# QuST-LLM: Integrating Large Language Models for Comprehensive Spatial Transcriptomics Analysis

arXiv: https://arxiv.org/abs/2406.14307 · HTML: https://mlsanity.com/paper/2406.14307/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 3 of its 20 references that are in the map.
- First posted on arXiv 20 Jun 2024.

## Builds on (most cited first, 3 of 3)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [QuST: QuPath Extension for Integrative Whole Slide Image and Spatial Transcriptomics Analysis](https://mlsanity.com/paper/2406.01613/) (2024)

## Built on by (most cited first, 3 of 3)

- [LLM4Cell: A Survey of Large Language and Agentic Models for Single-Cell Biology](https://mlsanity.com/paper/2510.07793/) (2025)
- [Generative Artificial Intelligence in Bioinformatics: A Systematic Review of Models, Applications, and Methodological Advances](https://mlsanity.com/paper/2511.03354/) (2025)
- [Evaluating Agentic Bioinformatics through Function, Evidence, and Validation](https://mlsanity.com/paper/2607.27556/) (2026)

## Abstract (arXiv)

In this paper, we introduce QuST-LLM, an innovative extension of QuPath that utilizes the capabilities of large language models (LLMs) to analyze and interpret spatial transcriptomics (ST) data. In addition to simplifying the intricate and high-dimensional nature of ST data by offering a comprehensive workflow that includes data loading, region selection, gene expression analysis, and functional annotation, QuST-LLM employs LLMs to transform complex ST data into understandable and detailed biological narratives based on gene ontology annotations, thereby significantly improving the interpretability of ST data. Consequently, users can interact with their own ST data using natural language. Hence, QuST-LLM provides researchers with a potent functionality to unravel the spatial and functional complexities of tissues, fostering novel insights and advancements in biomedical research. QuST-LLM is a part of QuST project. The source code is hosted on GitHub and documentation is available at (https://github.com/huangch/qust).