Zhenning Yang
Publications
scBench-Long: Verifiable Benchmarking of Long-Horizon Single-Cell Biology
Single-cell studies require analysts to convert raw measurements into specific biological claims through multi-step workflows and integration of metadata, assay context, and auxiliary evidence. Existing AI-biology benchmarks largely measure broad knowledge, executable workflows, or local analysis steps. We introduce scBench-Long, a benchmark for long-horizon single-cell biology in which agents must recover scientific conclusions from raw or near-raw data without prescribed methods. The benchmark contains 21 evaluations spanning melanoma CD8 T-cell reactivity, CD8 RNA+ATAC regulatory inference, human--monkey chimera development, KRAS-driven lung tumor aging, and lethal COVID-19 lung pathology. Tasks cover paired scRNA/TCR sequencing, RNA and chromatin profiling, cross-species transcriptomics, combinatorial scRNA-seq, single-nucleus RNA-seq, immune repertoires, ortholog maps, ligand--receptor resources, and validation evidence. Candidate claims are reproduced, reviewed, and converted into controlled answer vocabularies with deterministic grading and trajectory rubrics. Across 1,068 completed trajectories, the strongest model--harness pair passes 16/63 runs (25.4\%). scBench-Long evaluates whether agents can move beyond local analysis steps and make complex scientific claims that are supported by single-cell data.
Ambig-IaC: Multi-level Disambiguation for Interactive Cloud Infrastructure-as-Code Synthesis
The scale and complexity of modern cloud infrastructure have made Infrastructure-as-Code (IaC) essential for managing deployments. While large Language models (LLMs) are increasingly being used to generate IaC configurations from natural language, user requests are often underspecified. Unlike traditional code generation, IaC configurations cannot be executed cheaply or iteratively repaired, forcing the LLMs into an almost one-shot regime. We observe that ambiguity in IaC exhibits a tractable compositional structure: configurations decompose into three hierarchical axes (resources, topology, attributes) where higher-level decisions constrain lower-level ones. We propose a training-free, disagreement-driven framework that generates diverse candidate specifications, identifies structural disagreements across these axes, ranks them by informativeness, and produces targeted clarification questions that progressively narrow the configuration space. We introduce \textsc{Ambig-IaC}, a benchmark of 300 validated IaC tasks with ambiguous prompts, and an evaluation framework based on graph edit distance and embedding similarity. Our method outperforms the strongest baseline, achieving relative improvements of +18.4\% and +25.4\% on structure and attribute evaluations, respectively.