Paper Info
Title
Examination of Annealing Schedules for RNA Design.
Abstract
Computational Intelligence is frequently applied to solve RNA design problems, to construct RNA sequences that fold into biochemically useful structures and alignments. RNA Design’s NP-Hardness means that heuristic solutions, such as Evolutionary algorithms’ Simulated Annealing, are commonly used to more effectively search for RNA sequences that fold into the target structure. Examples of Simulated Annealing in RNA Design include SIMARD, the ERD approach, and RNAPredict, all which aim to return RNA Sequences as close as possible to the target structure. However, such methods only use a single simulated annealing cooling schedule even though literature covers many schedules with varied convergence and performances guarantees. Since existing RNA Design cooling schedule surveys only cover at most four RNA design problems over two simulated annealing variants, we investigate the performance of four major simulated annealing schedules with ten variants on twenty-nine RNA design sequences. Relevant findings include a) the insensitivity of geometric schedule parameters, b) that logarithmic cooling schedules can solve RNA Design problems not solved by other schedules, c) suggestions for adjusting geometric schedule stopping conditions, and d) identifying common issues in popular adaptive and non-adaptive schedules for RNA Design.
Year
DOI
Venue
2020
10.1109/CEC48606.2020.9185702
CEC
DocType
Citations 
PageRank 
Conference
0
0.34
References 
Authors
0
2
Name
Order
Citations
PageRank
Ryan McBride100.34
Herbert H. Tsang29219.08