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Optimus: a general purpose adaptive optimisation engine in R

View ORCID ProfileNicholas A. G. Johnson, View ORCID ProfileLiezel Tamon, View ORCID ProfileXin Liu, View ORCID ProfileAleksandr B. Sahakyan
doi: https://doi.org/10.1101/2022.01.18.476810
Nicholas A. G. Johnson
MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
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  • ORCID record for Nicholas A. G. Johnson
Liezel Tamon
MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
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Xin Liu
MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
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Aleksandr B. Sahakyan
MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
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  • ORCID record for Aleksandr B. Sahakyan
  • For correspondence: aleksandr.sahakyan@imm.ox.ac.uk
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Abstract

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.uk

Supplementary Information Supplementary information with more details, tutorials, and developer instructions is available.

Figure
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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 Statement

The authors have declared no competing interest.

Footnotes

  • http://github.com/SahakyanLab/Optimus

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 21, 2022.
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Optimus: a general purpose adaptive optimisation engine in R
Nicholas A. G. Johnson, Liezel Tamon, Xin Liu, Aleksandr B. Sahakyan
bioRxiv 2022.01.18.476810; doi: https://doi.org/10.1101/2022.01.18.476810
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Optimus: a general purpose adaptive optimisation engine in R
Nicholas A. G. Johnson, Liezel Tamon, Xin Liu, Aleksandr B. Sahakyan
bioRxiv 2022.01.18.476810; doi: https://doi.org/10.1101/2022.01.18.476810

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