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 (opens in a new tab)
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 (opens in a new tab), which is more accurate, but possibly slower in some cases. Default Value 'randomized' |
Returns
Defined in: generated/cluster/SpectralCoclustering.ts:29 (opens in a new tab)
Properties
_isDisposed
boolean=false
Defined in: generated/cluster/SpectralCoclustering.ts:27 (opens in a new tab)
_isInitialized
boolean=false
Defined in: generated/cluster/SpectralCoclustering.ts:26 (opens in a new tab)
_py
PythonBridge
Defined in: generated/cluster/SpectralCoclustering.ts:25 (opens in a new tab)
id
string
Defined in: generated/cluster/SpectralCoclustering.ts:22 (opens in a new tab)
opts
any
Defined in: generated/cluster/SpectralCoclustering.ts:23 (opens in a new tab)
Accessors
column_labels_
The bicluster label of each column.
Signature
column_labels_(): Promise<ArrayLike>;Returns
Promise<ArrayLike>
Defined in: generated/cluster/SpectralCoclustering.ts:404 (opens in a new tab)
columns_
Results of the clustering, like rows.
Signature
columns_(): Promise<ArrayLike[]>;Returns
Promise<ArrayLike[]>
Defined in: generated/cluster/SpectralCoclustering.ts:350 (opens in a new tab)
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:458 (opens in a new tab)
n_features_in_
Number of features seen during fit.
Signature
n_features_in_(): Promise<number>;Returns
Promise<number>
Defined in: generated/cluster/SpectralCoclustering.ts:431 (opens in a new tab)
py
Signature
py(): PythonBridge;Returns
PythonBridge
Defined in: generated/cluster/SpectralCoclustering.ts:81 (opens in a new tab)
Signature
py(pythonBridge: PythonBridge): void;Parameters
| Name | Type |
|---|---|
pythonBridge | PythonBridge |
Returns
void
Defined in: generated/cluster/SpectralCoclustering.ts:85 (opens in a new tab)
row_labels_
The bicluster label of each row.
Signature
row_labels_(): Promise<ArrayLike>;Returns
Promise<ArrayLike>
Defined in: generated/cluster/SpectralCoclustering.ts:377 (opens in a new tab)
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:323 (opens in a new tab)
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 (opens in a new tab)
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 (opens in a new tab)
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 (opens in a new tab)
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:242 (opens in a new tab)
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:279 (opens in a new tab)
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 (opens in a new tab)