Navid Naderializadeh

EvoPool improves variant effect prediction by integrating evolutionary information into protein language model embeddings using optimal transport.

COPTER improves protein representation by incorporating context using optimal transport, achieving better performance in drug target and perturbation response predictions.

PLMNovo improves de novo peptide sequencing by aligning spectrum and peptide embeddings using pre-trained protein language models.

This paper introduces an optimal transport-based method to aggregate residue-level protein language model embeddings into fixed-length representations, showing improved performance over average pooling for downstream tasks.