MolXPT: Wrapping Molecules with Text for Generative Pre-training

18 May 2023

Wei Zhang

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

45 / 45 papers shown

Title
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 47 1 0 20 Mar 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 53 3 0 03 Jan 2025
SMI-Editor: Edit-based SMILES Language Model with Fragment-level Supervision Kangjie Zheng Siyue Liang Junwei Yang Bin Feng Zequn Liu Wei Ju Zhiping Xiao Ming Zhang 73 1 0 07 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 Optimal Transport-Based Multi-Grained Alignments for Text-Molecule Retrieval Zijun Min Bingshuai Liu Li Zhang Jia Song Jinsong Su Song He Xiaochen Bo OT 65 1 0 04 Nov 2024
LLaMo: Large Language Model-based Molecular Graph Assistant Jinyoung Park Minseong Bae Dohwan Ko Hyunwoo J. Kim 39 1 0 31 Oct 2024
Chemical Language Model Linker: blending text and molecules with modular adapters Yifan Deng Spencer S. Ericksen Anthony Gitter 30 1 0 26 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 23 3 0 15 Oct 2024
Chain-of-Thoughts for Molecular Understanding Yunhui Jang Jaehyung Kim Sungsoo Ahn LRM AI4CE 33 1 0 08 Oct 2024
Dumpling GNN: Hybrid GNN Enables Better ADC Payload Activity Prediction Based on Chemical Structure Shengjie Xu Lingxi Xie 23 0 0 23 Sep 2024
Geometry Informed Tokenization of Molecules for Language Model Generation Xiner Li Limei Wang Youzhi Luo Carl N. Edwards Shurui Gui Yuchao Lin Heng Ji Shuiwang Ji 34 6 0 19 Aug 2024
Instruction-Based Molecular Graph Generation with Unified Text-Graph Diffusion Model Yuran Xiang Haiteng Zhao Chang Ma Zhi-Hong Deng 26 0 0 19 Aug 2024
HIGHT: Hierarchical Graph Tokenization for Graph-Language Alignment Yongqiang Chen Quanming Yao Juzheng Zhang James Cheng Yatao Bian 35 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 42 7 0 18 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 46 2 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 Sayan Ranu 40 2 0 03 Jun 2024
GLaD: Synergizing Molecular Graphs and Language Descriptors for Enhanced Power Conversion Efficiency Prediction in Organic Photovoltaic Devices Thao Nguyen Tiara Torres-Flores Changhyun Hwang Carl N. Edwards Ying Diao Heng Ji 32 0 0 23 May 2024
ALMol: Aligned Language-Molecule Translation LLMs through Offline Preference Contrastive Optimisation Dimitris Gkoumas 39 0 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 29 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 16 0 0 20 Mar 2024
MoleculeQA: A Dataset to Evaluate Factual Accuracy in Molecular Comprehension Xingyu Lu He Cao Zijing Liu Shengyuan Bai Leqing Chen Yuan Yao Hai-Tao Zheng Yu Li HILM 19 7 0 13 Mar 2024
Bridging Text and Molecule: A Survey on Multimodal Frameworks for Molecule Yi Xiao Xiangxin Zhou Qiang Liu Liang Wang AI4CE 32 3 0 07 Mar 2024
Large Language Models are In-Context Molecule Learners Jiatong Li Wei Liu Zhihao Ding Wenqi Fan Yuqiang Li Qing Li 40 5 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 51 19 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 85 11 0 28 Feb 2024
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning Qizhi Pei Lijun Wu Kaiyuan Gao Xiaozhuan Liang Yin Fang Jinhua Zhu Shufang Xie Tao Qin Rui Yan AI4CE 51 30 0 27 Feb 2024
L+M-24: Building a Dataset for Language + Molecules @ ACL 2024 Carl N. Edwards Qingyun Wang Lawrence Zhao Heng Ji 40 17 0 22 Feb 2024
ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback Henry W Sprueill Carl N. Edwards Khushbu Agarwal Mariefel V. Olarte Udishnu Sanyal Conrad Johnston Hongbin Liu Heng Ji Sutanay Choudhury LRM 33 7 0 15 Feb 2024
Leak, Cheat, Repeat: Data Contamination and Evaluation Malpractices in Closed-Source LLMs Simone Balloccu Patrícia Schmidtová Mateusz Lango Ondrej Dusek SILM ELM PILM 21 156 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 23 8 0 06 Feb 2024
From Words to Molecules: A Survey of Large Language Models in Chemistry Chang Liao Yemin Yu Yu Mei Ying Wei 30 16 0 02 Feb 2024
MolTailor: Tailoring Chemical Molecular Representation to Specific Tasks via Text Prompts Haoqiang Guo Sendong Zhao Hao Wang Yanrui Du Bing Qin AI4CE 21 8 0 21 Jan 2024
Large Language Models on Graphs: A Comprehensive Survey Bowen Jin Gang Liu Chi Han Meng Jiang Heng Ji Jiawei Han AI4CE 28 137 0 05 Dec 2023
InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug Discovery He Cao Zijing Liu Xingyu Lu Yuan Yao Yu Li 27 58 0 27 Nov 2023
Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst Design Henry W Sprueill Carl N. Edwards Mariefel V. Olarte Udishnu Sanyal Heng Ji Sutanay Choudhury LRM 34 10 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 Jindong Wang Xing Xie Zheng-Wei Zhang Yue Zhang HILM KELM 51 184 0 11 Oct 2023
BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations Qizhi Pei Wei Zhang Jinhua Zhu Kehan Wu Kaiyuan Gao Lijun Wu Yingce Xia Rui Yan 33 61 0 11 Oct 2023
From Artificially Real to Real: Leveraging Pseudo Data from Large Language Models for Low-Resource Molecule Discovery Yuhan Chen Nuwa Xi Yanrui Du Hao Wang Jianyu Chen Sendong Zhao Bing Qin 27 10 0 11 Sep 2023
Examining User-Friendly and Open-Sourced Large GPT Models: A Survey on Language, Multimodal, and Scientific GPT Models Kaiyuan Gao Su He Zhenyu He Jiacheng Lin Qizhi Pei Jie Shao Wei Zhang LM&MA SyDa 30 4 0 27 Aug 2023
What can Large Language Models do in chemistry? A comprehensive benchmark on eight tasks Taicheng Guo Kehan Guo B. Nan Zhengwen Liang Zhichun Guo Nitesh V. Chawla Olaf Wiest Xiangliang Zhang ELM 47 127 0 27 May 2023
Computational modeling of semantic change Nina Tahmasebi Haim Dubossarsky 34 6 0 13 Apr 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 44 107 0 12 Sep 2022
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 126 302 0 07 Oct 2021
Making Pre-trained Language Models Better Few-shot Learners Tianyu Gao Adam Fisch Danqi Chen 241 1,919 0 31 Dec 2020
MoleculeNet: A Benchmark for Molecular Machine Learning Zhenqin Wu Bharath Ramsundar Evan N. Feinberg Joseph Gomes C. Geniesse Aneesh S. Pappu K. Leswing Vijay S. Pande OOD 181 1,778 0 02 Mar 2017