# AblateCell: A Reproduce-then-Ablate Agent for Virtual Cell Repositories

arXiv: https://arxiv.org/abs/2604.19606 · HTML: https://mlsanity.com/paper/2604.19606/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 37 of its 58 references that are in the map.
- First posted on arXiv 21 Apr 2026.

## Builds on (most cited first, 30 of 37)

- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [SWE-agent: Agent-Computer Interfaces Enable Automated Software Engineering](https://mlsanity.com/paper/2405.15793/) (2024)
- [The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery](https://mlsanity.com/paper/2408.06292/) (2024)
- [Large Language Model based Multi-Agents: A Survey of Progress and Challenges](https://mlsanity.com/paper/2402.01680/) (2024)
- [The AI Scientist-v2: Workshop-Level Automated Scientific Discovery via Agentic Tree Search](https://mlsanity.com/paper/2504.08066/) (2025)
- [RepoCoder: Repository-Level Code Completion Through Iterative Retrieval and Generation](https://mlsanity.com/paper/2303.12570/) (2023)
- [CodeAgent: Enhancing Code Generation with Tool-Integrated Agent Systems for Real-World Repo-level Coding Challenges](https://mlsanity.com/paper/2401.07339/) (2024)
- [ResearchAgent: Iterative Research Idea Generation over Scientific Literature with Large Language Models](https://mlsanity.com/paper/2404.07738/) (2024)
- [SciCode: A Research Coding Benchmark Curated by Scientists](https://mlsanity.com/paper/2407.13168/) (2024)
- [CORE-Bench: Fostering the Credibility of Published Research Through a Computational Reproducibility Agent Benchmark](https://mlsanity.com/paper/2409.11363/) (2024)
- [From Automation to Autonomy: A Survey on Large Language Models in Scientific Discovery](https://mlsanity.com/paper/2505.13259/) (2025)
- [Agentic AI for Scientific Discovery: A Survey of Progress, Challenges, and Future Directions](https://mlsanity.com/paper/2503.08979/) (2025)
- [From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery](https://mlsanity.com/paper/2508.14111/) (2025)
- [Paper2Code: Automating Code Generation from Scientific Papers in Machine Learning](https://mlsanity.com/paper/2504.17192/) (2025)
- [MLR-Bench: Evaluating AI Agents on Open-Ended Machine Learning Research](https://mlsanity.com/paper/2505.19955/) (2025)
- [How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities](https://mlsanity.com/paper/2409.11654/) (2024)
- [Modelling Cellular Perturbations with the Sparse Additive Mechanism Shift Variational Autoencoder](https://mlsanity.com/paper/2311.02794/) (2023)
- [A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers](https://mlsanity.com/paper/2508.21148/) (2025)
- [ResearchCodeBench: Benchmarking LLMs on Implementing Novel Machine Learning Research Code](https://mlsanity.com/paper/2506.02314/) (2025)
- [PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis](https://mlsanity.com/paper/2408.10609/) (2024)
- [LLMs for Science: Usage for Code Generation and Data Analysis](https://mlsanity.com/paper/2311.16733/) (2023)
- [Scientists' First Exam: Probing Cognitive Abilities of MLLM via Perception, Understanding, and Reasoning](https://mlsanity.com/paper/2506.10521/) (2025)
- [Probing Scientific General Intelligence of LLMs with Scientist-Aligned Workflows](https://mlsanity.com/paper/2512.16969/) (2025)
- [scDiffusion: conditional generation of high-quality single-cell data using diffusion model](https://mlsanity.com/paper/2401.03968/) (2024)
- [Paper2Agent: Reimagining Research Papers As Interactive and Reliable AI Agents](https://mlsanity.com/paper/2509.06917/) (2025)
- [REPRO-Bench: Can Agentic AI Systems Assess the Reproducibility of Social Science Research?](https://mlsanity.com/paper/2507.18901/) (2025)
- [RepoMaster: Autonomous Exploration and Understanding of GitHub Repositories for Complex Task Solving](https://mlsanity.com/paper/2505.21577/) (2025)
- [RExBench: Can coding agents autonomously implement AI research extensions?](https://mlsanity.com/paper/2506.22598/) (2025)
- [Process-Level Trajectory Evaluation for Environment Configuration in Software Engineering Agents](https://mlsanity.com/paper/2510.25694/) (2025)
- [AbGen: Evaluating Large Language Models in Ablation Study Design and Evaluation for Scientific Research](https://mlsanity.com/paper/2507.13300/) (2025)

## Abstract (arXiv)

Systematic ablations are essential to attribute performance gains in AI Virtual Cells, yet they are rarely performed because biological repositories are under-standardized and tightly coupled to domain-specific data and formats. While recent coding agents can translate ideas into implementations, they typically stop at producing code and lack a verifier that can reproduce strong baselines and rigorously test which components truly matter. We introduce AblateCell, a reproduce-then-ablate agent for virtual cell repositories that closes this verification gap. AblateCell first reproduces reported baselines end-to-end by auto-configuring environments, resolving dependency and data issues, and rerunning official evaluations while emitting verifiable artifacts. It then conducts closed-loop ablation by generating a graph of isolated repository mutations and adaptively selecting experiments under a reward that trades off performance impact and execution cost. Evaluated on three single-cell perturbation prediction repositories (CPA, GEARS, BioLORD), AblateCell achieves 88.9% (+29.9% to human expert) end-to-end workflow success and 93.3% (+53.3% to heuristic) accuracy in recovering ground-truth critical components. These results enable scalable, repository-grounded verification and attribution directly on biological codebases.