README.md

In zhifeiyan/bfcluster: Birkhoff-Fan Clustering

Birkhoff-Fan Clustering

bfcluster is an R package that provides an implementation of an ADMM algorithm for computing the solution to an semidefinite program (SDP) over the intersection of the Fantope and the Birkhoff polytope. The SDP can be used for community detection and link prediction in networks, and multivariate data clustering by choosing the appropriate input matrix. The ADMM algorithm is written in C++ using Rcpp and the Armadillo C++ library. The package also provides several class methods for analyzing and visualizing results and other utilities for clustering.

Supported in part by the National Science Foundation under grant DMS-1513621

Installation

Use devtools to install directly from GitHub:

library(devtools)
install_github("zhifeiyan/bfcluster")

Example Usage

library(bfcluster)
library(ggplot2)
set.seed(201612)

# Generate a random adjacency matrix from a network model with community structure
adj <- gen_adjmat(n = 120, k = 3, sizes = c(30, 40, 50), 
                  p_min = 0.3, p_max = 0.6, 
                  q_min = 0.01, q_max = 0.05, 
                  type = "sbm", self_loop = FALSE, perm = TRUE)$adjmat
p_adj <- plot(adj)
p_adj <- p_adj + ggtitle("An adjacency matrix with three communities")
print(p_adj)

# Compute SDP solution matrix
sol <- bfcluster(adj, nclust = 3, admm_penalty = 10)
plot(sol, k = 3, perm = TRUE)

# Permute the adjacency matrix using label estimates obtained from SDP solution
perm_id <- permute(sol, k = 3)$perm_id
p_perm_adj <- plot(adj[perm_id, perm_id])
p_perm_adj <- p_perm_adj + ggtitle("Permuted adjacency matrix according to label estimates")
print(p_perm_adj)

zhifeiyan/bfcluster documentation built on May 4, 2019, 11:21 p.m.