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This study investigates the current landscape and future directions of protein foundation model research. While recent advancements have transformed protein science and engineering, the field lacks a comprehensive benchmark for fair…

Biomolecules · Quantitative Biology 2025-06-19 Zhangyang Gao , Hao Wang , Cheng Tan , Chenrui Xu , Mengdi Liu , Bozhen Hu , Linlin Chao , Xiaoming Zhang , Stan Z. Li

Many benchmarks for automated causal inference evaluate a system's performance based on a single numerical output, such as an Average Treatment Effect (ATE). This approach conflates two distinct steps in causal analysis: identification -…

Artificial Intelligence · Computer Science 2026-05-15 Ayush Sawarni , Jiyuan Tan , Vasilis Syrgkanis

The field of artificial intelligence (AI) in quantitative investment has seen significant advancements, yet it lacks a standardized benchmark aligned with industry practices. This gap hinders research progress and limits the practical…

Computational Finance · Quantitative Finance 2025-04-29 Saizhuo Wang , Hao Kong , Jiadong Guo , Fengrui Hua , Yiyan Qi , Wanyun Zhou , Jiahao Zheng , Xinyu Wang , Lionel M. Ni , Jian Guo

More scientists are now using AI, but prior studies have examined only how they use it 'at the desk' for computer-based work. However, given that scientific work often happens 'beyond the desk' at lab and field sites, we conducted the first…

Human-Computer Interaction · Computer Science 2026-03-23 Irene Hou , Alexander Qin , Lauren Cheng , Philip J. Guo

Data-driven scientific discovery requires the iterative integration of scientific domain knowledge, statistical expertise, and an understanding of data semantics to make nuanced analytical decisions, e.g., about which variables,…

Variant and gene interpretation are fundamental to personalized medicine and translational biomedicine. However, traditional approaches are manual and labor-intensive. Generative language models (LMs) can facilitate this process,…

Artificial Intelligence · Computer Science 2025-10-15 Owen Queen , Harrison G. Zhang , James Zou

From professional research to everyday planning, many tasks are bottlenecked by wide-scale information seeking, which is more repetitive than cognitively complex. With the rapid development of Large Language Models (LLMs), automated search…

Computation and Language · Computer Science 2025-08-29 Ryan Wong , Jiawei Wang , Junjie Zhao , Li Chen , Yan Gao , Long Zhang , Xuan Zhou , Zuo Wang , Kai Xiang , Ge Zhang , Wenhao Huang , Yang Wang , Ke Wang

Developing safe, aligned agentic AI systems requires comprehensive empirical testing, yet many existing benchmarks neglect crucial themes aligned with biology and economics, both time-tested fundamental sciences describing our needs and…

Multiagent Systems · Computer Science 2025-12-01 Roland Pihlakas

Translational medicine turns underspecified development goals into evidence synthesis that must combine literature, trials, patents, and quantitative multi-omics analysis while preserving identifiers, uncertainty, and retrievable…

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require…

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

Large language models (LLMs) are increasingly capable of generating functional source code, raising concerns about authorship, accountability, and security. While detecting AI-generated code is critical, existing datasets and benchmarks are…

Machine Learning · Computer Science 2026-02-03 Daniil Orel , Dilshod Azizov , Indraneil Paul , Yuxia Wang , Iryna Gurevych , Preslav Nakov

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…

Benchmarks play a significant role in how technology companies communicate about model capabilities and how researchers and the public understand generative AI systems. However, existing benchmarks have been criticized for their failure to…

Human-Computer Interaction · Computer Science 2026-04-29 Charlotte Li , Nick Hagar , Sachita Nishal , Jeremy Gilbert , Nick Diakopoulos

Recent advances in large language models (LLMs) have enabled AI agents to autonomously generate scientific proposals, conduct experiments, author papers, and perform peer reviews. Yet this flood of AI-generated research content collides…

Machine learning-based modeling of physical systems has experienced increased interest in recent years. Despite some impressive progress, there is still a lack of benchmarks for Scientific ML that are easy to use but still challenging and…

Large language models (LLMs) are increasingly used as simulated participants in social science experiments, but their behavior is often unstable and highly sensitive to design choices. Prior evaluations frequently conflate base-model…

Artificial Intelligence · Computer Science 2026-02-03 Xuan Liu , Haoyang Shang , Zizhang Liu , Xinyan Liu , Yunze Xiao , Yiwen Tu , Haojian Jin

The application of deep learning methods, particularly foundation models, in biological research has surged in recent years. These models can be text-based or trained on underlying biological data, especially omics data of various types.…

Artificial Intelligence · Computer Science 2024-12-06 Yoav Kan-Tor , Michael Morris Danziger , Eden Zohar , Matan Ninio , Yishai Shimoni

Agents based on Large Language Models (LLMs) have shown promise for performing sophisticated software engineering tasks autonomously. In addition, there has been progress towards developing agents that can perform parts of the research…

Computation and Language · Computer Science 2026-04-23 Nicholas Edwards , Yukyung Lee , Yujun Audrey Mao , Yulu Qin , Sebastian Schuster , Najoung Kim
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