Updist {shipunov}

Educated distances for semi-supervised clustering

Description

Updates distance matrix to help link or unlink objects

Usage

  Updist(dst, link=NULL, unlink=NULL, dmax=max(dst), dmin=min(dst))

Arguments

dst

dist object

link

1-level list with the arbitrary number of components, each component is a numeric vector of row numbers for objects which you prefer to be linked

unlink

1-level list with the arbitrary number of components, each component is a numeric vector of row numbers for objects which you prefer to be not linked

dmax

Distance to set for not linked objects

dmin

Distance to set for linked objects

Details

This function borrows the idea of MPCKM semi-supervised k-means (Bilenko et al., 2004) but instead of updating distances on the run, it simply updates the distances object beforehand in accordance with 'link' and 'unlink' constraints.

Amazingly, it works as expected :) Please see the examples below.

References

Bilenko M., Basu S., Mooney R.J. 2004. Integrating constraints and metric learning in semi-supervised clustering. In: Proceedings of the twenty-first international conference on Machine learning. P. 11. ACM.

See Also

dist

Examples

iris.d <- dist(iris[, -5])
iris.km <- kmeans(iris.d, 3)
iris.h <- cutree(hclust(iris.d, method="ward.D"), k=3)

Misclass(iris.km$cluster, iris$Species, best=TRUE)
Misclass(iris.h, iris$Species, best=TRUE)

i.vv <- cbind(which(iris$Species == "versicolor"), which(iris$Species == "virginica"))
i.link <- list(sample(i.vv[, 2], 25), sample(i.vv[, 1], 25))
i.unlink <- list(i.vv[1, ], i.vv[2, ])

iris.upd <- Updist(iris.d, link=i.link, unlink=i.unlink)

iris.ukm <- kmeans(iris.upd, 3)
iris.uh <- cutree(hclust(iris.upd, method="ward.D"), k=3)

Misclass(iris.ukm$cluster, iris$Species, best=TRUE)
Misclass(iris.uh, iris$Species, best=TRUE)

## ===

aad <- dist(t(atmospheres))
plot(hclust(aad))

aadu <- Updist(aad, unlink=list(c("Earth", "Mercury")))
plot(hclust(aadu))