Towards 3D Molecule-Text Interpretation in Language Models

25 January 2024

Zhiyuan Liu

Papers citing "Towards 3D Molecule-Text Interpretation in Language Models"

36 / 36 papers shown

Title
How to Detect and Defeat Molecular Mirage: A Metric-Driven Benchmark for Hallucination in LLM-based Molecular Comprehension Hao Li Liuzhenghao Lv He Cao Zijing Liu Zhiyuan Yan Yu Wang Yonghong Tian Y. Li Li Yuan 22 0 0 10 Apr 2025
Multimodal Language Modeling for High-Accuracy Single Cell Transcriptomics Analysis and Generation Yaorui Shi Jiaqi Yang Sihang Li Junfeng Fang X. Wang Zhiyuan Liu Yang Zhang 63 0 0 12 Mar 2025
Bridging Molecular Graphs and Large Language Models Runze Wang Mingqi Yang Yanming Shen 52 0 0 05 Mar 2025
MV-CLAM: Multi-View Molecular Interpretation with Cross-Modal Projection via Language Model Sumin Ha Jun Hyeong Kim Yinhua Piao Sun Kim 34 0 0 23 Feb 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Sihang Li Junfeng Fang Yaorui Shi X. Wang Kenji Kawaguchi Tat-Seng Chua 87 3 0 18 Feb 2025
ChemDFM-X: Towards Large Multimodal Model for Chemistry Zihan Zhao B. Chen Jingpiao Li Lu Chen Liyang Wen ... Ziping Wan Yansi Li Zhongyang Dai Xin Chen Kai Yu AI4CE 35 3 0 03 Jan 2025
From Generalist to Specialist: A Survey of Large Language Models for Chemistry Yang Han Ziping Wan Lu Chen Kai Yu Xin Chen LM&MA 32 1 0 31 Dec 2024
GeomCLIP: Contrastive Geometry-Text Pre-training for Molecules Teng Xiao Chao Cui Huaisheng Zhu V. Honavar AI4CE CLIP 28 0 0 16 Nov 2024
Exploring Hierarchical Molecular Graph Representation in Multimodal LLMs Chengxin Hu Hao Li Yihe Yuan Jing Li Ivor Tsang 36 0 0 07 Nov 2024
Exploring Optimal Transport-Based Multi-Grained Alignments for Text-Molecule Retrieval Zijun Min Bingshuai Liu L. Zhang Jia Song Jinsong Su Song He Xiaochen Bo OT 57 1 0 04 Nov 2024
Chain-of-Thoughts for Molecular Understanding Yunhui Jang Jaehyung Kim Sungsoo Ahn LRM AI4CE 21 0 0 08 Oct 2024
Text-guided Diffusion Model for 3D Molecule Generation Yanchen Luo Junfeng Fang Sihang Li Zhiyuan Liu Jiancan Wu An Zhang Wenjie Du Xiang Wang 26 6 0 04 Oct 2024
An Investigation of Warning Erroneous Chat Translations in Cross-lingual Communication Yunmeng Li Jun Suzuki Makoto Morishita Kaori Abe Kentaro Inui 38 1 0 28 Aug 2024
UniMoT: Unified Molecule-Text Language Model with Discrete Token Representation Jiayuan Zhu Yunli Qi Yongqiang Chen Quanming Yao 16 1 0 01 Aug 2024
HIGHT: Hierarchical Graph Tokenization for Graph-Language Alignment Yongqiang Chen Quanming Yao Juzheng Zhang James Cheng Yatao Bian 22 4 0 20 Jun 2024
PRESTO: Progressive Pretraining Enhances Synthetic Chemistry Outcomes He Cao Yanjun Shao Zhiyuan Liu Zijing Liu Xiangru Tang Yuan Yao Yu Li AI4CE 18 5 0 19 Jun 2024
MolecularGPT: Open Large Language Model (LLM) for Few-Shot Molecular Property Prediction Yuyan Liu Sirui Ding Sheng Zhou Wenqi Fan Qiaoyu Tan 21 6 0 18 Jun 2024
A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery Yu Zhang Xiusi Chen Bowen Jin Sheng Wang Shuiwang Ji Wei Wang Jiawei Han 35 17 0 16 Jun 2024
