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Author:

Duan, Junbo (Duan, Junbo.) | Soussen, Charles (Soussen, Charles.) | Brie, David (Brie, David.) | Idier, Jerome (Idier, Jerome.) | Wang, Yu-Ping (Wang, Yu-Ping.) | Wan, Mingxi (Wan, Mingxi.) (Scholars:万明习)

Indexed by:

SCIE EI

Abstract:

Piecewise signals appear in many application fields. Here, we propose a framework for segmenting such signals based on the modeling of each piece using a parametric probability distribution. The proposed framework first models the segmentation as an optimization problem with sparsity regularization. Then, an algorithm based on dynamic programming is utilized for finding the optimal solution. However, dynamic programming often suffers from a heavy computational burden. Therefore, we further show that the proposed framework is parallelizable and propose using GPU-based parallel computing to accelerate the computation. This approach is highly desirable for the analysis of large volumes of data that are ubiquitous. The experiments on both the simulated and real genomic datasets from the next-generation sequencing demonstrate an improved performance in terms of both segmentation quality and computational speed.

Keyword:

dynamic programming next generation sequencing Parallel computing piecewise distribution segmentation algorithm

Author Community:

  • [ 1 ] [Duan, Junbo; Wan, Mingxi] Xi An Jiao Tong Univ, Dept Biomed Engn, Xian, Shaanxi, Peoples R China
  • [ 2 ] [Soussen, Charles] Univ Paris Sud, Cent Supelec CNRS Univ Paris Saclay, Lab Signaux & Syst, F-91192 Gif Sur Yvette, France
  • [ 3 ] [Brie, David] Univ Lorraine, CNRS, Ctr Rech Automat Nancy, Lorraine, France
  • [ 4 ] [Idier, Jerome] Ecole Cent Nantes, Lab Sci Numer Nantes, Nantes, France
  • [ 5 ] [Wang, Yu-Ping] Tulane Univ, Dept Biomed Engn, New Orleans, LA 70118 USA

Reprint Author's Address:

  • Xi An Jiao Tong Univ, Dept Biomed Engn, Xian, Shaanxi, Peoples R China.

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Source :

IEEE ACCESS

ISSN: 2169-3536

Year: 2019

Volume: 7

Page: 13217-13229

3 . 7 4 5

JCR@2019

3 . 3 6 7

JCR@2020

JCR Journal Grade:2

CAS Journal Grade:2

Cited Count:

WoS CC Cited Count: 1

SCOPUS Cited Count: 1

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 6

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