BiCluE - Exact and heuristic algorithms for weighted bi-cluster editing of biomedical data.

ABSTRACT:

Background

The explosion of biological data has dramatically reformed today's biology research. The biggest challenge to biologists and bioinformaticians is the integration and analysis of large quantity of data to provide meaningful insights. One major problem is the combined analysis of data from different types. Bi-cluster editing, as a special case of clustering, which partitions two different types of data simultaneously, might be used for several biomedical scenarios. However, the underlying algorithmic problem is NP-hard.

Results

Here we contribute with BiCluE, a software package designed to solve the weighted bi-cluster editing problem. It implements (1) an exact algorithm based on fixed-parameter tractability and (2) a polynomial-time greedy heuristics based on solving the hardest part, edge deletions, first. We evaluated its performance on artificial graphs. Afterwards we exemplarily applied our implementation on real world biomedical data, GWAS data in this case. BiCluE generally works on any kind of data types that can be modeled as (weighted or unweighted) bipartite graphs.

Conclusions

To our knowledge, this is the first software package solving the weighted bi-cluster editing problem. BiCluE as well as the supplementary results are available online at http://biclue.mpi-inf.mpg.de.

SUBMITTER: Sun P 

PROVIDER: S-EPMC4044484 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature