Rethinking Performance Measures of RNA Secondary Structure Problems
Frederic Runge Jörg K. H. Franke Daniel Fertmann Frank Hutter
Accurate RNA secondary structure prediction is vital for understanding
cellular regulation and disease mechanisms. Deep learning (DL) methods have
surpassed traditional algorithms by predicting complex features like
pseudoknots and multi-interacting base pairs. However, traditional distance
measures can hardly deal with such tertiary interactions and the currently used
evaluation measures (F1 score, MCC) have limitations. We propose the
Weisfeiler-Lehman graph kernel (WL) as an alternative metric. Embracing
graph-based metrics like WL enables fair and accurate evaluation of RNA
structure prediction algorithms. Further, WL provides informative guidance, as
demonstrated in an RNA design experiment.