# Leveraging Large Language Models for enzymatic reaction prediction and characterization

arXiv: https://arxiv.org/abs/2505.05616 · HTML: https://mlsanity.com/paper/2505.05616/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 19 of its 51 references that are in the map.
- First posted on arXiv 8 May 2025.

## Builds on (most cited first, 19 of 19)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
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- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
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- [QLoRA: Efficient Finetuning of Quantized LLMs](https://mlsanity.com/paper/2305.14314/) (2023)
- [Emergent Abilities of Large Language Models](https://mlsanity.com/paper/2206.07682/) (2022)
- [A Survey on Large Language Model based Autonomous Agents](https://mlsanity.com/paper/2308.11432/) (2023)
- [Calibrate Before Use: Improving Few-Shot Performance of Language Models](https://mlsanity.com/paper/2102.09690/) (2021)
- [Parameter-Efficient Fine-Tuning for Large Models: A Comprehensive Survey](https://mlsanity.com/paper/2403.14608/) (2024)
- [Parameter-Efficient Fine-Tuning Methods for Pretrained Language Models: A Critical Review and Assessment](https://mlsanity.com/paper/2312.12148/) (2023)
- [Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction](https://mlsanity.com/paper/1811.02633/) (2018)
- [What can Large Language Models do in chemistry? A comprehensive benchmark on eight tasks](https://mlsanity.com/paper/2305.18365/) (2023)
- [Few-shot Fine-tuning vs. In-context Learning: A Fair Comparison and Evaluation](https://mlsanity.com/paper/2305.16938/) (2023)
- [Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models](https://mlsanity.com/paper/2306.08018/) (2023)
- [LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset](https://mlsanity.com/paper/2402.09391/) (2024)
- [Retrosynthetic reaction prediction using neural sequence-to-sequence models](https://mlsanity.com/paper/1706.01643/) (2017)
- [14 Examples of How LLMs Can Transform Materials Science and Chemistry: A Reflection on a Large Language Model Hackathon](https://mlsanity.com/paper/2306.06283/) (2023)

## Abstract (arXiv)

Predicting enzymatic reactions is crucial for applications in biocatalysis, metabolic engineering, and drug discovery, yet it remains a complex and resource-intensive task. Large Language Models (LLMs) have recently demonstrated remarkable success in various scientific domains, e.g., through their ability to generalize knowledge, reason over complex structures, and leverage in-context learning strategies. In this study, we systematically evaluate the capability of LLMs, particularly the Llama-3.1 family (8B and 70B), across three core biochemical tasks: Enzyme Commission number prediction, forward synthesis, and retrosynthesis. We compare single-task and multitask learning strategies, employing parameter-efficient fine-tuning via LoRA adapters. Additionally, we assess performance across different data regimes to explore their adaptability in low-data settings. Our results demonstrate that fine-tuned LLMs capture biochemical knowledge, with multitask learning enhancing forward- and retrosynthesis predictions by leveraging shared enzymatic information. We also identify key limitations, for example challenges in hierarchical EC classification schemes, highlighting areas for further improvement in LLM-driven biochemical modeling.