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Spectrum (version 0.9)

Fast Adaptive Spectral Clustering for Single and Multi-View Data

Description

A self-tuning spectral clustering method for single or multi-view data. 'Spectrum' uses a new type of adaptive density aware kernel that strengthens connections in the graph based on common nearest neighbours. It uses a tensor product graph data integration and diffusion procedure to integrate different data sources and reduce noise. 'Spectrum' uses either the eigengap or multimodality gap heuristics to determine the number of clusters. The method is sufficiently flexible so that a wide range of Gaussian and non-Gaussian structures can be clustered with automatic selection of K.

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Version

Install

install.packages('Spectrum')

Monthly Downloads

299

Version

0.9

License

AGPL-3

Maintainer

Christopher John

Last Published

October 7th, 2019

Functions in Spectrum (0.9)

kernel_pca

kernel_pca: A kernel pca function
cluster_similarity

cluster_similarity: cluster a similarity matrix using the Ng method
estimate_k

estimate_k: estimate K using the eigengap or multimodality gap heuristics
brain

A brain cancer dataset
blobs

8 blob like structures
integrate_similarity_matrices

integrate_similarity_matrices: integrate similarity matrices using a tensor product graph linear combination and diffusion technique
circles

Three concentric circles
harmonise_ids

harmonise_ids: works on a list of similarity matrices to add entries of NA where there are missing observations between views
CNN_kernel

CNN_kernel: fast adaptive density-aware kernel
pca

pca: A pca function
sigma_finder

sigma_finder: heuristic to find sigma for the Ng kernel
Spectrum

Spectrum: Fast Adaptive Spectral Clustering for Single and Multi-view Data
ng_kernel

ng_kernel: Kernel from the Ng spectral clustering algorithm
misslfilled

A list of the blob data as similarity matrices with a missing entry in one filled with NAs
spirals

Two spirals wrapped around one another
missl

A list of the blob data as similarity matrices with a missing entry in one
mean_imputation

mean_imputation: mean imputation function for multi-view spectral clustering with missing data
rbfkernel_b

rbfkernel_b: fast self-tuning kernel
tsne

tsne: A tsne function for similarity matrices or ordinary data
umap

umap: A umap function for similarity matrices or ordinary data