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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.  ...  Hierarchical clustering and the quartet method In cluster analysis there are basically two methods for 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.  ...  From our analysis, it has been shown that our Reduced Variable Neighbourhood Search is fast and particularly effective for the quartet method of hierarchical clustering.  ... 
doi:10.1109/tkde.2009.188 fatcat:sdlzh2i2jnaslmtr6oedy3j4a4

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 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

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.  ...  From our analysis, it has been shown that our Reduced Variable Neighbourhood Search is fast and particularly effective for the quartet method of hierarchical clustering.  ... 
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.  ...  Shapes are clustered based on some distance measure to facilitate fast querying.  ... 
doi:10.1145/2461912.2461954 fatcat:xoo2opsdpvfqbksiapvozyzfzy

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.  ...  These two analysis tools are necessary for fast motion location on the coarse level. More methods with their visualization techniques are needed for quantitative detail motion analysis.  ... 
doi:10.3390/s20185224 pmid:32933203 pmcid:PMC7570504 fatcat:rggx5vefc5h7teympqq5jsvf64

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

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 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

Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference

Clément-Marie Train, Natasha M Glover, Gaston H Gonnet, Adrian M Altenhoff, Christophe Dessimoz
2017 Bioinformatics  
In addition we introduce a more scalable procedure for hierarchical orthologous group (HOG) clustering, which are several orders of magnitude faster on large datasets.  ...  Motivation: Accurate orthology inference is a fundamental step in many phylogenetics and comparative analysis. Many methods have been proposed, including OMA (Orthologous MAtrix).  ...  Computations were performed at the Vital-IT Center for highperformance computing of the SIB Swiss Institute of Bioinformatics, and on the University College London Computer Science cluster.  ... 
doi:10.1093/bioinformatics/btx229 pmid:28881964 pmcid:PMC5870696 fatcat:6nhrdpyjgjhsno5r5uwrosv64q

Species Tree Estimation Using ASTRAL: Practical Considerations [article]

Siavash Mirarab
2019 arXiv   pre-print
ASTRAL is a method for reconstructing species trees after inferring a set of gene trees and is increasingly used in phylogenomic analyses.  ...  This chapter discusses practical considerations in using ASTRAL, starting with a review of published results and pointing to the strengths and weaknesses of species tree estimation using ASTRAL.  ...  ASTRAL exploits this observation to compute CU branch lengths (with simplifying assumptions) using a fast algorithm for computing mean quartet frequencies "around" each branch (Fig 7b) .  ... 
arXiv:1904.03826v2 fatcat:pgs3adrzjng6dotvke23k6esqu

Multilocus inference of species trees and DNA barcoding

Diego Mallo, David Posada
2016 Philosophical Transactions of the Royal Society of London. Biological Sciences  
One contribution of 16 to a theme issue 'From DNA barcodes to biomes'.  ...  We thank the editors for the invitation to this special issue and two anonymous reviewers for their very helpful comments.  ...  D.P. also wants to acknowledge Paul Hebert and Mehrdad Hajibabaei for the invitation to the International Barcode of Life Conference that was held in Guelph, Canada, in 2015.  ... 
doi:10.1098/rstb.2015.0335 pmid:27481787 pmcid:PMC4971187 fatcat:fovihzzjfrbepn4eys3rvlfuvm

Molecular Phylogenetic Analyses and Real Life Data [article]

Kerstin Hoef-Emden
2005 arXiv   pre-print
A linear increase in the number of sequences results in an exponential increase of possible trees. Thus, inferring trees from molecular data was shown to be NP-hard.  ...  In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees.  ...  The best of the three possible 4-trees for each quartet are used to first assemble a large number of n-trees (quartet-puzzling) and finally to obtain a consensus n-tree.  ... 
arXiv:q-bio/0501030v2 fatcat:7svybdmbqzgvjfzpnpgs6jzm3m

Fast and scalable genome-wide inference of local tree topologies from large number of haplotypes based on tree consistent PBWT data structure [article]

Vladimir Shchur, Liliia Ziganurova, Richard Durbin
2019 bioRxiv   pre-print
In this work we describe a new approach for fast and scalable generation of local tree topologies relating large numbers of haplotypes.  ...  It is based on a data structure which we call tree consistent PBWT, a modification of PBWT data structure introduced by R. Durbin (2014).  ...  Acknowledgement We thank Stephen Schiffels for fruitful discussions and the idea of imbalance density.  ... 
doi:10.1101/542035 fatcat:3arcjkhhabduja5ynsbwomamkm
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