# Towards Applying Large Language Models to Complement Single-Cell Foundation Models

arXiv: https://arxiv.org/abs/2507.10039 · HTML: https://mlsanity.com/paper/2507.10039/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 15 of its 49 references that are in the map.
- First posted on arXiv 14 Jul 2025.

## Builds on (most cited first, 15 of 15)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- ["Why Should I Trust You?": Explaining the Predictions of Any Classifier](https://mlsanity.com/paper/1602.04938/) (2016)
- [Flamingo: a Visual Language Model for Few-Shot Learning](https://mlsanity.com/paper/2204.14198/) (2022)
- [Axiomatic Attribution for Deep Networks](https://mlsanity.com/paper/1703.01365/) (2017)
- [Towards General Text Embeddings with Multi-stage Contrastive Learning](https://mlsanity.com/paper/2308.03281/) (2023)
- [MTEB: Massive Text Embedding Benchmark](https://mlsanity.com/paper/2210.07316/) (2022)
- [Bias and Fairness in Large Language Models: A Survey](https://mlsanity.com/paper/2309.00770/) (2023)
- [mGTE: Generalized Long-Context Text Representation and Reranking Models for Multilingual Text Retrieval](https://mlsanity.com/paper/2407.19669/) (2024)
- [AnglE-optimized Text Embeddings](https://mlsanity.com/paper/2309.12871/) (2023)
- [Scientific Large Language Models: A Survey on Biological & Chemical Domains](https://mlsanity.com/paper/2401.14656/) (2024)
- [GISTEmbed: Guided In-sample Selection of Training Negatives for Text Embedding Fine-tuning](https://mlsanity.com/paper/2402.16829/) (2024)
- [Do Language Models Know the Way to Rome?](https://mlsanity.com/paper/2109.07971/) (2021)

## Built on by (most cited first, 1 of 1)

- [LLM4Cell: A Survey of Large Language and Agentic Models for Single-Cell Biology](https://mlsanity.com/paper/2510.07793/) (2025)

## Abstract (arXiv)

Single-cell foundation models such as scGPT represent a significant advancement in single-cell omics, with an ability to achieve state-of-the-art performance on various downstream biological tasks. However, these models are inherently limited in that a vast amount of information in biology exists as text, which they are unable to leverage. There have therefore been several recent works that propose the use of LLMs as an alternative to single-cell foundation models, achieving competitive results. However, there is little understanding of what factors drive this performance, along with a strong focus on using LLMs as an alternative, rather than complementary approach to single-cell foundation models. In this study, we therefore investigate what biological insights contribute toward the performance of LLMs when applied to single-cell data, and introduce scMPT; a model which leverages synergies between scGPT, and single-cell representations from LLMs that capture these insights. scMPT demonstrates stronger, more consistent performance than either of its component models, which frequently have large performance gaps between each other across datasets. We also experiment with alternate fusion methods, demonstrating the potential of combining specialized reasoning models with scGPT to improve performance. This study ultimately showcases the potential for LLMs to complement single-cell foundation models and drive improvements in single-cell analysis.