Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Adjacency-constrained hierarchical clustering of a band similarity
  matrix with application to Genomics   Motivation: Genomic data analyses such as Genome-Wide Association Studies
(GWAS) or Hi-C studies are often faced with the problem of partitioning
chromosomes into successive regions based on a similarity matrix of
high-resolution, locus-level measurements. An intuitive way of doing this is to
perform a modified Hierarchical Agglomerative Clustering (HAC), where only
adjacent clusters (according to the ordering of positions within a chromosome)
are allowed to be merged. A major practical drawback of this method is its
quadratic time and space complexity in the number of loci, which is typically
of the order of 10^4 to 10^5 for each chromosome. Results: By assuming that the
similarity between physically distant objects is negligible, we propose an
implementation of this adjacency-constrained HAC with quasi-linear complexity.
Our illustrations on GWAS and Hi-C datasets demonstrate the relevance of this
assumption, and show that this method highlights biologically meaningful
signals. Thanks to its small time and memory footprint, the method can be run
on a standard laptop in minutes or even seconds. Availability and
Implementation: Software and sample data are available as an R package,
adjclust, that can be downloaded from the Comprehensive R Archive Network
(CRAN).

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The categories of this paper are: cmp-lg
5
The categories of this paper are: gr-qc
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The categories of this paper are: nlin
31
The categories of this paper are: ao-sci
6
The categories of this paper are: astro-ph
7
The categories of this paper are: hep-th
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The categories of this paper are: solv-int
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The categories of this paper are: bayes-an
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The categories of this paper are: cond-mat
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The categories of this paper are: hep-ex
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The categories of this paper are: quant-ph
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The categories of this paper are: econ
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The categories of this paper are: chem-ph
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The categories of this paper are: plasm-ph
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The categories of this paper are: atom-ph
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The categories of this paper are: eess