scBench-Long: Verifiable Benchmarking of Long-Horizon Single-Cell Biology

AI agents are increasingly useful for biological data analysis, but existing benchmarks mostly test broad biological knowledge, executable workflows, or localized analysis steps rather than end-to-end scientific reasoning over spatial measurements. We introduce SpatialBench-Long, a benchmark for long-horizon spatial biology in which agents must recover biological claims from raw or near-raw data and calibrated experimental context without prescribed methods. SpatialBench-Long contains 24 evaluations across primary pancreatic ductal adenocarcinoma (PDAC), engineered glioblastoma organoids and in vivo tumors, Cas9 lineage-traced lung adenocarcinoma, and mouse optic nerve aging/intervention systems, spanning CosMx, Visium, Xenium, multiplexed error-robust fluorescence in situ hybridization (MERFISH), single-cell RNA sequencing (scRNA-seq), Slide-seq, Slide-tags, histology, and lineage-recording data. Candidate claims are hardened through reproduction, independent scientist review, and trajectory inspection. Final answers are graded deterministically over controlled vocabularies and symbols with companion rubrics capturing progress through key analysis chokepoints. Across the SpatialBench-Long benchmark, three model-harness pairs tie at 8/72 runs (11.1%): Gemini 3.5 Flash / Pi terminal coding harness, GPT-5.5 / Pi, and GPT-5.5 / OpenAI Codex. SpatialBench-Long tests whether agents can move beyond executing procedural analysis to deriving accurate scientific conclusions from complex spatial measurements.

Simultaneous measurement of multiple omics modalities in single cells enables researchers to gain a more comprehensive understanding of cellular states and regulatory mechanisms. However, due to high experimental costs, significant noise, and incomplete modality coverage, a variety of computational methods for modality translation have emerged in recent years. Despite the development of translation models, there is still a lack of systematic benchmark evaluation in terms of datasets, evaluation metrics, and influencing factors. To address this, we present scTranslation, a comprehensive benchmark for single-cell multi-omics modality translation tasks. It includes diverse translation datasets, integrates state-of-the-art models, and provides a comprehensive evaluation metrics. In addition, we assess model performance under different scenarios, such as feature selection, feature quality, and few-shot settings. These factors significantly affect model performance but have rarely been systematically studied before. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development. The benchmark is open-sourced to facilitate future research. The code is anonymously released at https://github.com/Bunnybeibei/scTranslation.

Artificial intelligence (AI) promises to accelerate biological research by automating computational analyses. Yet the ability of AI agents to execute on computational biology at the scale of complete research studies has not been systematically evaluated. Here we introduce BixBench3, a benchmark that measures the capacity of AI agents to process raw biological data through to scientific results. We designed BixBench3 tasks to mirror the delegation of work from a scientist to an agent: the scientist chooses the research question and high-level methods, then delegates implementation of all analyses to the agent. In each task, an agent receives a research objective, methodological guidance, and raw data derived from a published scientific study, and must execute a sequence of analyses to achieve the research objective. The data artifacts resulting from these analyses, such as peak call matrices or differential expression tables, are programmatically graded against the corresponding artifacts generated and reported in the original study. Across 20 BixBench3 tasks encompassing the generation of 138 unique artifacts, we find that 13 frontier models achieve scores ranging from 0.00 for Gemini 3.1 Flash Lite to 0.48 for GPT 5.6 Sol. Agents perform worse on tasks with larger raw datasets (0.36 on tasks with <100 GB versus 0.10 on tasks with >100 GB) and on analyses requiring more sequential steps (0.36 at 1-2 steps vs 0.24 at 3+). On average, agents use 6.8 hours, 102 million tokens, and $43 to complete each task, with the longest attempts consuming 24 hours, 1.07 billion tokens, and $525. Notably, the highest-scoring agents used fewer tokens and were cheaper than less performant options. These results reveal that LLMs vary substantially in their ability to (1) execute multiple sequential analysis steps coherently, (2) manage large quantities of raw data, and (3) work across scientific domains.