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MolXPT: Wrapping Molecules with Text for Generative Pre-training

Annual Meeting of the Association for Computational Linguistics (ACL), 2023

18 May 2023

Wei Zhang

ArXiv (abs)PDF HTML HuggingFace (1 upvotes)

Papers citing "MolXPT: Wrapping Molecules with Text for Generative Pre-training"

50 / 51 papers shown

Title
KnowMol: Advancing Molecular Large Language Models with Multi-Level Chemical Knowledge Zaifei Yang Hong Chang Ruibing Hou Shiguang Shan Xilin Chen 76 1 0 22 Oct 2025
Coder as Editor: Code-driven Interpretable Molecular Optimization Wenyu Zhu Chengzhu Li Xiaohe Tian Yifan Wang Yinjun Jia Jianhui Wang Bowen Gao Ya Zhang Wei-Ying Ma Yanyan Lan 57 1 0 16 Oct 2025
Reasoning-Enhanced Large Language Models for Molecular Property Prediction Jiaxi Zhuang Yaorui Shi Jue Hou Yunong He Mingwei Ye ... Linfeng Zhang Linfeng Zhang Linfeng Zhang Guolin Ke Hengxing Cai LRM 128 2 0 11 Oct 2025
Training Text-to-Molecule Models with Context-Aware Tokenization Seojin Kim Hyeontae Song J. Nam Jinwoo Shin 126 1 0 30 Aug 2025
MolErr2Fix: Benchmarking LLM Trustworthiness in Chemistry via Modular Error Detection, Localization, Explanation, and Revision Yuyang Wu Jinhui Ye Shuhao Zhang Lu Dai Yonatan Bisk Olexandr Isayev LRM 132 1 0 26 Aug 2025
CROP: Integrating Topological and Spatial Structures via Cross-View Prefixes for Molecular LLMs Jianting Tang Yubo Wang Haoyu Cao Linli Xu 72 1 0 09 Aug 2025
ChemHAS: Hierarchical Agent Stacking for Enhancing Chemistry Tools Zhucong Li Bowei Zhang Jin Xiao Zhijian Zhou Fenglei Cao Jiaqing Liang Yuan Qi 168 0 0 27 May 2025
Improving Chemical Understanding of LLMs via SMILES Parsing Yunhui Jang Jaehyung Kim SungSoo Ahn 140 3 0 22 May 2025
Chem42: a Family of chemical Language Models for Target-aware Ligand Generation A. Singh Engin Tekin Maryam Nadeem Nancy A. ElNaker Mohammad Amaan Sayeed Natalia Vassilieva Boulbaba Ben Amor 292 1 0 20 Mar 2025
ChemDFM-X: Towards Large Multimodal Model for ChemistryScience China Information Sciences (Sci. China Inf. Sci.), 2024 Zihan Zhao B. Chen Jingpiao Li Lu Chen Liyang Wen ... Ziping Wan Yansi Li Zhongyang Dai Xin Chen Kai Yu AI4CE 422 21 0 03 Jan 2025
SMI-Editor: Edit-based SMILES Language Model with Fragment-level SupervisionInternational Conference on Learning Representations (ICLR), 2024 Kangjie Zheng Siyue Liang Junwei Yang Bin Feng Zequn Liu Wei Ju Zhiping Xiao Ming Zhang 350 5 0 07 Dec 2024
GeomCLIP: Contrastive Geometry-Text Pre-training for MoleculesIEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2024 Teng Xiao Chao Cui Huaisheng Zhu V. Honavar AI4CE CLIP 333 3 0 16 Nov 2024
Exploring Optimal Transport-Based Multi-Grained Alignments for Text-Molecule RetrievalIEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2024 Zijun Min Bingshuai Liu Li Zhang Jia Song Jinsong Su Song He Xiaochen Bo OT 226 5 0 04 Nov 2024
LLaMo: Large Language Model-based Molecular Graph AssistantNeural Information Processing Systems (NeurIPS), 2024 Jinyoung Park Minseong Bae Dohwan Ko Hyunwoo J. Kim 199 15 0 31 Oct 2024
Chemical Language Model Linker: blending text and molecules with modular adaptersJournal of Chemical Information and Modeling (JCIM), 2024 Yifan Deng Spencer S. Ericksen Anthony Gitter 398 3 0 26 Oct 2024
Can Large Language Models Act as Ensembler for Multi-GNNs? Hanqi Duan Yao Cheng Jianxiang Yu Yao Liu Xiang Li AI4CE 242 0 0 22 Oct 2024
