  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.
