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Molecular Relational Learning (MRL) aims to understand interactions between molecular pairs, playing a critical role in advancing biochemical research. With the recent development of large language models (LLMs), a growing number of studies…

Machine Learning · Computer Science 2025-06-03 Zhuo Chen , Yizhen Zheng , Huan Yee Koh , Hongxin Xiang , Linjiang Chen , Wenjie Du , Yang Wang

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

Evaluation of Large Language Models (LLMs) is challenging because instruction-following necessitates alignment with human values and the required set of skills varies depending on the instruction. However, previous studies have mainly…

Computation and Language · Computer Science 2024-04-16 Seonghyeon Ye , Doyoung Kim , Sungdong Kim , Hyeonbin Hwang , Seungone Kim , Yongrae Jo , James Thorne , Juho Kim , Minjoon Seo

Large Language Models (LLMs) have shown impressive performance across various domains, but their ability to perform molecular reasoning remains underexplored. Existing methods mostly rely on general-purpose prompting, which lacks…

Molecular property prediction is a crucial foundation for drug discovery. In recent years, pre-trained deep learning models have been widely applied to this task. Some approaches that incorporate prior biological domain knowledge into the…

Machine Learning · Computer Science 2024-08-20 Tianyu Zhang , Yuxiang Ren , Chengbin Hou , Hairong Lv , Xuegong Zhang

Vision-language models (VLMs) have made substantial progress across a wide range of visual question answering benchmarks, spanning visual reasoning, document understanding, and multimodal dialogue. These improvements are evident in a wide…

Computer Vision and Pattern Recognition · Computer Science 2026-02-23 Dhruba Ghosh , Yuhui Zhang , Ludwig Schmidt

Molecules are graphs, but large language models~(LLMs) are usually asked to reason about them through linear strings. The most popular molecular representation, SMILES, compresses atoms, bonds, branches and rings into a compact sequence in…

Biomolecules · Quantitative Biology 2026-05-19 Zhiyuan Yan , Chen Liu , Boxuan Zhao , Kaiqing Lin , Jixiang Zhao , Yimi Wang , Liuzhenghao Lv , Hao Li , Shanzhuo Zhang , Li Yuan , Fanyang Mo

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal…

Machine Learning · Computer Science 2025-05-23 Ziqing Wang , Kexin Zhang , Zihan Zhao , Yibo Wen , Abhishek Pandey , Han Liu , Kaize Ding

Word alignment over parallel corpora has a wide variety of applications, including learning translation lexicons, cross-lingual transfer of language processing tools, and automatic evaluation or analysis of translation outputs. The great…

Computation and Language · Computer Science 2021-08-13 Zi-Yi Dou , Graham Neubig

While alignment of texts on the sentential level is often seen as being too coarse, and word alignment as being too fine-grained, bi- or multilingual texts which are aligned on a level in-between are a useful resource for many purposes.…

Computation and Language · Computer Science 2007-05-23 Lea Cyrus , Hendrik Feddes

Large language models (LLMs) are increasingly recognized as powerful tools for scientific discovery, particularly in molecular science. A fundamental requirement for these models is the ability to accurately understand molecular structures,…

Machine Learning · Computer Science 2025-05-23 Yunhui Jang , Jaehyung Kim , Sungsoo Ahn

In recent years, Large Language Models (LLMs) have achieved significant success in natural language processing (NLP) and various interdisciplinary areas. However, applying LLMs to chemistry is a complex task that requires specialized domain…

Machine Learning · Computer Science 2024-02-05 Chang Liao , Yemin Yu , Yu Mei , Ying Wei

The impressive performance of Large Language Model (LLM) has prompted researchers to develop Multi-modal LLM (MLLM), which has shown great potential for various multi-modal tasks. However, current MLLM often struggles to effectively address…

Computer Vision and Pattern Recognition · Computer Science 2024-12-24 Yeyuan Wang , Dehong Gao , Bin Li , Rujiao Long , Lei Yi , Xiaoyan Cai , Libin Yang , Jinxia Zhang , Shanqing Yu , Qi Xuan

Aligning molecular sequence representations (e.g., SMILES notations) with textual descriptions is critical for applications spanning drug discovery, materials design, and automated chemical literature analysis. Existing methodologies…

Artificial Intelligence · Computer Science 2025-11-25 Letian Chen , Runhan Shi , Gufeng Yu , Yang Yang

Molecular Relational Learning (MRL), aiming to understand interactions between molecular pairs, plays a pivotal role in advancing biochemical research. Recently, the adoption of large language models (LLMs), known for their vast knowledge…

Quantitative Methods · Quantitative Biology 2024-06-11 Junfeng Fang , Shuai Zhang , Chang Wu , Zhengyi Yang , Zhiyuan Liu , Sihang Li , Kun Wang , Wenjie Du , Xiang Wang

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text.…

Machine Learning · Computer Science 2023-07-17 Chen Qian , Huayi Tang , Zhirui Yang , Hong Liang , Yong Liu

Achieving better alignment between vision embeddings and Large Language Models (LLMs) is crucial for enhancing the abilities of Multimodal LLMs (MLLMs), particularly for recent models that rely on powerful pretrained vision encoders and…

Computer Vision and Pattern Recognition · Computer Science 2025-05-26 Jiachen Jiang , Jinxin Zhou , Bo Peng , Xia Ning , Zhihui Zhu

Large language models (LLMs) have transformed human writing by enhancing grammar correction, content expansion, and stylistic refinement. However, their widespread use raises concerns about authorship, originality, and ethics, even…

Computation and Language · Computer Science 2024-10-21 Zhen Tao , Zhiyu Li , Runyu Chen , Dinghao Xi , Wei Xu

While large language models demonstrate remarkable capabilities at task-specific applications through fine-tuning, extending these benefits across diverse languages is essential for broad accessibility. However, effective cross-lingual…

Computation and Language · Computer Science 2025-06-03 Danni Liu , Jan Niehues

Multimodal Large Language Models (MLLMs) have shown impressive results on various multimodal tasks. However, most existing MLLMs are not well suited for document-oriented tasks, which require fine-grained image perception and information…

Computer Vision and Pattern Recognition · Computer Science 2024-04-16 Ya-Qi Yu , Minghui Liao , Jihao Wu , Yongxin Liao , Xiaoyu Zheng , Wei Zeng