Y-Mol: A Multiscale Biomedical Knowledge-Guided Large Language Model for Drug Development Tengfei Ma Xuan Lin Tianle Li Chaoyi Li Long Chen ... Xibao Cai Xinyu Yang Daojian Zeng Dongsheng Cao Xiangxiang Zeng 136 6 0 15 Oct 2024
Dumpling GNN: Hybrid GNN Enables Better ADC Payload Activity Prediction Based on Chemical Structure Shengjie Xu Lingxi Xie 99 1 0 23 Sep 2024
Geometry Informed Tokenization of Molecules for Language Model Generation Xiner Li Limei Wang Youzhi Luo Carl Edwards Shurui Gui Yuchao Lin Heng Ji Shuiwang Ji 192 11 0 19 Aug 2024
Instruction-Based Molecular Graph Generation with Unified Text-Graph Diffusion Model Yuran Xiang Haiteng Zhao Chang Ma Zhi-Hong Deng 174 3 0 19 Aug 2024
HIGHT: Hierarchical Graph Tokenization for Molecule-Language Alignment Yongqiang Chen Quanming Yao Juzheng Zhang James Cheng Yatao Bian 271 4 0 20 Jun 2024
MolecularGPT: Open Large Language Model (LLM) for Few-Shot Molecular Property Prediction Yuyan Liu Sirui Ding Sheng Zhou Wenqi Fan Qiaoyu Tan 162 28 0 18 Jun 2024
Learning Multi-view Molecular Representations with Structured and Unstructured KnowledgeKnowledge Discovery and Data Mining (KDD), 2024 Yizhen Luo Kai Yang Massimo Hong Xing Yi Liu Zikun Nie Hao Zhou Zaiqing Nie 128 12 0 14 Jun 2024
TAGMol: Target-Aware Gradient-guided Molecule Generation Vineeth Dorna Subhalingam D Keshav Kolluru Shreshth Tuli Mrityunjay Singh Saurabh Singal N. M. A. Krishnan Jignesh M. Patel 208 7 0 03 Jun 2024
GLaD: Synergizing Molecular Graphs and Language Descriptors for Enhanced Power Conversion Efficiency Prediction in Organic Photovoltaic DevicesInternational Conference on Information and Knowledge Management (CIKM), 2024 Thao Nguyen Tiara Torres-Flores Changhyun Hwang Carl Edwards Ying Diao Heng Ji 133 1 0 23 May 2024
ALMol: Aligned Language-Molecule Translation LLMs through Offline Preference Contrastive Optimisation Dimitris Gkoumas 158 3 0 14 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 246 3 0 23 Apr 2024
Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model Peng Zhou Jianmin Wang Chunyan Li Zixu Wang Yiping Liu ... Xibao Cai Houtim Lai Wei Liu Longyue Wang Xiangxiang Zeng 230 5 0 20 Mar 2024
MoleculeQA: A Dataset to Evaluate Factual Accuracy in Molecular ComprehensionConference on Empirical Methods in Natural Language Processing (EMNLP), 2024 Xingyu Lu He Cao Zijing Liu Shengyuan Bai Leqing Chen Xingtai Lv Hai-Tao Zheng Yu-Feng Li HILM 188 13 0 13 Mar 2024
Materials science in the era of large language models: a perspectiveDigital Discovery (DD), 2024 Ge Lei Ronan Docherty Samuel J. Cooper 175 39 0 11 Mar 2024
Bridging Text and Molecule: A Survey on Multimodal Frameworks for Molecule Yi Xiao Xiangxin Zhou Qiang Liu Liang Wang AI4CE 140 5 0 07 Mar 2024
Large Language Models are In-Context Molecule Learners Jiatong Li Wei Liu Zhihao Ding Wenqi Fan Yuqiang Li Qing Li 485 14 0 07 Mar 2024
Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey Qizhi Pei Lijun Wu Ran Bi Jinhua Zhu Yue Wang Guoqing Liu Tao Qin Lijun Wu Rui Yan AI4CE 273 22 0 03 Mar 2024
ProtLLM: An Interleaved Protein-Language LLM with Protein-as-Word Pre-Training Le Zhuo Zewen Chi Minghao Xu Heyan Huang Heqi Zheng Conghui He Xian-Ling Mao Wentao Zhang 230 18 0 28 Feb 2024
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning Qizhi Pei Lijun Wu Ran Bi Xiaozhuan Liang Yin Fang Jinhua Zhu Shufang Xie Tao Qin Rui Yan AI4CE 351 55 0 27 Feb 2024
