Matteo Di Bernardo, Claire Peterson, Ege Topkoc, Matt Might, Iain M. Cheeseman · 2026 · arXiv (Cornell University)
DOI: 10.48550/arxiv.2610.22617 · cited by 0 works (OpenAlex) · open-access PDF
오랫동안 확립된 안정된 스크린은 세포 형태와 행동의 변화에 유전적 방해를 연결하지만, 현미경 데이터를 해석 가능한 결과로 바꾸는 것은 복잡하고 다일간의 분석이 필요합니다. 확립 된 파이프라인은이 데이터를 처리하지만, 연구자들은 여전히 매개 변수를 선택하고 출력을 검사하고 각 실험에 대한 실패를 해결합니다. 여기서 우리는 Brieflow-auto를, 코드 코드 플러그인으로 구현 된 파이프라인 특정 유틸리티를 소개하며, 코딩 대 언어 모델 (LLM)가 Open-source end-to-end 파이프라인 인 Brieflow를 작동하도록 허용합니다. 연구자는 실험적 사실을 제공하고 실행을 승인합니다. 에이전트는 인터랙티브 노
Machine translation (Meta M2M100); the English original follows.
Optical pooled screens connect genetic perturbations to changes in cell morphology and behavior, but turning the microscopy data into interpretable results takes complex, multi-day analyses. Established pipelines process this data, yet researchers still select parameters, inspect outputs, and resolve failures for each experiment. Here, we present Brieflow-auto, a pipeline-specific harness implemented as a Claude Code plugin that lets a coding large language model (LLM) operate Brieflow, an open-source end-to-end pipeline for optical pooled screening data. A researcher supplies experimental facts and approves the launch. An agent tunes parameters in an interactive notebook, and the harness validates the configuration, monitors execution, recovers from common failures, and checks output quality. For pipeline defects, the agent opens upstream issues proposing backward-compatible fixes for the broader community. In five previously analyzed screens, harness runs yielded more cells with a confident single-gene assignment than the original hand analyses. On a screen the pipeline was not designed for, the harness turned each failure into a reviewed upstream fix. More broadly, we propose that wrapping an established pipeline in a harness can substantially accelerate its use and the long-term reliability of its codebase.
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Topics: Pipeline (software), Coding (social sciences), Computer science, Process (computing), Reliability (semiconductor), Upstream (networking)
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