  Peptides are formed by the dehydration condensation of multiple amino acids.
The primary structure of a peptide can be represented either as an amino acid
sequence or as a molecular graph consisting of atoms and chemical bonds.
Previous studies have indicated that deep learning routes specific to
sequential and graphical peptide forms exhibit comparable performance on
downstream tasks. Despite the fact that these models learn representations of
the same modality of peptides, we find that they explain their predictions
differently. Considering sequential and graphical models as two experts making
inferences from different perspectives, we work on fusing expert knowledge to
enrich the learned representations for improving the discriminative
performance. To achieve this, we propose a peptide co-modeling method, RepCon,
which employs a contrastive learning-based framework to enhance the mutual
information of representations from decoupled sequential and graphical
end-to-end models. It considers representations from the sequential encoder and
the graphical encoder for the same peptide sample as a positive pair and learns
to enhance the consistency of representations between positive sample pairs and
to repel representations between negative pairs. Empirical studies of RepCon
and other co-modeling methods are conducted on open-source discriminative
datasets, including aggregation propensity, retention time, antimicrobial
peptide prediction, and family classification from Peptide Database. Our
results demonstrate the superiority of the co-modeling approach over
independent modeling, as well as the superiority of RepCon over other methods
under the co-modeling framework. In addition, the attribution on RepCon further
corroborates the validity of the approach at the level of model explanation.
