RT Journal Article
SR Electronic
T1 Optimus: a general purpose adaptive optimisation engine in R
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.01.18.476810
DO 10.1101/2022.01.18.476810
A1 Johnson, Nicholas A. G.
A1 Tamon, Liezel
A1 Liu, Xin
A1 Sahakyan, Aleksandr B.
YR 2022
UL http://biorxiv.org/content/early/2022/01/21/2022.01.18.476810.abstract
AB Motivation Many calculations in computational biology necessitate a use of a probabilistic optimisation protocol to determine a set of parameters that capture the system at a desired state in the configurational space. Here, we developed a flexible optimisation engine in R that can be plugged to any, simple or complex, modelling initiative through a few lucid interfacing functions, to perform a seamless optimisation with rigorous parameter sampling.Results Optimus features an acceptance ratio simulated annealing, acceptance ratio replica exchange, and adaptive thermoregulation, thus driving a Monte Carlo optimisation process in a flexible manner, through constrained acceptance frequency but unconstrained adaptive pseudo temperature regiments. We show the applicability of our R optimiser to a wide variety of problems spanning data analyses and computational biology tasks.Availability and Implementation Optimus is written and implemented in R, and is freely available from the http://github.com/SahakyanLab/Optimus repository.Contact aleksandr.sahakyan{at}imm.ox.ac.ukSupplementary Information Supplementary information with more details, tutorials, and developer instructions is available.The Optimus software logo depicting two gears (“Op”) that drag the system “s”, trapped in a “u” minimum, through a rough solution landscape into a more favourable solution with a deeper pseudo-energy minimum (“p”).Competing Interest StatementThe authors have declared no competing interest.