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al3c: high-performance software for parameter inference using Approximate Bayesian Computation
Author(s) -
Alexander Stram,
Paul Marjoram,
Gary K. Chen
Publication year - 2015
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/btv393
Subject(s) - computer science , scalability , approximate bayesian computation , software , inference , overhead (engineering) , source code , bayesian inference , bayesian probability , algorithm , parallel computing , theoretical computer science , distributed computing , programming language , database , artificial intelligence
The development of Approximate Bayesian Computation (ABC) algorithms for parameter inference which are both computationally efficient and scalable in parallel computing environments is an important area of research. Monte Carlo rejection sampling, a fundamental component of ABC algorithms, is trivial to distribute over multiple processors but is inherently inefficient. While development of algorithms such as ABC Sequential Monte Carlo (ABC-SMC) help address the inherent inefficiencies of rejection sampling, such approaches are not as easily scaled on multiple processors. As a result, current Bayesian inference software offerings that use ABC-SMC lack the ability to scale in parallel computing environments.

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