Experiments

The code for the experiments run in the manuscript are present in the experiments folder. The experiments folder is further divided into the following parts:

Section	Description
encode_llm	Common API for encoding amino acid sequences with various pLMs.
embedding_dbs	Scripts for generating databases of amino acid embeddings.
speed_bench	Scripts for benchmarking the speed of the various pLMs.
ppi_bench	Scripts for training pLM-based PPI inference models.
kw_bench	Scripts for training the protein annotation model.
sars_bench	Scripts for inferring SARS-CoV-2 v. Human PPI interactions.
mutation_bench	Scripts for calculating embeddings of mutants for the mutation analysis.