Repository

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.

A widespread practice in software development is to tailor coding agents to repositories using context files, such as AGENTS.md. Although this practice is strongly encouraged by agent developers, there is currently no rigorous investigation into whether such context files are actually effective for real-world tasks. In this work, we study this question and evaluate coding agents' task completion performance in two complementary settings: established SWE-bench tasks from popular repositories, with LLM-generated context files, and a novel collection of issues from repositories containing developer-committed context files. Surprisingly, we find that providing context files does not generally improve task success rates, while increasing inference cost by over 20% on average. This observation holds across different LLMs, coding agents, and for both LLM-generated and developer-committed context files. Specifically, we find that while instructions in the context files are well followed by coding agents, repository overviews, although popular and recommended by model providers, are not helpful. We conclude that while context files are useful for specifying non-standard coding practices, any attempts to improve performance should be rigorously evaluated before deployment.

The prohibitive cost of evaluating Large Language Models (LLMs) necessitates efficient alternatives to full-scale benchmarking. Prevalent approaches address this by identifying a small coreset of items to approximate full-benchmark performance. However, existing methods must estimate a reliable item profile from response patterns across many source models, which becomes statistically unstable when the source pool is small. This dependency is particularly limiting for newly released benchmarks with minimal historical evaluation data. We argue that discrete correctness labels are a lossy view of the model's decision process and fail to capture information encoded in hidden states. To address this, we introduce RepCore, which aligns heterogeneous hidden states into a unified latent space to construct representative coresets. Using these subsets for performance extrapolation, RepCore achieves precise estimation accuracy with as few as ten source models. Experiments on five benchmarks and over 200 models show consistent gains over output-based baselines in ranking correlation and estimation accuracy. Spectral analysis further indicates that the aligned representations contain separable components reflecting broad response tendencies and task-specific reasoning patterns.

AI agents increasingly act through tools and delegated authority, but general incident repositories rarely capture the mechanisms needed to compare public failures with agent-security evaluations. We present the Agent Incident Registry (AIR) (Project page: https://enkryptai.com/air), a source-linked catalog containing 487 records of agent-related events disclosed from 2022 through 2026. Each record includes supporting evidence, a stable identifier, and missingness-aware labels for causal role, disclosure class, mechanism, and outcome. Among the 336 generative-system records in which the agent acted, 81 involved realized harm (24%). Realized outcomes concentrate in in-the-wild and safety-failure records, while responsible disclosures and research demonstrations are overwhelmingly demonstrated; the aggregate share therefore characterizes collection composition rather than deployment risk. After initial curation, a second human reviewer checked all 487 records and their existing labels for completeness and correctness. In a deployment-analogue audit, InjecAgent's 1,054 cases occupy three of AIR's twelve surfaces and are all attacker-triggered, whereas AIR contains 92 no-adversary safety failures. AIR supports source-grounded case retrieval and evaluation-scope auditing, not failure-rate or control-efficacy estimation.

An agent skill is a folder containing a SKILL.md file with instructions for a language-model agent, optionally accompanied by scripts and reference files. The agent loads the skill when it judges that a task matches the skill description. Anthropic introduced the format in October 2025 as an open specification. Nine months later, public GitHub repositories hold millions of skill files. Skills are unlike the artifacts that software engineering researchers usually mine: they are written mainly in natural language, a model selects them probabilistically at run time, and no compiler or type checker verifies the selection. Skills also have no central registry or package manager; developers reuse them by copying folders between repositories. How developers write, reuse, and maintain skills is therefore an empirical question, and no existing dataset records this population. We present GitSkills, a dataset of 3,797,117 SKILL.md files collected from 282,200 public repositories in July 2026. The dataset retains every file occurrence with its repository, path, and content hash. We group identical files into 1,877,981 distinct contents and enrich one representative per group with the full text, parsed front matter, folder contents, repository metadata, and, for a subset, the commit history of the file. A single self-contained SQLite file supports research on the adoption, reuse, structure, authorship, maintenance, and security of agent skills.