Learning to design RNA

F Runge, D Stoll, S Falkner, F Hutter - arXiv preprint arXiv:1812.11951, 2018 - arxiv.org
Design problem is to find an RNA sequence which … RNA Design problem, dubbed LEARNA.
LEARNA uses deep reinforcement learning to train a policy network to sequentially design

Machine learning for RNA design: Learna

F Runge, F Hutter - RNA Design: Methods and Protocols, 2024 - Springer
… we describe machine learning approaches specifically developed for the design of RNAs,
with … of automated deep reinforcement learning algorithms for secondary structure-based RNA

Solving the RNA design problem with reinforcement learning

P Eastman, J Shi, B Ramsundar… - PLoS computational …, 2018 - journals.plos.org
… Similar to how an agent for Go can learn the optimal move to make given one of … an RNA
design agent could also learn the optimal design choice given one of many unique target RNA

RNA design rules from a massive open laboratory

J Lee, W Kladwang, M Lee, D Cantu… - Proceedings of the …, 2014 - National Acad Sciences
… to learn strategies for solving in vitro RNA design problems on … negative design rules—were
distilled by machine learning … in a dozen RNA secondary structure design tests, including the …

RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design

C Tan, Y Zhang, Z Gao, B Hu, S Li, Z Liu… - … Conference on Learning …, 2024 - openreview.net
… for the complex RNA tertiary structure and design an RNA designlearning scheme and a
secondary structure imposing strategy. … RNA design to uncover the relationships between RNA

Geometric deep learning of RNA structure

RJL Townshend, S Eismann, AM Watkins, R Rangan… - Science, 2021 - science.org
… the mechanisms of RNA function, designing synthetic RNAs, and discovering … of previously
unseen RNAs, we used a benchmark consisting of all RNAs that were included in the RNA-…

Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery

K Sato, M Hamada - Briefings in Bioinformatics, 2023 - academic.oup.com
… -targeted drug discovery and in the design of RNA aptamers, where RNA … of RNA secondary
structure, RNA aptamers and RNA drug discovery using machine learning, deep learning

[HTML][HTML] Deep learning in RNA structure studies

H Yu, Y Qi, Y Ding - Frontiers in Molecular Biosciences, 2022 - frontiersin.org
… deep learning to solve RNA problems, including predictions of RNA structures, non-canonical
G-quadruplex, RNA… Next, the experience of deep learning architecture design is presented …

A deep learning approach to programmable RNA switches

NM Angenent-Mari, AS Garruss, LR Soenksen… - Nature …, 2020 - nature.com
design, our objective in this study is to develop a deep-… lead to improved function in RNA
sensors. Instead, visualized … to visualize important RNA secondary structures learned by our …

Machine learning modeling of RNA structures: methods, challenges and future perspectives

KE Wu, JY Zou, H Chang - Briefings in Bioinformatics, 2023 - academic.oup.com
… We discuss the shortcomings that various design decisions entail and … learning but
differentiates data on RNA length rather than structural coarseness. The authors reason that RNA