params
(\*\*params)Set the parameters of this estimator. -
__init__(n_clusters=3, method='bistochastic', n_components=6, n_best=3, svd_method='randomized', n_svd_vecs=None, mini_batch=False, init='k-means++', n_init=10, n_jobs=1, random_state=None)
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biclusters_
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Convenient way to get row and column indicators together.
Returns the
rows_
andcolumns_
members.
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fit(X)
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Creates a biclustering for X.
Parameters: X : array-like, shape (n_samples, n_features)
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get_indices(i)
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Row and column indices of the i?th bicluster.
Only works if
rows_
andcolumns_
attributes exist.Returns: row_ind : np.array, dtype=np.intp
Indices of rows in the dataset that belong to the bicluster.
col_ind : np.array, dtype=np.intp
Indices of columns in the dataset that belong to the bicluster.
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get_params(deep=True)
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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.
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get_shape(i)
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Shape of the i?th bicluster.
Returns: shape : (int, int)
Number of rows and columns (resp.) in the bicluster.
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get_submatrix(i, data)
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Returns the submatrix corresponding to bicluster
i
.Works with sparse matrices. Only works if
rows_
andcolumns_
attributes exist.
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set_params(**params)
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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 :
cluster.bicluster.SpectralBiclustering()
2017-01-15 04:20:38
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