Operon-S1: a fast decision controller for long-horizon biomedical agents

Authors: Genoria AI Team : Yuejie Hou , Yueyuxiao Yang , Weiting Tang , Meng Yang

View a PDF of the paper titled Operon-S1: a fast decision controller for long-horizon biomedical agents, by Genoria AI Team: Yuejie Hou and 3 other authors

View PDF

HTML (experimental)

Abstract: Language-model agents now carry out long scientific work in biology, but their judgements about conventions, skills, errors, evidence and stopping are made inside the reasoning that does the work, where they cannot be measured, replaced or improved on their own. Here we present Operon-S1, a fast decision system, a System 1 for the agent, that separates judging from doing. A decision harness poses the agent's recurring judgements as closed questions at 13 decision points and acts only through fixed messages that never contain an answer, so any model that answers the questions can serve as the judge. Across seven life-science benchmarks, a local decision model took over these judgements in 0.6 s at the median for an in-loop request on CPU at no request cost, with no measurable change in the agent's score on five of six benchmarks, whereas the general language model that drives the agent, asked the same questions, accounted for 8.0% to 35.2% of task cost. Every decision is recorded with its consequence. Retraining on labels from task construction, verifiers or execution raised decision accuracy on every question in each of three trained versions, and a new version enters service only through a promotion gate. Task-level results in this study use the public checkpoint. The same closed decisions serve wet-laboratory protocol troubleshooting and the design of a germline target enrichment panel. Like the regulator of an operon, which switches genes on and off without making their products, Operon-S1 steers the agent without doing its work, and makes the agent's judgements a layer that can be measured, replaced and trained.

Comments:

40 pages, 5 figures, 3 tables, 5 Extended Data figures, 6 Extended Data tables

Subjects:

Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG)

Cite as:

arXiv:2610.41350 [cs.AI]

(or

arXiv:2610.41350v1 [cs.AI] for this version)

https://doi.org/10.48550/arXiv.2610.41350

Focus to learn more

arXiv-issued DOI via DataCite (pending registration)

Submission history

From: YueJie Hou [ view email ]

[v1]

Fri, 30 Oct 2026 07:07:09 UTC (7,826 KB)

Full-text links:

Access Paper:

View a PDF of the paper titled Operon-S1: a fast decision controller for long-horizon biomedical agents, by Genoria AI Team: Yuejie Hou and 3 other authors

View PDF

HTML (experimental)

TeX Source

view license

Additional Features

Audio Summary

Current browse context:

cs.AI

< prev

next >

new

recent

| 2026-10

Change to browse by:

cs

cs.LG

References & Citations

SciX

Google Scholar

Semantic Scholar

export BibTeX citation

Loading...

BibTeX formatted citation

loading...

Data provided by:

Bookmark

Bibliographic Tools

Bibliographic and Citation Tools

Bibliographic Explorer Toggle

Bibliographic Explorer ( What is the Explorer? )

Connected Papers Toggle

Connected Papers ( What is Connected Papers? )

Litmaps Toggle

Litmaps ( What is Litmaps? )

scite.ai Toggle

scite Smart Citations ( What are Smart Citations? )

Code, Data, Media

Code, Data and Media Associated with this Article

alphaXiv Toggle

alphaXiv ( What is alphaXiv? )

Links to Code Toggle

CatalyzeX Code Finder for Papers ( What is CatalyzeX? )

DagsHub Toggle

DagsHub ( What is DagsHub? )

GotitPub Toggle

Gotit.pub ( What is GotitPub? )

Huggingface Toggle

Hugging Face ( What is Huggingface? )

ScienceCast Toggle

ScienceCast ( What is ScienceCast? )

Demos

Demos

Replicate Toggle

Replicate ( What is Replicate? )

Spaces Toggle

Hugging Face Spaces ( What is Spaces? )

Spaces Toggle

TXYZ.AI ( What is TXYZ.AI? )

Related Papers

Recommenders and Search Tools

Link to Influence Flower

Influence Flower ( What are Influence Flowers? )

Core recommender toggle

CORE Recommender ( What is CORE? )

Author

Venue

Institution

Topic

About arXivLabs

arXivLabs: experimental projects with community collaborators

arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website.

Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them.

Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs .

Which authors of this paper are endorsers? |

Disable MathJax ( What is MathJax? )