eprintid: 4663
rev_number: 9
eprint_status: archive
userid: 282
dir: disk0/00/00/46/63
datestamp: 2021-12-10 01:12:31
lastmod: 2021-12-10 01:12:31
status_changed: 2021-12-10 01:12:31
type: conference_item
metadata_visibility: show
creators_name: Pham, Tuan Nghia
creators_name: Hoang, Thi Diep
creators_id: ngfam2211@gmail.com
creators_id: diepht@vnu.edu.vn
title: A Distributed Algorithm for the Parsimony Bootstrap Approximation
ispublished: pub
subjects: IT
divisions: fac_fit
abstract: Accelerating phylogenetic tree reconstruction and bootstrapping is critical, especially to support the study of the evolution of dangerous viruses. In this paper, we propose the MPBoot-MPI, a distributed algorithm efficiently implementing the idea of bootstrap approximation in MPBoot for a parallel computing environment of multiple computational nodes. MPBoot-MPI employs the master-worker paradigm and divides the work in MPBoot into three phases, each with a separate strategy to distribute computing among processes. Since the bootstrap trees are not calculated independently, processes must share results throughout task execution. We propose that when arriving at a checkpoint to report their results to the master process, worker processes apply a stochastic strategy to determine whether to perform the sending, thereby reducing the effect of latency caused by the large size of the message sent. Experiments on simulation and real benchmark datasets showed that MPBoot-MPI on multiple processes obtained MP scores and bootstrap accuracy comparable to MPBoot while achieving a promising speedup ratio. We implemented the proposed method in the MPBoot-MPI program, which is publicly accessible at https://github.com/diepthihoang/mpboot/tree/mpboot-mpi-dev.
date: 2021-11
date_type: completed
official_url: https://iisi.siit.tu.ac.th/KSE2021
contact_email: diepht@vnu.edu.vn
full_text_status: none
pres_type: paper
event_title: The 13th IEEE International Conference on Knowledge and Systems Engineering (KSE 2021)
event_location: Bangkok, Thailand & Online
event_dates: November 10-12, 2021
event_type: conference
refereed: TRUE
funders: Vietnam National Foundation for Science and Technology Development (NAFOSTED) under grant number 6/2020/STS02
citation:   Pham, Tuan Nghia and Hoang, Thi Diep  (2021) A Distributed Algorithm for the Parsimony Bootstrap Approximation.  In: The 13th IEEE International Conference on Knowledge and Systems Engineering (KSE 2021), November 10-12, 2021, Bangkok, Thailand & Online.