protein-representation-learning 9 protein-embedding 3 protein-modeling 3 protein 2 pre-training 2 protein-structure 2 protein-sequence 2 protein-protein-interaction 2 protein-design 1 ligand-binding 1 equivariant-network 1 diffusion-models 1 graph-neural-networks 1 protein-sequences 1 representation-learning 1 protein-language-model 1 protein-embeddings 1 pretrained-models 1 bioinformatics 1 graph-transformer 1 evolutionary-scale-modeling 1 recurrent-neural-networks 1 pytorch 1 codebook 1 masked-modeling 1 language-model 1 deep-learning 1 contrastive-learning 1 compound-protein-interaction 1 vocabulary 1 microenvironment 1 ppi-networks 1