Papers › Kirigami: large convolutional kernels improve deep learning-based RNA secondary...
Kirigami: large convolutional kernels improve deep learning-based RNA secondary structure prediction
Marc Harary, Chengxin Zhang
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.
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Methods
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections