  RNA, whose functionality is largely determined by its structure, plays an
important role in many biological activities. The prediction of pairwise
structural proximity between each nucleotide of an RNA sequence can
characterize the structural information of the RNA. Historically, this problem
has been tackled by machine learning models using expert-engineered features
and trained on scarce labeled datasets. Here, we find that the knowledge
learned by a protein-coevolution Transformer-based deep neural network can be
transferred to the RNA contact prediction task. As protein datasets are orders
of magnitude larger than those for RNA contact prediction, our findings and the
subsequent framework greatly reduce the data scarcity bottleneck. Experiments
confirm that RNA contact prediction through transfer learning using a publicly
available protein model is greatly improved. Our findings indicate that the
learned structural patterns of proteins can be transferred to RNAs, opening up
potential new avenues for research.
