# DeepSeq: High-Throughput Single-Cell RNA Sequencing Data Labeling via Web Search-Augmented Agentic Generative AI Foundation Models

arXiv: https://arxiv.org/abs/2506.13817 · HTML: https://mlsanity.com/paper/2506.13817/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Medical and scientific domain agents, one of 16 directions in LLM agents and tool use.
- Builds on 6 of its 25 references that are in the map.
- First posted on arXiv 14 Jun 2025.

## 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, 6 of 6)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [From Louvain to Leiden: guaranteeing well-connected communities](https://mlsanity.com/paper/1810.08473/) (2018)

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

- [A Survey of LLM-based Deep Search Agents: Paradigm, Optimization, Evaluation, and Challenges](https://mlsanity.com/paper/2508.05668/) (2025)

## Abstract (arXiv)

Generative AI foundation models offer transformative potential for processing structured biological data, particularly in single-cell RNA sequencing, where datasets are rapidly scaling toward billions of cells. We propose the use of agentic foundation models with real-time web search to automate the labeling of experimental data, achieving up to 82.5% accuracy. This addresses a key bottleneck in supervised learning for structured omics data by increasing annotation throughput without manual curation and human error. Our approach enables the development of virtual cell foundation models capable of downstream tasks such as cell-typing and perturbation prediction. As data volume grows, these models may surpass human performance in labeling, paving the way for reliable inference in large-scale perturbation screens. This application demonstrates domain-specific innovation in health monitoring and diagnostics, aligned with efforts like the Human Cell Atlas and Human Tumor Atlas Network.