A memetic-aided approach to hierarchical clustering from distance matrices: application to gene expression clustering and phylogeny.
We propose a heuristic approach to hierarchical clustering from distance matrices based on the use of memetic algorithms (MAs). By using MAs to solve some variants of the Minimum Weight Hamiltonian Path Problem on the input matrix, a sequence of the individual elements to be clustered (referred to as patterns) is first obtained. While this problem is also NP-hard, a probably optimal sequence is easy to find with the current advances for this problem and helps to prune the space of possible solutions and/or to guide the search performed by an actual clustering algorithm. This technique has been successfully applied to both a Branch-and-Bound algorithm, and to evolutionary algorithms and MAs. Experimental results are given in the context of phylogenetic inference and in the hierarchical clustering of gene expression data.
Cotta
Carlos
C
Dept. Lenguajes y Ciencias de la Computación, Universidad de Málaga ETSI Informática (3.2.49), Campus de Teatinos, 29071 Malaga, Spain. ccottap@lcc.uma.es
Moscato
Pablo
P
D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D005075:Biological Evolution; D002874:Chromosome Mapping / Q000379:methods; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008928:Mitochondria / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated; D010802:Phylogeny; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software