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A New Quartet Tree Heuristic for Hierarchical Clustering [article]

Rudi Cilibrasi, Paul M.B. Vitanyi
2006 arXiv   pre-print
We present a heuristic for reconstructing the optimal-weight tree, and a canonical manner to derive the quartet-topology weights from a given distance matrix.  ...  This contrasts to other heuristic search methods from biological phylogeny, like DNAML or quartet puzzling, which, repeatedly, incrementally construct a solution from a random order of objects, and subsequently  ...  Testing On Heterogenous Natural Data We test gross classification of files based on heterogenous data of markedly different file types: (i) Four mitochondrial gene sequences, from a black bear, polar bear  ... 
arXiv:cs/0606048v1 fatcat:dua32cdi2jhilp7xfvgdket5t4

Improved Variable Neighbourhood Search Heuristic for Quartet Clustering [chapter]

Sergio Consoli, Jan Korst, Steffen Pauws, Gijs Geleijnse
2019 Proceedings  
Given a set of n data objects and their pairwise dissimilarities, the goal of quartet clustering is to construct an optimal tree from the total number of possible combinations of quartet topologies on  ...  The latter is one of the most popular heuristic algorithms for tackling the MQTC problem.  ...  Sergio Consoli wants to dedicate this work with deepest respect to the memory of Professor Kenneth Darby-Dowman, a great scientist, an excellent manager, the best supervisor, a wonderful person, a real  ... 
doi:10.1007/978-3-030-15843-9_1 dblp:conf/icvns/ConsoliKPG18 fatcat:lx3htpoqm5exbf7d7xps5cru64

A Fast Quartet tree heuristic for hierarchical clustering

Rudi L. Cilibrasi, Paul M.B. Vitányi
2011 Pattern Recognition  
We present a Monte Carlo heuristic, based on randomized hill-climbing, for approximating the optimal weight tree, given the quartet topology weights.  ...  The problem and the solution heuristic has been extensively used for general hierarchical clustering of nontree-like (non-phylogeny) data in various domains and across domains with heterogeneous data.  ...  Conclusion We have introduced a new quartet tree problem, the Minimum Quartet Tree Cost (MQTC) problem, suited for general hierarchical clustering.  ... 
doi:10.1016/j.patcog.2010.08.033 fatcat:ukkxvptmsjhdlhanz6qtctyvhe

Heuristic Approaches for the Quartet Method of Hierarchical Clustering

Sergio Consoli, Kenneth Darby-Dowman, Gijs Geleijnse, Jan Korst, Steffen Pauws
2010 IEEE Transactions on Knowledge and Data Engineering  
Given a set of objects and their pairwise distances, we wish to determine a visual representation of the data. We use the quartet paradigm to compute a hierarchy of clusters of the objects.  ...  The method is based on an NP-hard graph optimization problem called the Minimum Quartet Tree Cost problem.  ...  This is the most effective heuristic for the Minimum Quartet Tree Cost problem.  ... 
doi:10.1109/tkde.2009.188 fatcat:sdlzh2i2jnaslmtr6oedy3j4a4

On the minimum quartet tree cost problem [article]

Sergio Consoli, Jan Korst, Gijs Geleijnse, Steffen Pauws
2018 arXiv   pre-print
Given a set of n data objects and their pairwise dissimilarities, the goal of the minimum quartet tree cost (MQTC) problem is to construct an optimal tree from the total number of possible combinations  ...  of quartet topologies on n, where optimality means that the sum of the dissimilarities of the embedded (or consistent) quartet topologies is minimal.  ...  Summary and Outlook We considered the minimum quartet tree cost (MQTC) problem, a challenging novel graph optimization problem suited for general hierarchical clustering.  ... 
arXiv:1807.00566v1 fatcat:rdxxvfyqfvb7dphwdjwd63vr7u

Top-Down Induction of Phylogenetic Trees [chapter]

Celine Vens, Eduardo Costa, Hendrik Blockeel
2010 Lecture Notes in Computer Science  
We propose a novel distance based method for phylogenetic tree reconstruction. Our method is based on a conceptual clustering method that extends the well-known decision tree learning approach.  ...  Third, the resulting trees can be used as classification trees to classify new sequences into subfamilies.  ...  Acknowledgments Celine Vens is a Postdoctoral Fellow of the Research Foundation -Flanders (FWO).  ... 
doi:10.1007/978-3-642-12211-8_6 fatcat:7d5ki3lz4nfdvkcc4yrum63t7y

The development and application of metaheuristics for problems in graph theory: a computational study

Sergio Consoli
2011 4OR  
The remaining heuristics are new approaches to the quartet method of hierarchical clustering.  ...  The proposed VNS for the quartet method of hierarchical clustering is specified in Algorithm 5.4.  ... 
doi:10.1007/s10288-011-0187-3 fatcat:uybenvacn5ebvfaklscfbt52km

