English
Related papers

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

200 papers

RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community…

Rapidly evolving AI exhibits increasingly strong autonomy and goal-directed capabilities, accompanied by derivative systemic risks that are more unpredictable, difficult to control, and potentially irreversible. However, current AI safety…

We introduce xbench, a dynamic, profession-aligned evaluation suite designed to bridge the gap between AI agent capabilities and real-world productivity. While existing benchmarks often focus on isolated technical skills, they may not…

We present SIR-Bench, a benchmark of 794 test cases for evaluating autonomous security incident response agents that distinguishes genuine forensic investigation from alert parroting. Derived from 129 anonymized incident patterns with…

Cryptography and Security · Computer Science 2026-04-15 Daniel Begimher , Cristian Leo , Jack Huang , Pat Gaw , Bonan Zheng

The existence of doublets in single-cell RNA sequencing (scRNA-seq) data poses a great challenge in downstream data analysis. Computational doublet-detection methods have been developed to remove doublets from scRNA-seq data. Yet, the…

Quantitative Methods · Quantitative Biology 2023-02-07 Nan Miles Xi , Angelos Vasilopoulos

Single-cell RNA sequencing has transformed biology by enabling the measurement of gene expression at cellular resolution, providing information for cell types, states, and disease contexts. Recently, single-cell foundation models have…

Machine Learning · Computer Science 2025-10-13 Oussama Kharouiche , Aris Markogiannakis , Xiao Fei , Michail Chatzianastasis , Michalis Vazirgiannis

The cell cycle is one of the most fundamental biological processes important for understanding normal physiology and various pathologies such as cancer. Single cell RNA sequencing technologies give an opportunity to analyse the cell cycle…

Quantitative Methods · Quantitative Biology 2022-08-11 Alexander Chervov , Andrei Zinovyev

AI-driven program repair uses AI models to repair buggy software by producing patches. Rapid advancements in AI surely impact state-of-the-art performance of program repair. Yet, grasping this progress requires frequent and standardized…

Software Engineering · Computer Science 2025-10-28 André Silva , Martin Monperrus

Applications of single-cell RNA sequencing in various biomedical research areas have been blooming. This new technology provides unprecedented opportunities to study disease heterogeneity at the cellular level. However, unique…

Genomics · Quantitative Biology 2021-10-26 Xinlei Mi , William Bekerman , Peter A. Sims , Peter D. Canoll , Jianhua Hu

As Large Language Models (LLMs) exhibit plateauing performance on conventional benchmarks, a pivotal challenge persists: evaluating their proficiency in complex, open-ended tasks characterizing genuine expert-level cognition. Existing…

Scientific sketches (e.g., models) offer a powerful lens into students' conceptual understanding, yet AI-powered automated assessment of such free-form, visually diverse artifacts remains a critical challenge. Existing solutions often treat…

Human-Computer Interaction · Computer Science 2025-10-21 Ehsan Latif , Zirak Khan , Xiaoming Zhai

AI agents are increasingly used to diagnose and mitigate failures in production systems, known as agentic Site Reliability Engineering (SRE). Current SRE benchmarks are limited to oversimplistic SRE tasks and are unfortunately hard to…

Artificial Intelligence · Computer Science 2026-05-14 Jackson Clark , Yiming Su , Saad Mohammad Rafid Pial , Yifang Tian , Lily Gniedziejko , Hans-Arno Jacobsen , Yinfang Chen , Tianyin Xu

We introduce ISO-Bench, a benchmark for coding agents to test their capabilities on real-world inference optimization tasks. These tasks were taken from vLLM and SGLang, two of the most popular LLM serving frameworks. Each task provides an…

Machine Learning · Computer Science 2026-02-24 Ayush Nangia , Shikhar Mishra , Aman Gokrani , Paras Chopra

Contemporary benchmarks for agentic artificial intelligence (AI) frequently evaluate safety through isolated task-level accuracy thresholds, implicitly treating autonomous systems as single points of failure. This single-channel paradigm…

Computers and Society · Computer Science 2026-02-24 Nelu D. Radpour

Modern AI progress has been driven by ML methods that are generalizable across settings and scalable to larger regimes. As large language models demonstrate advanced capabilities in reasoning, coding, and engineering tasks, it is…

Miscalibrated confidence scores are a practical obstacle to deploying AI in clinical settings. A model that is always overconfident offers no useful signal for deferral. We present a multi-agent framework that combines domain-specific…

Artificial Intelligence · Computer Science 2026-03-26 John Ray B. Martinez

Modern Large Language Model (LLM) agents promise end to end assistance with real-world software tasks, yet existing benchmarks evaluate LLM agents almost exclusively in pre-baked environments where every dependency is pre-installed. To fill…

Software Engineering · Computer Science 2025-07-15 Avi Arora , Jinu Jang , Roshanak Zilouchian Moghaddam

Recent advancements in integrating large language models (LLMs) with application programming interfaces (APIs) have gained significant interest in both academia and industry. Recent work demonstrates that these API-based agents exhibit…

Software Engineering · Computer Science 2025-01-24 Haiyang Shen , Yue Li , Desong Meng , Dongqi Cai , Sheng Qi , Li Zhang , Mengwei Xu , Yun Ma

Current agentic AI benchmarks predominantly evaluate task completion accuracy, while overlooking critical enterprise requirements such as cost-efficiency, reliability, and operational stability. Through systematic analysis of 12 main…

Artificial Intelligence · Computer Science 2025-11-19 Sushant Mehta

This paper presents DataSciBench, a comprehensive benchmark for evaluating Large Language Model (LLM) capabilities in data science. Recent related benchmarks have primarily focused on single tasks, easily obtainable ground truth, and…

Computation and Language · Computer Science 2025-02-20 Dan Zhang , Sining Zhoubian , Min Cai , Fengzu Li , Lekang Yang , Wei Wang , Tianjiao Dong , Ziniu Hu , Jie Tang , Yisong Yue
‹ Prev 1 8 9 10 Next ›