Abstract
Functional annotation of newly sequenced proteins remains a bottleneck in molecular biology: the number of sequences in public repositories grows far faster than the capacity for manual curation. Most computational approaches consider annotation as multi-label classification over a fixed ontology, which constrains predictions to a predefined label set. In this work we study the the protein annotation as a sequence-to-text generation problem. We fine-tune the 3B-parameter Ministral 3 base model with QLoRA (4-bit NF4 quantization with low-rank adapters) on sequence annotation pairs. We assess predictions with an LLM-as-expert protocol: a GPT model prompted as a senior molecular-biology curator scores organism identification as binary and function annotation quality. We conclude that QLoRA-fine-tuned compact LLMs can generate curator-style annotations with genuine biological value for a substantial subset of proteins. We also discuss future directions in data quality, model scaling, and evidence grounding that are needed to make the approach sufficiently reliable for practical use.
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Publication details
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- Open access
- Green open access
Cite this article
APA 7
Pavlyshenko, D., & Pavlyshenko, B. (2026). QLoRA Fine-Tuning of Ministral LLM for Sequence-to-Function Protein Annotation. https://omanscience.com/en/articles/qlora-fine-tuning-of-ministral-llm-for-sequence-to-function-protein-annotation
MLA 9
Pavlyshenko, Demian, and Bohdan Pavlyshenko. "QLoRA Fine-Tuning of Ministral LLM for Sequence-to-Function Protein Annotation." https://omanscience.com/en/articles/qlora-fine-tuning-of-ministral-llm-for-sequence-to-function-protein-annotation.
Chicago (author–date)
Pavlyshenko, Demian, and Bohdan Pavlyshenko. 2026. "QLoRA Fine-Tuning of Ministral LLM for Sequence-to-Function Protein Annotation." https://omanscience.com/en/articles/qlora-fine-tuning-of-ministral-llm-for-sequence-to-function-protein-annotation.
Harvard
Pavlyshenko, D. and Pavlyshenko, B. (2026) 'QLoRA Fine-Tuning of Ministral LLM for Sequence-to-Function Protein Annotation', Available at: https://omanscience.com/en/articles/qlora-fine-tuning-of-ministral-llm-for-sequence-to-function-protein-annotation.
Vancouver
Pavlyshenko D, Pavlyshenko B. QLoRA Fine-Tuning of Ministral LLM for Sequence-to-Function Protein Annotation. https://omanscience.com/en/articles/qlora-fine-tuning-of-ministral-llm-for-sequence-to-function-protein-annotation
IEEE
D. Pavlyshenko, and B. Pavlyshenko, "QLoRA Fine-Tuning of Ministral LLM for Sequence-to-Function Protein Annotation," https://omanscience.com/en/articles/qlora-fine-tuning-of-ministral-llm-for-sequence-to-function-protein-annotation.