diceR (version 0.3.0)

PAC: Proportion of Ambiguous Clustering

Description

Given a consensus matrix, returns the proportion of ambiguous clusters (PAC). This is a robust way to assess clustering performance.

Usage

PAC(cm, lower = 0, upper = 1)

Arguments

cm

consensus matrix. Should be symmetric and values between 0 and 1.

lower

the lower bound that determines what is ambiguous

upper

the upper bound that determines what is ambiguous

Value

the PAC is a score used in clustering performance. The lower it is the better, because we want minimal ambiguity amongst the consensus.

Details

Since a consensus matrix is symmetric, we only look at its lower (or upper) triangular matrix. The proportion of entries strictly between lower and upper is the PAC. In a perfect clustering, the consensus matrix would consist of only 0s and 1s, and the PAC assessed on the (0, 1) interval would have a perfect score of 0. Using a (0.1, 0.9) interval for defining ambiguity is common as well.

The PAC is not, strictly speaking, an internal validity index. Originally used to choose the optimal number of clusters, here we use it to assess cluster stability. However, PAC is still agnostic any gold standard clustering result so we use it like an internal validity index.

References

Senbabaoglu, Y., Michailidis, G., & Li, J. Z. (2014). Critical limitations of consensus clustering in class discovery. Scientific reports, 4.

Examples

# NOT RUN {
set.seed(1)
x <- replicate(100, rbinom(100, 4, 0.2))
y <- consensus_matrix(x)
PAC(y, lower = 0.05, upper = 0.95)
# }