Search results for "Brown clustering"

showing 4 items of 4 documents

Fast dendrogram-based OTU clustering using sequence embedding

2014

Biodiversity assessment is an important step in a metagenomic processing pipeline. The biodiversity of a microbial metagenome is often estimated by grouping its 16S rRNA reads into operational taxonomic units or OTUs. These metagenomic datasets are typically large and hence require effective yet accurate computational methods for processing.In this paper, we introduce a new hierarchical clustering method called CRiSPy-Embed which aims to produce high-quality clustering results at a low computational cost. We tackle two computational issues of the current OTU hierarchical clustering approach: (1) the compute-intensive sequence alignment operation for building the distance matrix and (2) the …

Brown clusteringCURE data clustering algorithmSingle-linkage clusteringCorrelation clusteringCanopy clustering algorithmData miningBiologyHierarchical clustering of networksCluster analysiscomputer.software_genrecomputerHierarchical clusteringProceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics
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GenClust: A genetic algorithm for clustering gene expression data

2005

Abstract Background Clustering is a key step in the analysis of gene expression data, and in fact, many classical clustering algorithms are used, or more innovative ones have been designed and validated for the task. Despite the widespread use of artificial intelligence techniques in bioinformatics and, more generally, data analysis, there are very few clustering algorithms based on the genetic paradigm, yet that paradigm has great potential in finding good heuristic solutions to a difficult optimization problem such as clustering. Results GenClust is a new genetic algorithm for clustering gene expression data. It has two key features: (a) a novel coding of the search space that is simple, …

Clustering high-dimensional dataDNA ComplementaryComputer scienceRand indexCorrelation clusteringOligonucleotidesEvolutionary algorithmlcsh:Computer applications to medicine. Medical informaticscomputer.software_genreBiochemistryPattern Recognition AutomatedBiclusteringOpen Reading FramesStructural BiologyCURE data clustering algorithmConsensus clusteringGenetic algorithmCluster AnalysisCluster analysislcsh:QH301-705.5Molecular BiologyGene expression data Clustering Evolutionary algorithmsOligonucleotide Array Sequence AnalysisModels StatisticalBrown clusteringHeuristicGene Expression ProfilingApplied MathematicsComputational BiologyComputer Science Applicationslcsh:Biology (General)Gene Expression RegulationMutationlcsh:R858-859.7Data miningSequence AlignmentcomputerSoftwareAlgorithmsBMC Bioinformatics
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Twister Tries

2015

Many commonly used data-mining techniques utilized across research fields perform poorly when used for large data sets. Sequential agglomerative hierarchical non-overlapping clustering is one technique for which the algorithms’ scaling properties prohibit clustering of a large amount of items. Besides the unfavorable time complexity of O(n 2 ), these algorithms have a space complexity of O(n 2 ), which can be reduced to O(n) if the time complexity is allowed to rise to O(n 2 log2 n). In this paper, we propose the use of locality-sensitive hashing combined with a novel data structure called twister tries to provide an approximate clustering for average linkage. Our approach requires only lin…

ta113Hierarchical agglomerative clusteringta112Fuzzy clusteringBrown clusteringComputer scienceSingle-linkage clusteringcomputer.software_genreHierarchical clusteringLocality-sensitive hashingData setCURE data clustering algorithmlocality-sensitive hashingaverage linkageData miningHierarchical clustering of networkslinear complexityCluster analysishierarchical clusteringAlgorithmcomputerTime complexityProceedings of the 2015 ACM SIGMOD International Conference on Management of Data
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Scalable Hierarchical Clustering: Twister Tries with a Posteriori Trie Elimination

2015

Exact methods for Agglomerative Hierarchical Clustering (AHC) with average linkage do not scale well when the number of items to be clustered is large. The best known algorithms are characterized by quadratic complexity. This is a generally accepted fact and cannot be improved without using specifics of certain metric spaces. Twister tries is an algorithm that produces a dendrogram (i.e., Outcome of a hierarchical clustering) which resembles the one produced by AHC, while only needing linear space and time. However, twister tries are sensitive to rare, but still possible, hash evaluations. These might have a disastrous effect on the final outcome. We propose the use of a metaheuristic algor…

ta113Theoretical computer scienceBrown clusteringComputer scienceCorrelation clusteringSingle-linkage clusteringHierarchical clusteringCURE data clustering algorithmhierrchial clusteringCanopy clustering algorithmHierarchical clustering of networksCluster analysisclustering2015 IEEE Symposium Series on Computational Intelligence
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