Kirigami: large convolutional kernels improve deep learning-based RNA secondary structure prediction

• URL: http://arxiv.org/abs/2406.02381v2
• Date: Thu, 6 Jun 2024 14:04:32 GMT
• Title: Kirigami: large convolutional kernels improve deep learning-based RNA secondary structure prediction
• Authors: Marc Harary, Chengxin Zhang,
• Abstract summary: We introduce a novel fully convolutional neural network (FCN) architecture for predicting the secondary structure of ribonucleic acid (RNA) molecules. We employ deep learning to estimate the probability of base pairing between nucleotide residues. On a widely adopted, standardized test set comprised of 1,305 molecules, the accuracy of our method exceeds that of current state-of-the-art (SOTA) secondary structure prediction software.
• Score: 0.0
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: We introduce a novel fully convolutional neural network (FCN) architecture for predicting the secondary structure of ribonucleic acid (RNA) molecules. Interpreting RNA structures as weighted graphs, we employ deep learning to estimate the probability of base pairing between nucleotide residues. Unique to our model are its massive 11-pixel kernels, which we argue provide a distinct advantage for FCNs on the specialized domain of RNA secondary structures. On a widely adopted, standardized test set comprised of 1,305 molecules, the accuracy of our method exceeds that of current state-of-the-art (SOTA) secondary structure prediction software, achieving a Matthews Correlation Coefficient (MCC) over 11-40% higher than that of other leading methods on overall structures and 58-400% higher on pseudoknots specifically.

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