Evaluating task specific finetuning for protein language models

Prediction methods inputting embeddings from protein Language Models (pLMs) have reached or even surpassed state-of-the-art (SOTA) performance on many protein prediction tasks. In natural language processing (NLP) fine-tuning Language Models has become the de facto standard. In contrast, most protein-prediction tasks do not backpropagate to the pLM. Here, we compared the use of pretrained embeddings to fine-tuning three SOTA pLMs (ESM2, ProtT5, Ankh) on eight different tasks. Two results stood out: (1) task-specific supervised fine-tunig mostly increased downstream prediction performance. (2) Parameter-efficient fine-tuning could reach similar improvements consuming substantially fewer resources. These findings suggest task-specific fine-tuning as a generic improvement of pLM-based prediction methods. To help kick-off such an advance, we provided easy-to-use notebooks for parameter efficient fine-tuning of ProtT5 for per-protein (pooling) and per-residue prediction tasks at (link will be added in final version).