Qualitative organization of collections of shapes via quartet analysis

Shi-Sheng Huang, Ariel Shamir, Chao-Hui Shen, Hao Zhang, Alla Sheffer, Shi-Min Hu, Daniel Cohen-Or
2013 ACM Transactions on Graphics  
Figure 1 : A heterogeneous collection of shapes is organized in a hierarchical categorization tree (middle) via quartet-based qualitative analysis.  ...  Combining the information from many quartets computed across a shape collection using several distance measures, we create a hierarchical structure we call categorization tree of the shape collection.  ...  Lastly, at any time the user can switch back to the C-tree display to choose a different shape as a starting point for a new exploration.  ... 
doi:10.1145/2461912.2461954 fatcat:xoo2opsdpvfqbksiapvozyzfzy

Clustering by Compression

R. Cilibrasi, P.M.B. Vitanyi
2005 IEEE Transactions on Information Theory  
To extract a hierarchy of clusters from the distance matrix, we determine a dendrogram (binary tree) by a new quartet method and a fast heuristic to implement it.  ...  We present a new method for clustering based on compression.  ...  Teemu Roos and Henri Tirry for implementing a visualization of the clustering process.  ... 
doi:10.1109/tit.2005.844059 fatcat:imrem6kkszbfjhh6aom6udfhga

Algorithmic Clustering of Music Based on String Compression

Rudi Cilibrasi, Paul Vitányi, Ronald de Wolf
2004 Computer Music Journal  
Acknowledgments We thank John Tromp and Mike Paunovich for useful discussions, and the editors of Computer Music Journal and anonymous referees for pointers to the literature and for many comments that  ...  Below, we describe a heuristic method, developed first for the experiments reported here, that searches for a tree of minimal total cost.  ...  If it lies squarely within a cluster of pieces by a particular composer, then that would be a plausible candidate composer for the new piece. A fourth area to examine lies in the quartet method.  ... 
doi:10.1162/0148926042728449 fatcat:suy4dbx5anexhic4xgdxcwzmrm

A memetic-aided approach to hierarchical clustering from distance matrices: application to gene expression clustering and phylogeny

Carlos Cotta, Pablo Moscato
2003 Biosystems (Amsterdam. Print)  
We propose a heuristic approach to hierarchical clustering from distance matrices based on the use of memetic algorithms (MAs).  ...  Experimental results are given in the context of phylogenetic inference and in the hierarchical clustering of gene expression data.  ...  Saitou for having sent him (back in 1989) a copy of his Neighbor-Joining paper (Saitou and Nei, 1987) . Finally, we thank the reviewers for their useful comments and suggestions. C.  ... 
doi:10.1016/s0303-2647(03)00136-9 pmid:14642660 fatcat:flflf3nepbd2pfrqzjc2b3ymwm

Clustering by compression [article]

Rudi Cilibrasi and Paul Vitanyi (CWI and University of Amsterdam)
2004 arXiv   pre-print
To extract a hierarchy of clusters from the distance matrix, we determine a dendrogram (binary tree) by a new quartet method and a fast heuristic to implement it.  ...  We present a new method for clustering based on compression.  ...  implementing a visualization of the clustering process.  ... 
arXiv:cs/0312044v2 fatcat:7kxq7xadyzd2xnup36aqxrnboq

A Phylogenetic Approach to Music Performance Analysis

Elad Liebman, Eitan Ornoy, Benny Chor
2012 Journal of New Music Research  
Taking samples from 29 different performances of two pieces from Bach's sonatas for solo violin, we construct a 'phylogenetic' tree, representing the relationship between those performances.  ...  Such, for example, are studies made of interpretation approaches to piano compositions  ...  Acknowledgements We would like to thank Sagi Snir, for supplying us with his code implementation of the Rao-Snir quartet max-cut heuristic; Dorottya Fabian, for her contribution to collecting the recordings  ... 
doi:10.1080/09298215.2012.668194 fatcat:ep2dazlipvctzdfipj63dmbf7i

Visual Browse and Exploration in Motion Capture Data with Phylogenetic Tree of Context-Aware Poses

Songle Chen, Xuejian Zhao, Bingqing Luo, Zhixin Sun
2020 Sensors  
Second, to construct a meaningful neighborhood for user browsing, it further merges logical similarity measures of pose with the weight quartets and casts the isolated representative poses into a structure  ...  of phylogenetic tree.  ...  (4) We provide KNN-based motion ranking and AP-based motion clustering with the proposed Euclidean distance on latent space for motion exploration.  ... 
doi:10.3390/s20185224 pmid:32933203 pmcid:PMC7570504 fatcat:rggx5vefc5h7teympqq5jsvf64

Robust analysis of phylogenetic tree space

Martin R Smith
2021 Systematic Biology  
My recommendations for tree space validation and visualization are implemented in a new graphical user interface in the 'TreeDist' R package.  ...  its tree space unsuitable for many purposes.  ...  information (CI), path (Pt), Kendall-Colijn (KC) and quartet (Q) metrics, and a new metric (SV) derived from vector representations of trees.  ... 
doi:10.1093/sysbio/syab100 pmid:34963003 fatcat:gtgueajsxraatgek5zwm72fxwi
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