arXiv subjects

Arjun Banerjee

Publications and source records attributed to Arjun Banerjee.

5 recordsLinked to original sources

arXiv2026

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.

cs.AI↗

arXiv2026

BioSecBench-Refusal: A paired metric for performance and alignment in agentic biosecurity risk assessment

As AI agents are incorporated into life science workflows, the capabilities that speed discovery might also enable misuse. We present BioSecBench-Refusal, a benchmark for risk identification and refusal behavior for biological research tasks. The benchmark pairs 61 Routine tasks, legitimate analyses adapted from the published literature, with 46 Red-Team tasks, fictional scenarios that resemble real research but conceal a biosecurity hazard. Across 16 model-harness configurations, refusal rates ranged from 7 percent to 74 percent on Routine tasks and 1 percent to 62 percent on Red-Team tasks, with many configurations refusing legitimate Routine work at comparable or higher rates than concealed hazards. Refusals were most often triggered by provider API filters applied prior to agentic reasoning. However, models given room to reason showed the potential to identify more real threats. We release BioSecBench-Refusal as a tool for model developers to calibrate capability and caution for agentic biotech research and development.

cs.CR↗

arXiv2026

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.

q-bio.GN↗

arXiv2025

Automated Neuron Labelling Enables Generative Steering and Interpretability in Protein Language Models

Protein language models (PLMs) encode rich biological information, yet their internal neuron representations are poorly understood. We introduce the first automated framework for labeling every neuron in a PLM with biologically grounded natural language descriptions. Unlike prior approaches relying on sparse autoencoders or manual annotation, our method scales to hundreds of thousands of neurons, revealing individual neurons are selectively sensitive to diverse biochemical and structural properties. We then develop a novel neuron activation-guided steering method to generate proteins with desired traits, enabling convergence to target biochemical properties like molecular weight and instability index as well as secondary and tertiary structural motifs, including alpha helices and canonical Zinc Fingers. We finally show that analysis of labeled neurons in different model sizes reveals PLM scaling laws and a structured neuron space distribution.

cs.LG↗

arXiv2012

Characterizing price index behavior through fluctuation dynamics

We study the nature of fluctuations in variety of price indices involving companies listed on the New York Stock Exchange. The fluctuations at multiple scales are extracted through the use of wavelets belonging to Daubechies basis. The fact that these basis sets satisfy vanishing moments conditions makes them ideal to extract local polynomial trends, through the low pass or `average coefficients'. Subtracting the trends from the original time series yields the fluctuations, at different scales, depending on the level of low-pass coefficients used for finding the `average behavior'. The fluctuations are then studied using wavelet based multifractal detrended fluctuation analysis to analyze their self-similar and non-statistical properties. Due to the multifractality of such time series, they deviate from Gaussian behavior in different frequency regimes. Their departure from random matrix theory predictions in such regimes is also analyzed. These deviations and non-statistical properties of the fluctuations can be instrumental in throwing significant light on the dynamics of financial markets.

q-fin.ST↗