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Molecular function is largely determined by structure. Accurately aligning molecular structure with natural language is therefore essential for enabling large language models (LLMs) to reason about downstream chemical tasks. However, the…

Computation and Language · Computer Science 2026-05-11 Feiyang Cai , Guijuan He , Yi Hu , Jingjing Wang , Joshua Luo , Tianyu Zhu , Srikanth Pilla , Gang Li , Ling Liu , Feng Luo

In the field of chemical structure recognition, the task of converting molecular images into machine-readable data formats such as SMILES string stands as a significant challenge, primarily due to the varied drawing styles and conventions…

Computer Vision and Pattern Recognition · Computer Science 2025-03-12 Yufan Chen , Ching Ting Leung , Yong Huang , Jianwei Sun , Hao Chen , Hanyu Gao

Large Language Models (LLMs) have transformed how people interact with artificial intelligence (AI) systems, achieving state-of-the-art results in various tasks, including scientific discovery and hypothesis generation. However, the lack of…

Computation and Language · Computer Science 2024-11-06 Sikun Guo , Amir Hassan Shariatmadari , Guangzhi Xiong , Albert Huang , Eric Xie , Stefan Bekiranov , Aidong Zhang

Formal models are essential to specifying large, complex computer systems and verifying their correctness, but are notoriously expensive to write and maintain. Recent advances in generative AI show promise in generating certain forms of…

Artificial Intelligence · Computer Science 2026-01-29 Qian Cheng , Ruize Tang , Emilie Ma , Finn Hackett , Peiyang He , Yiming Su , Ivan Beschastnikh , Yu Huang , Xiaoxing Ma , Tianyin Xu

Small molecules are essential to drug discovery, and graph-language models hold promise for learning molecular properties and functions from text. However, existing molecule-text datasets are limited in scale and informativeness,…

Biomolecules · Quantitative Biology 2025-06-03 Yihan Zhu , Gang Liu , Eric Inae , Meng Jiang

Deep learning is now widely used in drug discovery, providing significant acceleration and cost reduction. As the most fundamental building block, molecular representation is essential for predicting molecular properties to enable various…

Machine Learning · Computer Science 2024-04-22 Haoqiang Guo , Sendong Zhao , Haochun Wang , Yanrui Du , Bing Qin

Despite the remarkable advancements and widespread applications of deep neural networks, their ability to perform reasoning tasks remains limited, particularly in domains requiring structured, abstract thought. In this paper, we investigate…

Computation and Language · Computer Science 2025-09-16 Satyam Goyal , Soham Dan

Large language models (LLMs) have made impressive progress in chemistry applications. However, the community lacks an LLM specifically designed for chemistry. The main challenges are two-fold: firstly, most chemical data and scientific…

Data preparation is a central and time-consuming stage in data analysis workflows. Traditionally, commercial tools have relied on graphical user interfaces (GUIs) to simplify data preparation, allowing users to define transformations…

Databases · Computer Science 2026-05-12 Jingzhe Xu , Rui Wang , Jiannan Wang , Guoliang Li

General-purposed embodied agents are designed to understand the users' natural instructions or intentions and act precisely to complete universal tasks. Recently, methods based on foundation models especially Vision-Language-Action models…

Generative AI agents, software systems powered by Large Language Models (LLMs), are emerging as a promising approach to automate cybersecurity tasks. Among the others, penetration testing is a challenging field due to the task complexity…

Cryptography and Security · Computer Science 2024-10-29 Luca Gioacchini , Marco Mellia , Idilio Drago , Alexander Delsanto , Giuseppe Siracusano , Roberto Bifulco

Recovering editable CAD programs from images or 3D observations is central to AI-assisted design, but progress is difficult to measure because existing evaluations are fragmented across datasets, modalities, and metrics. We introduce…

Computer Vision and Pattern Recognition · Computer Science 2026-05-12 Anna C. Doris , Jacob Thomas Sony , Ghadi Nehme , Era Syla , Amin Heyrani Nobari , Faez Ahmed

Large Language Models (LLMs) have achieved remarkable success in code generation tasks, powering various applications like code completion, debugging, and programming assistance. However, existing benchmarks such as HumanEval, MBPP, and…

Machine Learning · Computer Science 2025-05-09 Manik Sheokand , Parth Sawant

Large Language Model (LLM) agents have shown great potential for solving real-world problems and promise to be a solution for tasks automation in industry. However, more benchmarks are needed to systematically evaluate automation agents…

Artificial Intelligence · Computer Science 2025-07-16 Yinsheng Li , Zhen Dong , Yi Shao

Leveraging Multi-modal Large Language Models (MLLMs) to create embodied agents offers a promising avenue for tackling real-world tasks. While language-centric embodied agents have garnered substantial attention, MLLM-based embodied agents…

Creativity is a fundamental aspect of intelligence, involving the ability to generate novel and appropriate solutions across diverse contexts. While Large Language Models (LLMs) have been extensively evaluated for their creative…

Computer Vision and Pattern Recognition · Computer Science 2025-03-20 Xinyu Fang , Zhijian Chen , Kai Lan , Lixin Ma , Shengyuan Ding , Yingji Liang , Xiangyu Zhao , Farong Wen , Zicheng Zhang , Guofeng Zhang , Haodong Duan , Kai Chen , Dahua Lin

Large Language Models (LLMs) with their strong task-handling capabilities have shown remarkable advancements across a spectrum of fields, moving beyond natural language understanding. However, their proficiency within the chemistry domain…

Computer Vision and Pattern Recognition · Computer Science 2026-02-02 Khiem Le , Zhichun Guo , Kaiwen Dong , Xiaobao Huang , Bozhao Nan , Roshni Iyer , Xiangliang Zhang , Olaf Wiest , Wei Wang , Ting Hua , Nitesh V. Chawla

As Vision-Language Models (VLMs) increasingly gain traction in medical applications, clinicians are progressively expecting AI systems not only to generate textual diagnoses but also to produce corresponding medical images that integrate…

Computer Vision and Pattern Recognition · Computer Science 2025-11-19 Junjie Yang , Yuhao Yan , Gang Wu , Yuxuan Wang , Ruoyu Liang , Xinjie Jiang , Xiang Wan , Fenglei Fan , Yongquan Zhang , Feiwei Qin , Changmiao Wang

In contrast to their remarkable performance on general knowledge QA, the true abilities of Large Language Models (LLMs) in tasks demanding deep, specialized reasoning, such as in protein biology, have yet to be thoroughly investigated.…

Quantitative Methods · Quantitative Biology 2025-12-30 Dingyi Rong , Zijian Chen , Qi Jia , Kaiwei Zhang , Haotian Lu , Guangtao Zhai , Ning Liu

The advancement and extensive application of large language models (LLMs) have been remarkable, including their use in scientific research assistance. However, these models often generate scientifically incorrect or unsafe responses, and in…

Computation and Language · Computer Science 2024-11-28 Haochen Zhao , Xiangru Tang , Ziran Yang , Xiao Han , Xuanzhi Feng , Yueqing Fan , Senhao Cheng , Di Jin , Yilun Zhao , Arman Cohan , Mark Gerstein