Annotation Vocabulary (Might Be) All You Need

Abstract

Protein Language Models (pLMs) have revolutionized the computational modeling of protein systems, building numerical embeddings that are centered around structural features. To enhance the breadth of biochemically relevant properties available in protein embeddings, we engineered the Annotation Vocabulary, a transformer readable language of protein properties defined by structured ontologies. We trained Annotation Transformers (AT) from the ground up to recover masked protein property inputs without reference to amino acid sequences, building a new numerical feature space on protein descriptions alone. We leverage AT representations in various model architectures, for both protein representation and generation. To showcase the merit of Annotation Vocabulary integration, we performed 515 diverse downstream experiments. Using a novel loss function and only $3 in commercial compute, our premier representation model CAMP produces state-of-the-art embeddings for five out of 15 common datasets with competitive performance on the rest; highlighting the computational efficiency of latent space curation with Annotation Vocabulary. To standardize the comparison of de novo generated protein sequences, we suggest a new sequence alignment-based score that is more flexible and biologically relevant than traditional language modeling metrics. Our generative model, GSM, produces high alignment scores from annotation-only prompts with a BERT-like generation scheme. Of particular note, many GSM hallucinations return statistically significant BLAST hits, where enrichment analysis shows properties matching the annotation prompt even when the ground truth has low sequence identity to the entire training set. Overall, the Annotation Vocabulary toolbox presents a promising pathway to replace traditional tokens with members of ontologies and knowledge graphs, enhancing transformer models in specific domains. The concise, accurate, and efficient descriptions of proteins by the Annotation Vocabulary offers a novel way to build numerical representations of proteins for protein annotation and design.