[2605.28655] AutoScientists: Self-Organizing Agent Teams for Long-Running Scientific Experimentation

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Computer Science > Artificial Intelligence

arXiv:2605.28655 (cs)

[Submitted on 27 May 2026]

Title:AutoScientists: Self-Organizing Agent Teams for Long-Running Scientific Experimentation

Authors:Shanghua Gao, Ada Fang, Marinka Zitnik<br>View a PDF of the paper titled AutoScientists: Self-Organizing Agent Teams for Long-Running Scientific Experimentation, by Shanghua Gao and 2 other authors

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Abstract:Scientific research proceeds through iterative cycles of hypothesis generation, experiment design, execution, and revision. AI agents can automate parts of this process, but existing approaches typically follow a single research trajectory or coordinate through a central planner with fixed objectives. As a result, they struggle to sustain parallel exploration, adapt as experimental evidence changes, or preserve knowledge of failed directions over long-running experiments. We introduce AutoScientists, a decentralized team of AI agents for long-running computational scientific experimentation. Agents interpret a shared experimental state, self-organize into teams around promising hypotheses, critique proposals before using experimental compute, and share successes and failures to reduce redundant exploration. Under matched experimental budgets, AutoScientists improves over prior AI agents across biomedical machine learning, language-model training optimization, and protein fitness prediction. On BioML-Bench, spanning biomedical imaging, protein engineering, single-cell omics, and drug discovery, AutoScientists achieves a mean leaderboard percentile of 74.4% across 24 tasks, improving over the strongest AI agent by +8.33%. On GPT training optimization, AutoScientists reaches a target validation bits-per-byte 1.9x faster than Autoresearch and continues discovering improvements from a starting champion where the single-agent approach finds none (7 vs. 0 accepted improvements). On ProteinGym fitness prediction, AutoScientists discovers a method for ACE2-Spike binding that improves over the current state-of-the-art model by +12.5% in Spearman correlation. Applied without modification across all 217 ProteinGym assays, the same method improves over the prior state of the art by +6.5% (Spearman correlation).

Subjects:

Artificial Intelligence (cs.AI)

Cite as:<br>arXiv:2605.28655 [cs.AI]

(or<br>arXiv:2605.28655v1 [cs.AI] for this version)

https://doi.org/10.48550/arXiv.2605.28655

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arXiv-issued DOI via DataCite (pending registration)

Submission history<br>From: Shanghua Gao [view email]<br>[v1]<br>Wed, 27 May 2026 15:56:12 UTC (1,975 KB)

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