Francesca Young

Prediction of virus-host association using protein language models and multiple instance learning

This paper introduces EvoMIL, a deep learning method that predicts virus-host associations using protein language models and multiple instance learning, achieving improved accuracy in both prokaryotic and eukaryotic hosts.

PLM-interact: extending protein language models to predict protein-protein interactions

PLM-interact improves PPI prediction by jointly encoding protein pairs, achieving 16-28% AUPR gains across multiple species.

From a single sequence to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2 protein sequences

This paper shows that protein language models can assess mutation effects in SARS-CoV-2 spike protein without multiple sequence alignments, capturing evolutionary constraints and variant properties.