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Machine learning has the potential to automate molecular design and drastically accelerate the discovery of new functional compounds. Towards this goal, generative models and reinforcement learning (RL) using string and graph…

Machine Learning · Computer Science 2022-02-02 Daniel Flam-Shepherd , Alexander Zhigalin , Alán Aspuru-Guzik

Multi-agent large language model frameworks are promising for complex multi step reasoning, yet existing systems remain weak for scientific and knowledge intensive domains due to static prompts and agent roles, rigid workflows, and…

Artificial Intelligence · Computer Science 2026-03-04 Yichao Feng , Haoran Luo , Zhenghong Lin , Yiqun Sun , Pengfei Wei , Lawrence B. Hsieh , Anh Tuan Luu

Large language models (LLMs) can perform complex reasoning by generating intermediate reasoning steps. Providing these steps for prompting demonstrations is called chain-of-thought (CoT) prompting. CoT prompting has two major paradigms. One…

Computation and Language · Computer Science 2022-10-10 Zhuosheng Zhang , Aston Zhang , Mu Li , Alex Smola

Structure-Based Drug Design (SBDD) has revolutionized drug discovery by enabling the rational design of molecules for specific protein targets. Despite significant advancements in improving docking scores, advanced 3D-SBDD generative models…

Biomolecules · Quantitative Biology 2025-03-04 Bowen Gao , Yanwen Huang , Yiqiao Liu , Wenxuan Xie , Wei-Ying Ma , Ya-Qin Zhang , Yanyan Lan

Despite recent advancements in language models (LMs), their application to dialogue management (DM) problems and ability to carry on rich conversations remain a challenge. We use reinforcement learning (RL) to develop a dialogue agent that…

Computation and Language · Computer Science 2022-06-02 Yinlam Chow , Aza Tulepbergenov , Ofir Nachum , MoonKyung Ryu , Mohammad Ghavamzadeh , Craig Boutilier

Large language models excel on static benchmarks, but their ability as self-learning agents in dynamic environments remains unclear. We evaluate three prompting strategies: self-reflection, heuristic mutation, and planning across dynamic…

Artificial Intelligence · Computer Science 2025-08-12 Annie Wong , Thomas Bäck , Aske Plaat , Niki van Stein , Anna V. Kononova

Emerging reasoning models hold promise for automating scientific discovery. However, their training is hindered by a critical supervision gap: experimental outcomes are abundant, whereas intermediate reasoning steps are rarely documented at…

Biomolecules · Quantitative Biology 2026-03-24 Zequn Liu , Kehan Wu , Shufang Xie , Zekun Guo , Wei Zhang , Tao Qin , Renhe Liu , Yingce Xia

Code generation models based on large language models (LLMs) have gained wide adoption, but challenges remain in ensuring safety, accuracy, and controllability, especially for complex tasks. Existing methods often lack dynamic integration…

Software Engineering · Computer Science 2025-10-13 Aofan Liu , Haoxuan Li , Bin Wang , Ao Yang , Hui Li

Medical dialogue generation aims to provide automatic and accurate responses to assist physicians to obtain diagnosis and treatment suggestions in an efficient manner. In medical dialogues two key characteristics are relevant for response…

Computation and Language · Computer Science 2021-05-14 Dongdong Li , Zhaochun Ren , Pengjie Ren , Zhumin Chen , Miao Fan , Jun Ma , Maarten de Rijke

Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in…

Machine Learning · Computer Science 2025-10-03 Dongki Kim , Wonbin Lee , Sung Ju Hwang

Artificial intelligence has demonstrated immense potential in scientific research. Within molecular science, it is revolutionizing the traditional computer-aided paradigm, ushering in a new era of deep learning. With recent progress in…

Biomolecules · Quantitative Biology 2024-03-22 Yi Xiao , Xiangxin Zhou , Qiang Liu , Liang Wang

Large Language Models (LLMs) exhibit strong mathematical reasoning when trained on high-quality Chain-of-Thought (CoT) that articulates intermediate steps, yet costly CoT curation hinders further progress. While existing remedies such as…

Artificial Intelligence · Computer Science 2026-04-17 Zhuo Wang , Zhuo Zhang , Yafu Li , Yu Cheng , Lizhen Qu , Zenglin Xu

Multi-Agent Debate (MAD) has shown promise in leveraging collective intelligence to improve reasoning and reduce hallucinations, yet it remains unclear how information exchange shapes the underlying ability. Empirically, MAD exhibits…

Multiagent Systems · Computer Science 2026-03-03 Dan Qiao , Binbin Chen , Fengyu Cai , Jianlong Chen , Wenhao Li , Fuxin Jiang , Zuzhi Chen , Hongyuan Zha , Tieying Zhang , Baoxiang Wang

We introduce a technique for multi-document grounded multi-turn synthetic dialog generation that incorporates three main ideas. First, we control the overall dialog flow using taxonomy-driven user queries that are generated with…

Computation and Language · Computer Science 2024-09-19 Young-Suk Lee , Chulaka Gunasekara , Danish Contractor , Ramón Fernandez Astudillo , Radu Florian

With the emergence of diffusion models as a frontline generative model, many researchers have proposed molecule generation techniques with conditional diffusion models. However, the unavoidable discreteness of a molecule makes it difficult…

Machine Learning · Computer Science 2025-06-05 Jinho Chang , Jong Chul Ye

The ability to perform Chain-of-Thought (CoT) reasoning marks a major milestone for multimodal models (MMs), enabling them to solve complex visual reasoning problems. Yet a critical question remains: is such reasoning genuinely grounded in…

Computer Vision and Pattern Recognition · Computer Science 2025-12-10 Jusheng Zhang , Kaitong Cai , Xiaoyang Guo , Sidi Liu , Qinhan Lv , Ruiqi Chen , Jing Yang , Yijia Fan , Xiaofei Sun , Jian Wang , Ziliang Chen , Liang Lin , Keze Wang

Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-like properties). In addition, the molecules that LLMs…

Interleaved-Modal Chain-of-Thought (I-MCoT) advances vision-language reasoning, such as Visual Question Answering (VQA). This paradigm integrates specially selected visual evidence from the input image into the context of Vision-Language…

Computer Vision and Pattern Recognition · Computer Science 2026-04-21 Xiping Li , Jianghong Ma

Search-integrated reasoning enables language agents to transcend static parametric knowledge by actively querying external sources. However, training these agents via reinforcement learning is hindered by the multi-scale credit assignment…

Artificial Intelligence · Computer Science 2026-02-04 Bowei He , Minda Hu , Zenan Xu , Hongru Wang , Licheng Zong , Yankai Chen , Chen Ma , Xue Liu , Pluto Zhou , Irwin King

The rapid advancement of artificial intelligence, particularly autonomous agentic systems based on Large Language Models (LLMs), presents new opportunities to accelerate drug discovery by improving in-silico modeling and reducing dependence…