# CellVerse: Do Large Language Models Really Understand Cell Biology?

arXiv: https://arxiv.org/abs/2505.07865 · HTML: https://mlsanity.com/paper/2505.07865/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Builds on 23 of its 60 references that are in the map.
- First posted on arXiv 9 May 2025.

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

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [Efficient Memory Management for Large Language Model Serving with PagedAttention](https://mlsanity.com/paper/2309.06180/) (2023)
- [Measuring Mathematical Problem Solving With the MATH Dataset](https://mlsanity.com/paper/2103.03874/) (2021)
- [Qwen2.5 Technical Report](https://mlsanity.com/paper/2412.15115/) (2024)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [MathVista: Evaluating Mathematical Reasoning of Foundation Models in Visual Contexts](https://mlsanity.com/paper/2310.02255/) (2023)
- [Competition-Level Code Generation with AlphaCode](https://mlsanity.com/paper/2203.07814/) (2022)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [Large Language Models for Mathematical Reasoning: Progresses and Challenges](https://mlsanity.com/paper/2402.00157/) (2024)
- [SciBench: Evaluating College-Level Scientific Problem-Solving Abilities of Large Language Models](https://mlsanity.com/paper/2307.10635/) (2023)
- [MathPrompter: Mathematical Reasoning using Large Language Models](https://mlsanity.com/paper/2303.05398/) (2023)
- [GeoQA: A Geometric Question Answering Benchmark Towards Multimodal Numerical Reasoning](https://mlsanity.com/paper/2105.14517/) (2021)
- [SciEval: A Multi-Level Large Language Model Evaluation Benchmark for Scientific Research](https://mlsanity.com/paper/2308.13149/) (2023)
- [SciAssess: Benchmarking LLM Proficiency in Scientific Literature Analysis](https://mlsanity.com/paper/2403.01976/) (2024)
- [Symbol-LLM: Towards Foundational Symbol-centric Interface For Large Language Models](https://mlsanity.com/paper/2311.09278/) (2023)
- [Geneverse: A collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research](https://mlsanity.com/paper/2406.15534/) (2024)

## Built on by (most cited first, 5 of 5)

- [MME-Emotion: A Holistic Evaluation Benchmark for Emotional Intelligence in Multimodal Large Language Models](https://mlsanity.com/paper/2508.09210/) (2025)
- [LLM4Cell: A Survey of Large Language and Agentic Models for Single-Cell Biology](https://mlsanity.com/paper/2510.07793/) (2025)
- [SC-Arena: A Natural Language Benchmark for Single-Cell Reasoning with Knowledge-Augmented Evaluation](https://mlsanity.com/paper/2602.23199/) (2026)
- [Plausibility Is Not Prediction: Contrastive Evidence for LLM-Based Cellular Perturbation Reasoning](https://mlsanity.com/paper/2606.01042/) (2026)
- [OmicsLM: A Multimodal Large Language Model for Multi-Sample Omics Reasoning](https://mlsanity.com/paper/2605.06728/) (2026)

## Abstract (arXiv)

Recent studies have demonstrated the feasibility of modeling single-cell data as natural languages and the potential of leveraging powerful large language models (LLMs) for understanding cell biology. However, a comprehensive evaluation of LLMs' performance on language-driven single-cell analysis tasks still remains unexplored. Motivated by this challenge, we introduce CellVerse, a unified language-centric question-answering benchmark that integrates four types of single-cell multi-omics data and encompasses three hierarchical levels of single-cell analysis tasks: cell type annotation (cell-level), drug response prediction (drug-level), and perturbation analysis (gene-level). Going beyond this, we systematically evaluate the performance across 14 open-source and closed-source LLMs ranging from 160M to 671B on CellVerse. Remarkably, the experimental results reveal: (1) Existing specialist models (C2S-Pythia) fail to make reasonable decisions across all sub-tasks within CellVerse, while generalist models such as Qwen, Llama, GPT, and DeepSeek family models exhibit preliminary understanding capabilities within the realm of cell biology. (2) The performance of current LLMs falls short of expectations and has substantial room for improvement. Notably, in the widely studied drug response prediction task, none of the evaluated LLMs demonstrate significant performance improvement over random guessing. CellVerse offers the first large-scale empirical demonstration that significant challenges still remain in applying LLMs to cell biology. By introducing CellVerse, we lay the foundation for advancing cell biology through natural languages and hope this paradigm could facilitate next-generation single-cell analysis.