Arjun Banerjee
Publications
BioSecBench-Surveillance: A Verifiable Benchmark for AI Agents in Pathogen Genomic Surveillance
As pathogen genomic surveillance scales, the bottleneck is shifting from data generation to analysis. We present BioSecBench-Surveillance, a verifiable benchmark of 100 evaluations testing whether AI agents can infer the right analysis pipeline from raw sequencing data and surveillance context. Each evaluation gives an agent only the data and context a human analyst would have, then grades its structured answer deterministically. The tasks span seven categories, from taxonomic classification to genetic-engineering detection, across diverse sample types and sequencing technologies. Across 3,962 gradable attempts from sixteen model-harness pairs, the strongest configuration cleared only about half. Opus 4.8 with PI led at 50.2 percent, with a 95 percent confidence interval of 40.1 to 60.3 percent across 83 evaluations, tied with GPT-5.5 with Codex at 50.2 percent, with a 95 percent confidence interval of 40.8 to 59.6 percent, followed by Opus 4.7 with PI at 49.6 percent, with a 95 percent confidence interval of 40.0 to 59.2 percent, and Sonnet 4.6 with PI at 48.6 percent, with a 95 percent confidence interval of 38.9 to 58.3 percent. Even when agents invoked the correct workflows, their mistakes came from the choices around them, such as which references, thresholds, filters, and normalization to apply. BioSecBench-Surveillance provides a standard for measuring whether agents can be trusted to perform genomic surveillance when the next outbreak arrives.
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.