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Large Language Models (LLMs) and Vision Language Models (VLMs) have recently shown promising capabilities in various scientific domain. In particular, these advances have opened new opportunities in drug discovery, where the ability to…

Artificial Intelligence · Computer Science 2026-05-13 Jueon Park , Wonjune Jang , Jiwoo Lee , Yein Park , Jaewoo Kang

Recent advances in large language models (LLMs) have enabled molecular reasoning for property prediction. However, toxicity arises from complex biological mechanisms beyond chemical structure, necessitating mechanistic reasoning for…

Quantitative Methods · Quantitative Biology 2026-04-09 Jueon Park , Wonjune Jang , Chanhwi Kim , Yein Park , Jaewoo Kang

Large language models (LLMs) have achieved impressive results across a range of natural language processing tasks, but their potential to generate harmful content has raised serious safety concerns. Current toxicity detectors primarily rely…

Computation and Language · Computer Science 2025-10-20 Zhiqiang Kou , Junyang Chen , Xin-Qiang Cai , Ming-Kun Xie , Biao Liu , Changwei Wang , Lei Feng , Yuheng Jia , Gang Niu , Masashi Sugiyama , Xin Geng

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…

Large Language Models (LLMs) have shown growing potential in molecular sciences, but they often produce chemically inaccurate descriptions and struggle to recognize or justify potential errors. This raises important concerns about their…

Chemical Physics · Physics 2025-10-29 Yuyang Wu , Jinhui Ye , Shuhao Zhang , Lu Dai , Yonatan Bisk , Olexandr Isayev

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and…

Machine Learning · Computer Science 2024-03-11 Zhiqiang Zhong , Kuangyu Zhou , Davide Mottin

Multimodal large language models (MLLMs) have made impressive progress in many applications in recent years. However, chemical MLLMs that can handle cross-modal understanding and generation remain underexplored. To fill this gap, we propose…

Machine Learning · Computer Science 2025-08-05 Qian Tan , Dongzhan Zhou , Peng Xia , Wanhao Liu , Wanli Ouyang , Lei Bai , Yuqiang Li , Tianfan Fu

The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our…

Biomolecules · Quantitative Biology 2024-12-20 He Cao , Zijing Liu , Xingyu Lu , Yuan Yao , Yu Li

In the molecular domain, numerous studies have explored the use of multimodal large language models (LLMs) to construct a general-purpose, multi-task molecular model. However, these efforts are still far from achieving a truly universal…

Machine Learning · Computer Science 2025-10-31 Chengxin Hu , Hao Li , Yihe Yuan , Zezheng Song , Chenyang Zhao , Haixin Wang

In the pursuit of developing Large Language Models (LLMs) that adhere to societal standards, it is imperative to detect the toxicity in the generated text. The majority of existing toxicity metrics rely on encoder models trained on specific…

Computation and Language · Computer Science 2024-11-15 Hyukhun Koh , Dohyung Kim , Minwoo Lee , Kyomin Jung

The rapid advancement of multimodal large language models (MLLMs) has significantly enhanced performance across benchmarks. However, data contamination-unintentional memorization of benchmark data during model training-poses critical…

Computer Vision and Pattern Recognition · Computer Science 2025-09-23 Dingjie Song , Sicheng Lai , Mingxuan Wang , Shunian Chen , Lichao Sun , Benyou Wang

Large language models (LLMs) have become integral to our professional workflows and daily lives. Nevertheless, these machine companions of ours have a critical flaw: the huge amount of data which endows them with vast and diverse knowledge,…

Computation and Language · Computer Science 2024-05-21 Tinh Son Luong , Thanh-Thien Le , Linh Ngo Van , Thien Huu Nguyen

Multimodal Large Language Models (MLLMs) excel at recognizing individual visual elements and reasoning over simple linear diagrams. However, when faced with complex topological structures involving branching paths, converging flows, and…

Artificial Intelligence · Computer Science 2026-04-24 Qiang Xu , Shengyuan Bai , Yu Wang , He Cao , Leqing Chen , Yuanyuan Liu , Bin Feng , Zijing Liu , Yu Li

Chemistry plays a crucial role in many domains, such as drug discovery and material science. While large language models (LLMs) such as GPT-4 exhibit remarkable capabilities on natural language processing tasks, existing research indicates…

Artificial Intelligence · Computer Science 2024-08-13 Botao Yu , Frazier N. Baker , Ziqi Chen , Xia Ning , Huan Sun

In an era of rapidly evolving internet technology, the surge in multimodal content, including videos, has expanded the horizons of online communication. However, the detection of toxic content in this diverse landscape, particularly in…

Artificial Intelligence · Computer Science 2024-07-16 Krishanu Maity , A. S. Poornash , Sriparna Saha , Pushpak Bhattacharyya

The spread of toxic content online is an important problem that has adverse effects on user experience online and in our society at large. Motivated by the importance and impact of the problem, research focuses on developing solutions to…

Computation and Language · Computer Science 2023-08-11 Xinlei He , Savvas Zannettou , Yun Shen , Yang Zhang

The modeling of bio-molecular system across molecular scales remains a central challenge in scientific research. Large language models (LLMs) are increasingly applied to bio-molecular discovery, yet systematic evaluation across multi-scale…

Machine Learning · Computer Science 2026-04-07 Yaxin Xu , Yue Zhou , Tianyu Zhao , Fengwei An , Zhixiang Ren

Chemical reaction and retrosynthesis prediction are fundamental tasks in drug discovery. Recently, large language models (LLMs) have shown potential in many domains. However, directly applying LLMs to these tasks faces two major challenges:…

Machine Learning · Computer Science 2025-05-06 Xuan Lin , Qingrui Liu , Hongxin Xiang , Daojian Zeng , Xiangxiang Zeng

Language is a deep-rooted means of perpetration of stereotypes and discrimination. Large Language Models (LLMs), now a pervasive technology in our everyday lives, can cause extensive harm when prone to generating toxic responses. The…

Software Engineering · Computer Science 2026-02-06 Simone Corbo , Luca Bancale , Valeria De Gennaro , Livia Lestingi , Vincenzo Scotti , Matteo Camilli

Large Language Models (LLMs) have the potential to accelerate small molecule drug design due to their ability to reason about information from diverse sources and formats. However, their practical utility remains unclear due to the lack of…

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