ml_power_iteration: Spark ML - Power Iteration Clustering

In rstudio/sparklyr: R Interface to Apache Spark

Spark ML – Power Iteration Clustering

Description

Power iteration clustering (PIC) is a scalable and efficient algorithm for clustering vertices of a graph given pairwise similarities as edge properties, described in the paper "Power Iteration Clustering" by Frank Lin and William W. Cohen. It computes a pseudo-eigenvector of the normalized affinity matrix of the graph via power iteration and uses it to cluster vertices. spark.mllib includes an implementation of PIC using GraphX as its backend. It takes an RDD of (srcId, dstId, similarity) tuples and outputs a model with the clustering assignments. The similarities must be nonnegative. PIC assumes that the similarity measure is symmetric. A pair (srcId, dstId) regardless of the ordering should appear at most once in the input data. If a pair is missing from input, their similarity is treated as zero.

Usage

ml_power_iteration(
  x,
  k = 4,
  max_iter = 20,
  init_mode = "random",
  src_col = "src",
  dst_col = "dst",
  weight_col = "weight",
  ...
)

Arguments

x	A 'spark_connection' or a 'tbl_spark'.
k	The number of clusters to create.
max_iter	The maximum number of iterations to run.
init_mode	This can be either "random", which is the default, to use a random vector as vertex properties, or "degree" to use normalized sum similarities.
src_col	Column in the input Spark dataframe containing 0-based indexes of all source vertices in the affinity matrix described in the PIC paper.
dst_col	Column in the input Spark dataframe containing 0-based indexes of all destination vertices in the affinity matrix described in the PIC paper.
weight_col	Column in the input Spark dataframe containing non-negative edge weights in the affinity matrix described in the PIC paper.
...	Optional arguments. Currently unused.

Value

A 2-column R dataframe with columns named "id" and "cluster" describing the resulting cluster assignments

Examples

## Not run: 

library(sparklyr)

sc <- spark_connect(master = "local")

r1 <- 1
n1 <- 80L
r2 <- 4
n2 <- 80L

gen_circle <- function(radius, num_pts) {
  # generate evenly distributed points on a circle centered at the origin
  seq(0, num_pts - 1) %>%
    lapply(
      function(pt) {
        theta <- 2 * pi * pt / num_pts

        radius * c(cos(theta), sin(theta))
      }
    )
}

guassian_similarity <- function(pt1, pt2) {
  dist2 <- sum((pt2 - pt1)^2)

  exp(-dist2 / 2)
}

gen_pic_data <- function() {
  # generate points on 2 concentric circle centered at the origin and then
  # compute pairwise Gaussian similarity values of all unordered pair of
  # points
  n <- n1 + n2
  pts <- append(gen_circle(r1, n1), gen_circle(r2, n2))
  num_unordered_pairs <- n * (n - 1) / 2

  src <- rep(0L, num_unordered_pairs)
  dst <- rep(0L, num_unordered_pairs)
  sim <- rep(0, num_unordered_pairs)

  idx <- 1
  for (i in seq(2, n)) {
    for (j in seq(i - 1)) {
      src[[idx]] <- i - 1L
      dst[[idx]] <- j - 1L
      sim[[idx]] <- guassian_similarity(pts[[i]], pts[[j]])
      idx <- idx + 1
    }
  }

  dplyr::tibble(src = src, dst = dst, sim = sim)
}

pic_data <- copy_to(sc, gen_pic_data())

clusters <- ml_power_iteration(
  pic_data,
  src_col = "src", dst_col = "dst", weight_col = "sim", k = 2, max_iter = 40
)
print(clusters)

## End(Not run)

rstudio/sparklyr documentation built on Sept. 18, 2024, 6:10 a.m.