English
Related papers

Related papers: scBench: Evaluating AI Agents on Single-Cell RNA-s…

200 papers

AI-driven drug response prediction holds great promise for advancing personalized cancer treatment. However, the inherent heterogenity of cancer and high cost of data generation make accurate prediction challenging. In this study, we…

Machine Learning · Computer Science 2025-05-14 Till Rossner , Ziteng Li , Jonas Balke , Nikoo Salehfard , Tom Seifert , Ming Tang

RNA velocity is a model of gene expression dynamics designed to analyze single-cell RNA sequencing (scRNA-seq) data, and it has recently gained significant attention. However, despite its popularity, the model has raised several concerns,…

Applications · Statistics 2025-05-07 Elena Sabbioni , Enrico Bibbona , Gianluca Mastrantonio , Guido Sanguinetti

We present Doctorina MedBench, a comprehensive evaluation framework for agent-based medical AI based on the simulation of realistic physician-patient interactions. Unlike traditional medical benchmarks that rely on solving standardized test…

Computation and Language · Computer Science 2026-03-30 Anna Kozlova , Stanislau Salavei , Pavel Satalkin , Hanna Plotnitskaya , Sergey Parfenyuk

The rapid growth of AI agent ecosystems is transforming how complex tasks are delegated and executed, creating a new challenge of identifying suitable agents for a given task. Unlike traditional tools, agent capabilities are often…

Artificial Intelligence · Computer Science 2026-04-27 Bin Wu , Arastun Mammadli , Xiaoyu Zhang , Emine Yilmaz

The transition to agentic Root Cause Analysis (RCA) necessitates benchmarks that evaluate active reasoning rather than passive classification. However, current frameworks fail to reconcile ecological validity with reproducibility. We…

Software Engineering · Computer Science 2026-03-03 Yilun Wang , Guangba Yu , Haiyu Huang , Zirui Wang , Yujie Huang , Pengfei Chen , Michael R. Lyu

Computer-Using Agents (CUAs) are rapidly extending large language models (LLMs) beyond text-based reasoning toward action execution in more complex environments, such as web browsers and graphical user interfaces (GUIs). However, existing…

As language models (LMs) evolve from chat assistants to long-horizon agents capable of multi-step reasoning and tool use, existing benchmarks remain largely confined to structured or exam-style tasks that fall short of real-world…

On June 25th, 2018, Huang et al. published a computational method SAVER on Nature Methods for imputing dropout gene expression levels in single cell RNA sequencing (scRNA-seq) data. Huang et al. performed a set of comprehensive benchmarking…

Applications · Statistics 2019-08-21 Wei Vivian Li , Jingyi Jessica Li

Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to analyze gene expression at the cellular level. By providing data on gene expression for each individual cell, scRNA-seq generates large datasets with thousands of…

Computational Complexity · Computer Science 2025-02-11 Md Romizul Islam , Swakkhar Shatabda

Large language models are increasingly used for medical guidance, but women's health remains under-evaluated in benchmark design. We present the Women's Health Benchmark (WHBench), a targeted evaluation suite of 47 expert-crafted scenarios…

Computation and Language · Computer Science 2026-04-02 Sneha Maurya , Pragya Saboo , Girish Kumar

RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…

Genomics · Quantitative Biology 2026-05-25 Christopher Thron , Farhad Jafari

As AI agents expand into high-stakes domains like network system operations, evaluating their real-world reliability becomes increasingly critical. However, existing benchmarks risk contamination due to static design, show high statistical…

Networking and Internet Architecture · Computer Science 2026-03-17 Yajie Zhou , Jiajun Ruan , Eric S. Wang , Sadjad Fouladi , Francis Y. Yan , Kevin Hsieh , Zaoxing Liu

Autonomous agents have rapidly matured as task executors and seen widespread deployment via harnesses such as OpenClaw. Safety concerns have rightly drawn growing research attention, and beneath them lie the values silently steering agent…

Artificial Intelligence · Computer Science 2026-05-12 Haonan Dong , Qiguan Feng , Kehan Jiang , Haoran Ye , Xin Zhang , Guojie Song

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA,…

Quantitative Methods · Quantitative Biology 2024-12-13 Yuchen Ren , Zhiyuan Chen , Lifeng Qiao , Hongtai Jing , Yuchen Cai , Sheng Xu , Peng Ye , Xinzhu Ma , Siqi Sun , Hongliang Yan , Dong Yuan , Wanli Ouyang , Xihui Liu

AI agents hold growing promise for accelerating scientific discovery; yet, a lack of frontier evaluations hinders adoption into real workflows. Expert-written benchmarks have proven effective at measuring AI reasoning, but most at this…

Rigorous security-focused evaluation of large language model (LLM) agents is imperative for establishing trust in their safe deployment throughout the software development lifecycle. However, existing benchmarks largely rely on synthetic…

Machine Learning · Computer Science 2025-10-23 Hwiwon Lee , Ziqi Zhang , Hanxiao Lu , Lingming Zhang

Training web agents to navigate complex, real-world websites requires them to master $\textit{subtasks}$ - short-horizon interactions on multiple UI components (e.g., choosing the correct date in a date picker, or scrolling in a container…

Deep research, in which an agent searches the open web, collects evidence, and derives an answer through extended reasoning, is a prominent use case for frontier language models. Frontier deep research products score high on existing…

Artificial Intelligence · Computer Science 2026-05-21 Sixiong Xie , Zhuofan Shi , Haiyang Shen , Jiuzheng Wang , Siqi Zhong , Mugeng Liu , Chongyang Pan , Peilun Jia , Baoqing Sun , Xiang Jing , Yun Ma

Enterprises increasingly need AI systems that can answer sales-leader questions over live, customized CRM data, but most available models do not expose transparent, repeatable evidence of quality. This paper describes the Sales Research…

Artificial Intelligence · Computer Science 2026-02-20 Deepanjan Bhol

LLM development has aroused great interest in Sequential Recommendation (SR) applications. However, comprehensive evaluation of SR models remains lacking due to the limitations of the existing benchmarks: 1) an overemphasis on accuracy,…

Information Retrieval · Computer Science 2026-04-14 Jianhong Li , Zeheng Qian , Wangze Ni , Haoyang Li , Hongwei Yao , Yang Bai , Kui Ren