{"repo":"Genentech/AssayBench","free":true,"listed":false,"github":"https://github.com/Genentech/AssayBench","clone":"git clone https://github.com/Genentech/AssayBench.git","description":"AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents","language":"Python","stars":12,"topics":["benchmark","biology","crispr","llms","metrics","screen"],"license":"MIT","category":"ai-agents","readme_excerpt":"AssayBench A benchmark for evaluating machine learning models on phenotypic screen prediction. :globe with meridians: Website :octocat: Code :hugs: Dataset :page with curl: Paper 0. News We released a website with interactive data visualization! 1. Installation Or install directly from the repository: Or clone and install in editable mode: This installs the assaybench package, which provides: - AssayBenchDataset — loads screens and splits from HuggingFace ( Genentech/assaybench ) - RankingMetrics — computes ranking metrics (adjusted nDCG, precision, FDR, etc.) With uv You can add it to your project with 2. Usage Loading data and scoring a model Each example in the dataset contains a question prompt describing a CRISPR screen, along with ground-truth relevance genes and relevance scores . To evaluate a model, pass its predicted gene ranking (a plain list[str] ) together with the ground-truth genes and scores to RankingMetrics.evaluate() : See examples/load data.ipynb for a complete walkthrough. Dataset fields Each screen returned by get train test split() is a dictionary with the following fields: Field Type Description --- --- --- question str The prompt describing the screen and ranking task relevance genes list[str] All genes in the screen library relevance scores list[float] Thresholded percentile scores for each gene (higher = more relevant) hit list[bool] Whether each gene is a hit in the screen dataset name str Screen identifier screen ids list[int] BioGRID screen ID(s)","default_branch":null,"files":null,"tree":[],"storefront":"/r/Genentech","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/Genentech/AssayBench/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}