We describe systems and methods for generating and training convolutional neural networks using biological sequences and relevance scores derived from structural, biochemical, population and evolutionary data. The convolutional neural networks take as input biological sequences and additional information and output molecular phenotypes. Biological sequences may include DNA, RNA and protein sequences. Molecular phenotypes may include protein-DNA interactions, protein-RNA interactions, protein-protein interactions, splicing patterns, polyadenylation patterns, and microRNA-RNA interactions, which may be described using numerical, categorical or ordinal attributes. Intermediate layers of the convolutional neural networks are weighted using relevance score sequences, for example, conservation tracks. The resulting molecular phenotype convolutional neural networks may be used in genetic testing, to identify drug targets, to identify patients that respond similarly to a drug, to ascertain health risks, or to connect patients that have similar molecular phenotypes.