Learning Multi-view Molecular Representations with Structured and Unstructured Knowledge Yizhen Luo Kai Yang Massimo Hong Xing Yi Liu Zikun Nie Hao Zhou Zaiqing Nie 33 2 0 14 Jun 2024
MolX: Enhancing Large Language Models for Molecular Learning with A Multi-Modal Extension Khiem Le Zhichun Guo Kaiwen Dong Xiaobao Huang B. Nan Roshni G. Iyer Xiangliang Zhang Olaf Wiest Wei Wang Nitesh V. Chawla 29 8 0 10 Jun 2024
ReactXT: Understanding Molecular "Reaction-ship" via Reaction-Contextualized Molecule-Text Pretraining Zhiyuan Liu Yaorui Shi An Zhang Sihang Li Enzhi Zhang Xiang Wang Kenji Kawaguchi Tat-Seng Chua 25 10 0 23 May 2024
ProtT3: Protein-to-Text Generation for Text-based Protein Understanding Zhiyuan Liu An Zhang Hao Fei Enzhi Zhang Xiang Wang Kenji Kawaguchi Tat-Seng Chua 44 14 0 21 May 2024
Atomas: Hierarchical Alignment on Molecule-Text for Unified Molecule Understanding and Generation Yikun Zhang Geyan Ye Chaohao Yuan Bo Han Long-Kai Huang Jianhua Yao Wei Liu Yu Rong 21 3 0 23 Apr 2024
MolBind: Multimodal Alignment of Language, Molecules, and Proteins Teng Xiao Chao Cui Huaisheng Zhu V. Honavar AI4CE 19 6 0 13 Mar 2024
Bridging Text and Molecule: A Survey on Multimodal Frameworks for Molecule Yi Xiao Xiangxin Zhou Qiang Liu Liang Wang AI4CE 27 3 0 07 Mar 2024
Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey Qizhi Pei Lijun Wu Kaiyuan Gao Jinhua Zhu Yue Wang Zun Wang Tao Qin Rui Yan AI4CE 41 19 0 03 Mar 2024
Prospect Personalized Recommendation on Large Language Model-based Agent Platform Jizhi Zhang Keqin Bao Wenjie Wang Yang Zhang Wentao Shi Wanhong Xu Fuli Feng Tat-Seng Chua LLMAG 29 16 0 28 Feb 2024
LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset Botao Yu Frazier N. Baker Ziqi Chen Xia Ning Huan Sun LM&MA 29 15 0 14 Feb 2024
MolTC: Towards Molecular Relational Modeling In Language Models Junfeng Fang Shuai Zhang Chang Wu Zhengyi Yang Zhiyuan Liu Sihang Li Kun Wang Wenjie Du Xiang Wang 14 18 0 06 Feb 2024
EXGC: Bridging Efficiency and Explainability in Graph Condensation Junfeng Fang Xinglin Li Yongduo Sui Yuan Gao Guibin Zhang Kun Wang Xiang Wang Xiangnan He DD 49 18 0 05 Feb 2024
Interactive Molecular Discovery with Natural Language Zheni Zeng Bangchen Yin Shipeng Wang Jia-Rou Liu Cheng Yang Haishen Yao Xingzhi Sun Maosong Sun Guotong Xie Zhiyuan Liu AI4CE 11 12 0 21 Jun 2023
BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models Junnan Li Dongxu Li Silvio Savarese Steven C. H. Hoi VLM MLLM 244 4,186 0 30 Jan 2023
A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language Bing-Huang Su Dazhao Du Zhao-Qing Yang Yujie Zhou Jiangmeng Li Anyi Rao Haoran Sun Zhiwu Lu Ji-Rong Wen 38 107 0 12 Sep 2022
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 106 294 0 07 Oct 2021
Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs Zhao Xu Youzhi Luo Xuan Zhang Xinyi Xu Yaochen Xie Meng Liu Kaleb Dickerson Cheng Deng Maho Nakata Shuiwang Ji 33 39 0 30 Sep 2021
Conceptual 12M: Pushing Web-Scale Image-Text Pre-Training To Recognize Long-Tail Visual Concepts Soravit Changpinyo P. Sharma Nan Ding Radu Soricut VLM 273 845 0 17 Feb 2021