Fine-tuning protein language models boosts predictions across diverse tasks

Robert Schmirler (), Michael Heinzinger and Burkhard Rost
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Robert Schmirler: Chair of Bioinformatics & Computational Biology - i12
Michael Heinzinger: Chair of Bioinformatics & Computational Biology - i12
Burkhard Rost: Chair of Bioinformatics & Computational Biology - i12

Nature Communications, 2024, vol. 15, issue 1, 1-10

Abstract: Abstract Prediction methods inputting embeddings from protein language models have reached or even surpassed state-of-the-art performance on many protein prediction tasks. In natural language processing fine-tuning large language models has become the de facto standard. In contrast, most protein language model-based protein predictions do not back-propagate to the language model. Here, we compare the fine-tuning of three state-of-the-art models (ESM2, ProtT5, Ankh) on eight different tasks. Two results stand out. Firstly, task-specific supervised fine-tuning almost always improves downstream predictions. Secondly, parameter-efficient fine-tuning can reach similar improvements consuming substantially fewer resources at up to 4.5-fold acceleration of training over fine-tuning full models. Our results suggest to always try fine-tuning, in particular for problems with small datasets, such as for fitness landscape predictions of a single protein. For ease of adaptability, we provide easy-to-use notebooks to fine-tune all models used during this work for per-protein (pooling) and per-residue prediction tasks.

Date: 2024
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DOI: 10.1038/s41467-024-51844-2

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