# scReader: Prompting Large Language Models to Interpret scRNA-seq Data

arXiv: https://arxiv.org/abs/2412.18156 · HTML: https://mlsanity.com/paper/2412.18156/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 13 of its 43 references that are in the map.
- First posted on arXiv 24 Dec 2024.

## Builds on (most cited first, 13 of 13)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [LlamaFactory: Unified Efficient Fine-Tuning of 100+ Language Models](https://mlsanity.com/paper/2403.13372/) (2024)
- [BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains](https://mlsanity.com/paper/2402.10373/) (2024)
- [A Survey of GPT-3 Family Large Language Models Including ChatGPT and GPT-4](https://mlsanity.com/paper/2310.12321/) (2023)
- [BioRAG: A RAG-LLM Framework for Biological Question Reasoning](https://mlsanity.com/paper/2408.01107/) (2024)
- [Resolving the Imbalance Issue in Hierarchical Disciplinary Topic Inference via LLM-based Data Augmentation](https://mlsanity.com/paper/2310.05318/) (2023)
- [Temporal Inductive Path Neural Network for Temporal Knowledge Graph Reasoning](https://mlsanity.com/paper/2309.03251/) (2023)
- [Hierarchical Interdisciplinary Topic Detection Model for Research Proposal Classification](https://mlsanity.com/paper/2209.13519/) (2022)
- [NEEDED: Introducing Hierarchical Transformer to Eye Diseases Diagnosis](https://mlsanity.com/paper/2212.13408/) (2022)
- [Enhanced Gene Selection in Single-Cell Genomics: Pre-Filtering Synergy and Reinforced Optimization](https://mlsanity.com/paper/2406.07418/) (2024)

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

- [scPilot: Large Language Model Reasoning Toward Automated Single-Cell Analysis and Discovery](https://mlsanity.com/paper/2602.11609/) (2026)
- [A Survey of Large Language Models in Discipline-specific Research: Challenges, Methods and Opportunities](https://mlsanity.com/paper/2507.08425/) (2025)
- [scLLM-DSC: LLM-Knowledge Enhanced Cross-Modal Deep Structural Clustering for Single-Cell RNA Sequencing](https://mlsanity.com/paper/2606.13007/) (2026)

## Abstract (arXiv)

Large language models (LLMs) have demonstrated remarkable advancements, primarily due to their capabilities in modeling the hidden relationships within text sequences. This innovation presents a unique opportunity in the field of life sciences, where vast collections of single-cell omics data from multiple species provide a foundation for training foundational models. However, the challenge lies in the disparity of data scales across different species, hindering the development of a comprehensive model for interpreting genetic data across diverse organisms. In this study, we propose an innovative hybrid approach that integrates the general knowledge capabilities of LLMs with domain-specific representation models for single-cell omics data interpretation. We begin by focusing on genes as the fundamental unit of representation. Gene representations are initialized using functional descriptions, leveraging the strengths of mature language models such as LLaMA-2. By inputting single-cell gene-level expression data with prompts, we effectively model cellular representations based on the differential expression levels of genes across various species and cell types. In the experiments, we constructed developmental cells from humans and mice, specifically targeting cells that are challenging to annotate. We evaluated our methodology through basic tasks such as cell annotation and visualization analysis. The results demonstrate the efficacy of our approach compared to other methods using LLMs, highlighting significant improvements in accuracy and interoperability. Our hybrid approach enhances the representation of single-cell data and offers a robust framework for future research in cross-species genetic analysis.