# Fine-Tuning and Prompt Engineering of LLMs, for the Creation of Multi-Agent AI for Addressing Sustainable Protein Production Challenges

arXiv: https://arxiv.org/abs/2506.20598 · HTML: https://mlsanity.com/paper/2506.20598/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Placed in Medical and scientific domain agents, one of 16 directions in LLM agents and tool use.
- Builds on 23 of its 38 references that are in the map.
- First posted on arXiv 25 Jun 2025.

## Placed in

- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 23 of 23)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [Large Language Models are Zero-Shot Reasoners](https://mlsanity.com/paper/2205.11916/) (2022)
- [Pre-train, Prompt, and Predict: A Systematic Survey of Prompting Methods in Natural Language Processing](https://mlsanity.com/paper/2107.13586/) (2021)
- [The Rise and Potential of Large Language Model Based Agents: A Survey](https://mlsanity.com/paper/2309.07864/) (2023)
- [Video-ChatGPT: Towards Detailed Video Understanding via Large Vision and Language Models](https://mlsanity.com/paper/2306.05424/) (2023)
- [A Survey on Large Language Models for Code Generation](https://mlsanity.com/paper/2406.00515/) (2024)
- [A Prompt Pattern Catalog to Enhance Prompt Engineering with ChatGPT](https://mlsanity.com/paper/2302.11382/) (2023)
- [AgentVerse: Facilitating Multi-Agent Collaboration and Exploring Emergent Behaviors](https://mlsanity.com/paper/2308.10848/) (2023)
- [Agentic Retrieval-Augmented Generation: A Survey on Agentic RAG](https://mlsanity.com/paper/2501.09136/) (2025)
- [A Comprehensive Capability Analysis of GPT-3 and GPT-3.5 Series Models](https://mlsanity.com/paper/2303.10420/) (2023)
- [Large Language Models for Robotics: Opportunities, Challenges, and Perspectives](https://mlsanity.com/paper/2401.04334/) (2024)
- [KoLA: Carefully Benchmarking World Knowledge of Large Language Models](https://mlsanity.com/paper/2306.09296/) (2023)
- [Learning to Route LLMs with Confidence Tokens](https://mlsanity.com/paper/2410.13284/) (2024)
- [Beyond Self-Talk: A Communication-Centric Survey of LLM-Based Multi-Agent Systems](https://mlsanity.com/paper/2502.14321/) (2025)
- [A Survey of Prompt Engineering Methods in Large Language Models for Different NLP Tasks](https://mlsanity.com/paper/2407.12994/) (2024)
- [Let GPT be a Math Tutor: Teaching Math Word Problem Solvers with Customized Exercise Generation](https://mlsanity.com/paper/2305.14386/) (2023)
- [A Study on the Calibration of In-context Learning](https://mlsanity.com/paper/2312.04021/) (2023)
- [Summarization for Generative Relation Extraction in the Microbiome Domain](https://mlsanity.com/paper/2506.08647/) (2025)

## Built on by (most cited first, 2 of 2)

- [Tools as Continuous Flow for Evolving Agentic Reasoning](https://mlsanity.com/paper/2605.07339/) (2026)
- [Foundation-Model-Based Agents in Industrial Automation: Purposes, Capabilities, and Open Challenges](https://mlsanity.com/paper/2605.02592/) (2026)

## Abstract (arXiv)

The global demand for sustainable protein sources has accelerated the need for intelligent tools that can rapidly process and synthesise domain-specific scientific knowledge. In this study, we present a proof-of-concept multi-agent Artificial Intelligence (AI) framework designed to support sustainable protein production research, with an initial focus on microbial protein sources. Our Retrieval-Augmented Generation (RAG)-oriented system consists of two GPT-based LLM agents: (1) a literature search agent that retrieves relevant scientific literature on microbial protein production for a specified microbial strain, and (2) an information extraction agent that processes the retrieved content to extract relevant biological and chemical information. Two parallel methodologies, fine-tuning and prompt engineering, were explored for agent optimisation. Both methods demonstrated effectiveness at improving the performance of the information extraction agent in terms of transformer-based cosine similarity scores between obtained and ideal outputs. Mean cosine similarity scores were increased by up to 25%, while universally reaching mean scores of ≥ 0.89 against ideal output text. Fine-tuning overall improved the mean scores to a greater extent (consistently of ≥ 0.94) compared to prompt engineering, although lower statistical uncertainties were observed with the latter approach. A user interface was developed and published for enabling the use of the multi-agent AI system, alongside preliminary exploration of additional chemical safety-based search capabilities