A Fast Construction Algorithm for the Incidence Matrices of a Class of Symmetric Balanced Incomplete Block Designs

Lee, Ju‐Hyun; Kang, Sungkwon; Choi, Hoo‐Kyun

doi:10.1007/978-3-540-24768-5_2

Cited by 4 publications

(3 citation statements)

References 7 publications

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“…The second (‘block’) approach subsets pairs that are more likely to have elements in common, which limits data replication [see also ( Kleinheksel and Somani, 2016 )]. The final (‘design’) approach uses a projective plane ( Lee et al., 2004 ) or symmetric balanced incomplete block design to create subsets of elements such that any pair of elements is observed exactly once across all the subsets.…”

Section: Introductionmentioning

confidence: 99%

Novel approach for parallelizing pairwise comparison problems as applied to detecting segments identical by decent in whole-genome data

Sapin

2021

Bioinformatics

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Motivation Pairwise comparison problems arise in many areas of science. In genomics, datasets are already large and getting larger, and so operations that require pairwise comparisons—either on pairs of SNPs or pairs of individuals—are extremely computationally challenging. We propose a generic algorithm for addressing pairwise comparison problems that breaks a large problem (of order n2 comparisons) into multiple smaller ones (each of order n comparisons), allowing for massive parallelization. Results We demonstrated that this approach is very efficient for calling identical by descent (IBD) segments between all pairs of individuals in the UK Biobank dataset, with a 250-fold savings in time and 750-fold savings in memory over the standard approach to detecting such segments across the full dataset. This efficiency should extend to other methods of IBD calling and, more generally, to other pairwise comparison tasks in genomics or other areas of science.

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Section: Introductionmentioning

confidence: 99%

Novel approach for parallelizing pairwise comparison problems as applied to detecting segments identical by decent in whole-genome data

Sapin

2021

Bioinformatics

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“…An algorithm to construct projective planes was proposed by Lee et al [10]. The construction of D can be derived from Theorem 2.…”

Section: Design Approachmentioning

confidence: 99%

Pairwise Element Computation with MapReduce

Kiefer¹,

Volk²,

Lehner³

2010

Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing

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In this paper, we present a parallel method to evaluate functions on pairs of elements. It is a challenge to partition the Cartesian product of a set with itself in order to parallelize the function evaluation on all pairs. Our solution uses (a) replication of set elements to allow for partitioning and (b) aggregation of the results gathered for different copies of an element. Based on an execution model with nodes that execute tasks on local data without online communication, we present a generic algorithm and show how it can be implemented with MapReduce. Three different distribution schemes that define the partitioning of the Cartesian product are introduced, compared, and evaluated. Any one of the distribution schemes can be used to derive and implement a specific algorithm for parallel pairwise element computation.

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“…The second ("block") approach subsets pairs that are more likely to have elements in common, which limits data replication (see also (Kleinheksel and Somani 2016)). The final ("design") approach uses a projective plane (Lee et al 2004) or symmetric balanced incomplete block design to create subsets of elements such that any pair of elements is observed exactly once across all the subsets.…”

Section: Introductionmentioning

confidence: 99%

Novel Approach for Parallelizing Pairwise Comparison Problems as Applied to Detecting Segments Identical By Decent in Whole-Genome Data

Sapin

2020

Preprint

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AbstractMotivationPairwise comparison problems arise in many areas of science. In genomics, datasets are already large and getting larger, and so operations that require pairwise comparisons—either on pairs of SNPs or pairs of individuals—are extremely computationally challenging. We propose a generic algorithm for addressing pairwise comparison problems that breaks a large problem (of order n2 comparisons) into multiple smaller ones (each of order n comparisons), allowing for massive parallelization.ResultsWe demonstrated that this procedure is very efficient for calling identical by descent (IBD) segments between all pairs of individuals in the UK Biobank dataset, with a user time savings roughly 180-fold over the traditional (non-parallel) approach to detecting such segments. This efficiency should extend to other methods of IBD calling and, more generally, to other pairwise comparison tasks in genomics or other areas of science.Contactemmanuel.sapin@colorado.edu

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A Fast Construction Algorithm for the Incidence Matrices of a Class of Symmetric Balanced Incomplete Block Designs

Cited by 4 publications

References 7 publications

Novel approach for parallelizing pairwise comparison problems as applied to detecting segments identical by decent in whole-genome data

Novel approach for parallelizing pairwise comparison problems as applied to detecting segments identical by decent in whole-genome data

Pairwise Element Computation with MapReduce

Novel Approach for Parallelizing Pairwise Comparison Problems as Applied to Detecting Segments Identical By Decent in Whole-Genome Data

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