# SCTA: An Agentic Framework for Stable and Interpretable Target Gene Discovery from Single-Cell RNA Sequencing

arXiv: https://arxiv.org/abs/2607.23821 · HTML: https://mlsanity.com/paper/2607.23821/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Medical and scientific domain agents, one of 16 directions in LLM agents and tool use.
- Builds on 7 of its 61 references that are in the map.
- First posted on arXiv 26 Jul 2026.

## Placed in

- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 7 of 7)

- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [Data Interpreter: An LLM Agent For Data Science](https://mlsanity.com/paper/2402.18679/) (2024)
- [CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis](https://mlsanity.com/paper/2407.09811/) (2024)
- [scAgent: Universal Single-Cell Annotation via a LLM Agent](https://mlsanity.com/paper/2504.04698/) (2025)

## Abstract (arXiv)

Identifying therapeutic target genes from single-cell RNA sequencing (scRNA-seq) data remains a fundamental challenge in translational biology. Unlike bulk assays, scRNA-seq captures heterogeneous cellular states and rare subpopulations, but this same heterogeneity makes target discovery highly sensitive to analytical choices throughout the pipeline, including preprocessing, cell population selection, differential expression analysis, and downstream biological interpretation. As a result, existing workflows and general-purpose analysis agents often produce unstable or difficult-to-interpret target hypotheses, limiting their reliability for disease-focused discovery. We present SCTA (Single-Cell Target Agent), a decision-centric agentic framework for stable and interpretable target gene discovery from scRNA-seq data. Rather than treating analysis as a single general-purpose reasoning task, SCTA decomposes target discovery into specialized agents aligned with key decision points in the single-cell pipeline and constrains downstream reasoning with structured biological evidence. In a representative ablation study on hereditary chronic pancreatitis, we demonstrate that SCTA's full evidence integration yields the most stable target selection across independent runs among the tested configurations, while recovering biologically coherent, disease-relevant mechanisms validated in prior studies. These results suggest that decision-aware agent orchestration tailored to the structure of single-cell analysis can improve the robustness, interpretability, and practical utility of target discovery in precision medicine.