@inproceedings{liu-etal-2026-gardener,
title = "Gardener: An Agentic {AI} System for Single-Cell {RNA} Sequence Analysis",
author = "Liu, Junhan and
Liu, Zhenke and
Shi, Yongcheng and
Yu, Peilin and
Zhang, Minxing and
Zhang, Jiapeng",
editor = "Durrett, Greg and
Jian, Ping",
booktitle = "Proceedings of the 64th Annual Meeting of the {A}ssociation for {C}omputational {L}inguistics (Volume 3: System Demonstrations)",
month = jul,
year = "2026",
address = "San Diego, California, United States",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/2026.acl-demo.40/",
pages = "408--417",
ISBN = "979-8-89176-392-0",
abstract = "Gardener is an interactive agentic system for single-cell RNA-seq (scRNA-seq) analysis that enables expert-steered, iterative workflows under strict data-residency requirements. Existing large language model (LLM)-based analysis agents commonly encode workflow progress as implicit conversational state and rely on cloud-centric execution, which hinders traceability and auditability and complicates keeping sensitive expression data on-device. Gardener grounds cloud-side reasoning in a local, on-device scientific engine and an Experiment Management Kernel (EMK) that externalizes analysis progress as persistent, immutable snapshots linked by lineage. This explicit state representation supports rollback, branching, and comparison of alternative analysis paths while reusing prior computation. Gardener enforces data isolation by design: cloud-hosted LLMs operate only on snapshot identifiers and sanitized summaries, while raw expression matrices and local artifacts remain on the user{'}s device. A local graphical user interface (GUI) provides human-in-the-loop steering and inspection of workflow state and outputs. Gardener is released as an open-source desktop application for macOS and Windows under the Apache License 2.0."
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%0 Conference Proceedings
%T Gardener: An Agentic AI System for Single-Cell RNA Sequence Analysis
%A Liu, Junhan
%A Liu, Zhenke
%A Shi, Yongcheng
%A Yu, Peilin
%A Zhang, Minxing
%A Zhang, Jiapeng
%Y Durrett, Greg
%Y Jian, Ping
%S Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 3: System Demonstrations)
%D 2026
%8 July
%I Association for Computational Linguistics
%C San Diego, California, United States
%@ 979-8-89176-392-0
%F liu-etal-2026-gardener
%X Gardener is an interactive agentic system for single-cell RNA-seq (scRNA-seq) analysis that enables expert-steered, iterative workflows under strict data-residency requirements. Existing large language model (LLM)-based analysis agents commonly encode workflow progress as implicit conversational state and rely on cloud-centric execution, which hinders traceability and auditability and complicates keeping sensitive expression data on-device. Gardener grounds cloud-side reasoning in a local, on-device scientific engine and an Experiment Management Kernel (EMK) that externalizes analysis progress as persistent, immutable snapshots linked by lineage. This explicit state representation supports rollback, branching, and comparison of alternative analysis paths while reusing prior computation. Gardener enforces data isolation by design: cloud-hosted LLMs operate only on snapshot identifiers and sanitized summaries, while raw expression matrices and local artifacts remain on the user’s device. A local graphical user interface (GUI) provides human-in-the-loop steering and inspection of workflow state and outputs. Gardener is released as an open-source desktop application for macOS and Windows under the Apache License 2.0.
%U https://aclanthology.org/2026.acl-demo.40/
%P 408-417
Markdown (Informal)
[Gardener: An Agentic AI System for Single-Cell RNA Sequence Analysis](https://aclanthology.org/2026.acl-demo.40/) (Liu et al., ACL 2026)
ACL
- Junhan Liu, Zhenke Liu, Yongcheng Shi, Peilin Yu, Minxing Zhang, and Jiapeng Zhang. 2026. Gardener: An Agentic AI System for Single-Cell RNA Sequence Analysis. In Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 3: System Demonstrations), pages 408–417, San Diego, California, United States. Association for Computational Linguistics.