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

ICML 2025 Workshop FM4LS Submission31 Authors

Keywords: Single cell, RNA sequencing, web search, agentic, generative AI, foundation models, structured data labeling

TL;DR: DeepSeq uses web search-augmented agentic generative AI foundation models (e.g., GPT-4o) to label single-cell RNA-seq data with up to 82.5% accuracy, enabling scalable and reproducible annotation without manual curation.

Abstract: 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.

Submission Number: 31