# MetaBench: A Multi-task Benchmark for Assessing LLMs in Metabolomics

arXiv: https://arxiv.org/abs/2510.14944 · HTML: https://mlsanity.com/paper/2510.14944/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 9 of its 40 references that are in the map.
- First posted on arXiv 16 Oct 2025.

## Builds on (most cited first, 9 of 9)

- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [BERTScore: Evaluating Text Generation with BERT](https://mlsanity.com/paper/1904.09675/) (2019)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [A Comprehensive Overview of Large Language Models](https://mlsanity.com/paper/2307.06435/) (2023)
- [Pre-trained Language Models in Biomedical Domain: A Systematic Survey](https://mlsanity.com/paper/2110.05006/) (2021)
- [Benchmarking large language models for biomedical natural language processing applications and recommendations](https://mlsanity.com/paper/2305.16326/) (2023)
- [BERT-based Ranking for Biomedical Entity Normalization](https://mlsanity.com/paper/1908.03548/) (2019)
- [Incorporating Metabolic Information into LLMs for Anomaly Detection in Clinical Time-Series](https://mlsanity.com/paper/2410.12830/) (2024)

## Abstract (arXiv)

Large Language Models (LLMs) have demonstrated remarkable capabilities on general text; however, their proficiency in specialized scientific domains that require deep, interconnected knowledge remains largely uncharacterized. Metabolomics presents unique challenges with its complex biochemical pathways, heterogeneous identifier systems, and fragmented databases. To systematically evaluate LLM capabilities in this domain, we introduce MetaBench, the first benchmark for metabolomics assessment. Curated from authoritative public resources, MetaBench evaluates five capabilities essential for metabolomics research: knowledge, understanding, grounding, reasoning, and research. Our evaluation of 25 open- and closed-source LLMs reveals distinct performance patterns across metabolomics tasks: while models perform well on text generation tasks, cross-database identifier grounding remains challenging even with retrieval augmentation. Model performance also decreases on long-tail metabolites with sparse annotations. With MetaBench, we provide essential infrastructure for developing and evaluating metabolomics AI systems, enabling systematic progress toward reliable computational tools for metabolomics research.