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SpectralCoclustering

Spectral Co-Clustering algorithm (Dhillon, 2001).

Clusters rows and columns of an array X to solve the relaxed normalized cut of the bipartite graph created from X as follows: the edge between row vertex i and column vertex j has weight X\[i, j\].

The resulting bicluster structure is block-diagonal, since each row and each column belongs to exactly one bicluster.

Supports sparse matrices, as long as they are nonnegative.

Read more in the User Guide.

Python Reference

Constructors

constructor()

Signature

new SpectralCoclustering(opts?: object): SpectralCoclustering;

Parameters

Name Type Description
opts? object -
opts.init? ArrayLike[] Method for initialization of k-means algorithm; defaults to ‘k-means++’. Default Value 'k-means++'
opts.mini_batch? boolean Whether to use mini-batch k-means, which is faster but may get different results. Default Value false
opts.n_clusters? number The number of biclusters to find. Default Value 3
opts.n_init? number 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. Default Value 10
opts.n_svd_vecs? number Number of vectors to use in calculating the SVD. Corresponds to ncv when svd\_method=arpack and n\_oversamples when svd\_method is ‘randomized`.
opts.random_state? number Used for randomizing the singular value decomposition and the k-means initialization. Use an int to make the randomness deterministic. See Glossary.
opts.svd_method? "randomized" | "arpack" Selects the algorithm for finding singular vectors. May be ‘randomized’ or ‘arpack’. If ‘randomized’, use sklearn.utils.extmath.randomized\_svd, which may be faster for large matrices. If ‘arpack’, use scipy.sparse.linalg.svds, which is more accurate, but possibly slower in some cases. Default Value 'randomized'

Returns

SpectralCoclustering

Defined in: generated/cluster/SpectralCoclustering.ts:29

Methods

dispose()

Disposes of the underlying Python resources.

Once dispose() is called, the instance is no longer usable.

Signature

dispose(): Promise<void>;

Returns

Promise<void>

Defined in: generated/cluster/SpectralCoclustering.ts:146

fit()

Create a biclustering for X.

Signature

fit(opts: object): Promise<any>;

Parameters

Name Type Description
opts object -
opts.X? ArrayLike[] Training data.
opts.y? any Not used, present for API consistency by convention.

Returns

Promise<any>

Defined in: generated/cluster/SpectralCoclustering.ts:163

get_indices()

Row and column indices of the i’th bicluster.

Only works if rows\_ and columns\_ attributes exist.

Signature

get_indices(opts: object): Promise<ArrayLike>;

Parameters

Name Type Description
opts object -
opts.i? number The index of the cluster.

Returns

Promise<ArrayLike>

Defined in: generated/cluster/SpectralCoclustering.ts:205

get_metadata_routing()

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Signature

get_metadata_routing(opts: object): Promise<any>;

Parameters

Name Type Description
opts object -
opts.routing? any A MetadataRequest encapsulating routing information.

Returns

Promise<any>

Defined in: generated/cluster/SpectralCoclustering.ts:244

get_shape()

Shape of the i’th bicluster.

Signature

get_shape(opts: object): Promise<number>;

Parameters

Name Type Description
opts object -
opts.i? number The index of the cluster.

Returns

Promise<number>

Defined in: generated/cluster/SpectralCoclustering.ts:282

get_submatrix()

Return the submatrix corresponding to bicluster i.

Signature

get_submatrix(opts: object): Promise<ArrayLike[]>;

Parameters

Name Type Description
opts object -
opts.data? ArrayLike[] The data.
opts.i? number The index of the cluster.

Returns

Promise<ArrayLike[]>

Defined in: generated/cluster/SpectralCoclustering.ts:319

init()

Initializes the underlying Python resources.

This instance is not usable until the Promise returned by init() resolves.

Signature

init(py: PythonBridge): Promise<void>;

Parameters

Name Type
py PythonBridge

Returns

Promise<void>

Defined in: generated/cluster/SpectralCoclustering.ts:94

Properties

_isDisposed

boolean = false

Defined in: generated/cluster/SpectralCoclustering.ts:27

_isInitialized

boolean = false

Defined in: generated/cluster/SpectralCoclustering.ts:26

_py

PythonBridge

Defined in: generated/cluster/SpectralCoclustering.ts:25

id

string

Defined in: generated/cluster/SpectralCoclustering.ts:22

opts

any

Defined in: generated/cluster/SpectralCoclustering.ts:23

Accessors

column_labels_

The bicluster label of each column.

Signature

column_labels_(): Promise<ArrayLike>;

Returns

Promise<ArrayLike>

Defined in: generated/cluster/SpectralCoclustering.ts:444

columns_

Results of the clustering, like rows.

Signature

columns_(): Promise<ArrayLike[]>;

Returns

Promise<ArrayLike[]>

Defined in: generated/cluster/SpectralCoclustering.ts:390

feature_names_in_

Names of features seen during fit. Defined only when X has feature names that are all strings.

Signature

feature_names_in_(): Promise<ArrayLike>;

Returns

Promise<ArrayLike>

Defined in: generated/cluster/SpectralCoclustering.ts:498

n_features_in_

Number of features seen during fit.

Signature

n_features_in_(): Promise<number>;

Returns

Promise<number>

Defined in: generated/cluster/SpectralCoclustering.ts:471

py

Signature

py(): PythonBridge;

Returns

PythonBridge

Defined in: generated/cluster/SpectralCoclustering.ts:81

Signature

py(pythonBridge: PythonBridge): void;

Parameters

Name Type
pythonBridge PythonBridge

Returns

void

Defined in: generated/cluster/SpectralCoclustering.ts:85

row_labels_

The bicluster label of each row.

Signature

row_labels_(): Promise<ArrayLike>;

Returns

Promise<ArrayLike>

Defined in: generated/cluster/SpectralCoclustering.ts:417

rows_

Results of the clustering. rows\[i, r\] is true if cluster i contains row r. Available only after calling fit.

Signature

rows_(): Promise<ArrayLike[]>;

Returns

Promise<ArrayLike[]>

Defined in: generated/cluster/SpectralCoclustering.ts:363