SpatialAgent: An autonomous AI agent for spatial biology Article Swipe

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Hanchen Wang , Yichun He , Paula P. Coelho , Mauro Bucci , Arshad Nazir , Bob Chen , Linh Trinh , Serena Zhang , Kexin Huang , Vineethkrishna Chandrasekar , Douglas Chung , Minsheng Hao , Ana Carolina Leote , Yong-Ju Lee , Bo Li , Tianyu Liu , Jin Liu , Romain Lopez , Lucas Tawaun , Mingyu Ma , Nikita Makarov , Lisa McGinnis , Linna Peng , Stephen Ra , Gabriele Scalia , Avtar Singh , Liming Tao , Masatoshi Uehara , Chenyu Wang , Runmin Wei , Ryan Copping , Orit Rozenblatt‐Rosen , Jure Leskovec , Aviv Regev ·

YOU? · · 2025 · Open Access · · DOI: https://doi.org/10.1101/2025.04.03.646459

Advances in AI are transforming scientific discovery, yet spatial biology, a field that deciphers the molecular organization within tissues, remains constrained by labor-intensive workflows. Here, we present SpatialAgent, a fully autonomous AI agent dedicated for spatial-biology research. SpatialAgent integrates large language models with dynamic tool execution and adaptive reasoning. SpatialAgent spans the entire research pipeline, from experimental design to multimodal data analysis and hypothesis generation. Tested on multiple datasets comprising two million cells from human brain, heart, and a mouse colon colitis model, SpatialAgent’s performance surpassed the best computational methods, matched or outperformed human scientists across key tasks, and scaled across tissues and species. By combining autonomy with human collaboration, SpatialAgent establishes a new paradigm for AI-driven discovery in spatial biology.

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Type: preprint
Language: en
Landing Page: https://doi.org/10.1101/2025.04.03.646459
PDF: https://www.biorxiv.org/content/biorxiv/early/2025/04/06/2025.04.03.646459.full.pdf
OA Status: green
Cited By: 14
References: 28
Related Works: 10
OpenAlex ID: https://openalex.org/W4409201831

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DOI: https://doi.org/10.1101/2025.04.03.646459

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Title: SpatialAgent: An autonomous AI agent for spatial biology

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Type: preprint

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Language: en

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Publication year: 2025

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Publication date: 2025-04-06

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Authors: Hanchen Wang, Yichun He, Paula P. Coelho, Mauro Bucci, Arshad Nazir, Bob Chen, Linh Trinh, Serena Zhang, Kexin Huang, Vineethkrishna Chandrasekar, Douglas Chung, Minsheng Hao, Ana Carolina Leote, Yong-Ju Lee, Bo Li, Tianyu Liu, Jin Liu, Romain Lopez, Lucas Tawaun, Mingyu Ma, Nikita Makarov, Lisa McGinnis, Linna Peng, Stephen Ra, Gabriele Scalia, Avtar Singh, Liming Tao, Masatoshi Uehara, Chenyu Wang, Runmin Wei, Ryan Copping, Orit Rozenblatt‐Rosen, Jure Leskovec, Aviv Regev

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Landing page: https://doi.org/10.1101/2025.04.03.646459

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PDF URL: https://www.biorxiv.org/content/biorxiv/early/2025/04/06/2025.04.03.646459.full.pdf

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Concepts: Computer science, Biology, Computational biology, Artificial intelligence

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Cited by: 14

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Citations by year (recent): 2025: 14

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