L+M-24: Building a Dataset for Language + Molecules @ ACL 2024 Carl Edwards Qingyun Wang Lawrence Zhao Heng Ji 218 30 0 22 Feb 2024
ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback Henry W Sprueill Carl Edwards Khushbu Agarwal Mariefel V. Olarte Udishnu Sanyal Conrad Johnston Hongbin Liu Heng Ji Sutanay Choudhury LRM 355 14 0 15 Feb 2024
A quantitative analysis of knowledge-learning preferences in large language models in molecular science Pengfei Liu Jun Tao Zhixiang Ren 96 3 0 06 Feb 2024
Leak, Cheat, Repeat: Data Contamination and Evaluation Malpractices in Closed-Source LLMsConference of the European Chapter of the Association for Computational Linguistics (EACL), 2024 Simone Balloccu Patrícia Schmidtová Mateusz Lango Ondrej Dusek SILM ELM PILM 345 246 0 06 Feb 2024
Professional Agents -- Evolving Large Language Models into Autonomous Experts with Human-Level Competencies Zhixuan Chu Yan Wang Feng Zhu Lu Yu Longfei Li Jinjie Gu LLMAG 163 11 0 06 Feb 2024
From Words to Molecules: A Survey of Large Language Models in Chemistry Chang Liao Yemin Yu Yu Mei Ying Wei 168 27 0 02 Feb 2024
MolTailor: Tailoring Chemical Molecular Representation to Specific Tasks via Text PromptsAAAI Conference on Artificial Intelligence (AAAI), 2024 Haoqiang Guo Sendong Zhao Hao Wang Yanrui Du Bing Qin AI4CE 207 13 0 21 Jan 2024
Large Language Models on Graphs: A Comprehensive SurveyIEEE Transactions on Knowledge and Data Engineering (TKDE), 2023 Sara Szymkuć Gang Liu Chi Han Meng Jiang Heng Ji Jiawei Han AI4CE 271 239 0 05 Dec 2023
InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug DiscoveryInternational Conference on Computational Linguistics (COLING), 2023 He Cao Zijing Liu Xingyu Lu Xingtai Lv Yu-Feng Li 236 85 0 27 Nov 2023
Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst DesignConference on Empirical Methods in Natural Language Processing (EMNLP), 2023 Henry W Sprueill Carl Edwards Mariefel V. Olarte Udishnu Sanyal Heng Ji Sutanay Choudhury LRM 248 13 0 22 Oct 2023
Survey on Factuality in Large Language Models: Knowledge, Retrieval and Domain-Specificity Cunxiang Wang Xiaoze Liu Yuanhao Yue Xiangru Tang Tianhang Zhang ... Linyi Yang Yongfeng Zhang Xing Xie Zheng Zhang Yue Zhang HILM KELM 359 248 0 11 Oct 2023
BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language AssociationsConference on Empirical Methods in Natural Language Processing (EMNLP), 2023 Qizhi Pei Wei Zhang Jinhua Zhu Kehan Wu Ran Bi Lijun Wu Ziheng Lu Rui Yan 232 100 0 11 Oct 2023
From Artificially Real to Real: Leveraging Pseudo Data from Large Language Models for Low-Resource Molecule DiscoveryAAAI Conference on Artificial Intelligence (AAAI), 2023 Yuhan Chen Nuwa Xi Yanrui Du Hao Wang Jianyu Chen Sendong Zhao Bing Qin 256 14 0 11 Sep 2023
Examining User-Friendly and Open-Sourced Large GPT Models: A Survey on Language, Multimodal, and Scientific GPT Models Ran Bi Su He Zhenyu He Jiacheng Lin Qizhi Pei Jie Shao Wei Zhang LM&MA SyDa 138 14 0 27 Aug 2023
What can Large Language Models do in chemistry? A comprehensive benchmark on eight tasksNeural Information Processing Systems (NeurIPS), 2023 Taicheng Guo Kehan Guo B. Nan Zhengwen Liang Zhichun Guo Nitesh Chawla Olaf Wiest Xiangliang Zhang ELM 442 204 0 27 May 2023

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MolXPT: Wrapping Molecules with Text for Generative Pre-training

Papers citing "MolXPT: Wrapping Molecules with Text for Generative Pre-training"