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java.lang.Objectprocope.methods.clustering.HierarchicalClusteringTrees
public class HierarchicalClusteringTrees
Implements hierarchical agglomerative clustering in O(n2) time and space complexity. It utilizes a nearest neighbor chain method as described in
Murthag, F.
Complexities of Hierarchic Clustering Algorithms: State of the Art
Computational Statistics Quarterly, 1984, 1, 101-113
Supports single linkage, complete linkage, UPGMA and WPGMA clustering
Note: As there are seems to be a confusion in the literature about UPGMA and WPGMA we adapt the notation of the paper above. UPGMA calculates the average of two clusters as the average similarty between all members. For WPGMA the similarity of a merged cluster to any other cluster is the arithmetic mean of the two merged clusters to that other cluster.
Trees
This class does not directly compute a clustering but a tree which represents the order of agglomerations and the similarities at which the subclusters were merged. You have to apply a cutoff value on that tree afterwards to cut the tree and get clusters.
Note: This class contains only static members and is not instantiatable.
Method Summary | |
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static HierarchicalTreeNode |
clusterSimilarities(ProteinNetwork net,
HierarchicalLinkage linkage)
Performs agglomerative hierarchical clustering on a given network using a given linkage method. |
static HierarchicalTreeNode |
clusterSimilarities(ProteinNetwork net,
HierarchicalLinkage linkage,
Set<Integer> proteins)
Performs agglomerative hierarchical clustering on a given network using a given linkage method. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static HierarchicalTreeNode clusterSimilarities(ProteinNetwork net, HierarchicalLinkage linkage)
net
- similarity network to be clusteredlinkage
- linkage
to be used
public static HierarchicalTreeNode clusterSimilarities(ProteinNetwork net, HierarchicalLinkage linkage, Set<Integer> proteins)
net
- similarity network to be clusteredlinkage
- linkage
to be usedproteins
- only cluster this given set of proteins
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