Pre-training Molecular Graph Representation with 3D Geometry

7 October 2021

Jian Tang

Papers citing "Pre-training Molecular Graph Representation with 3D Geometry"

50 / 169 papers shown

Title
Could Chemical LLMs benefit from Message Passing Jiaqing Xie Ziheng Chi 35 0 0 14 May 2024
SubGDiff: A Subgraph Diffusion Model to Improve Molecular Representation Learning Jiying Zhang Zijing Liu Yu Wang Yu Li DiffM 45 1 0 09 May 2024
Delayed Bottlenecking: Alleviating Forgetting in Pre-trained Graph Neural Networks Zhe Zhao Pengkun Wang Xu Wang Haibin Wen Xiaolong Xie Zhengyang Zhou Qingfu Zhang Yang Wang AI4CE CLL 20 0 0 23 Apr 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
On the Scalability of GNNs for Molecular Graphs Maciej Sypetkowski Frederik Wenkel Farimah Poursafaei Nia Dickson Karush Suri Philip Fradkin Dominique Beaini GNN AI4CE 36 11 0 17 Apr 2024
Harnessing the Power of Large Language Model for Uncertainty Aware Graph Processing Zhenyu Qian Yiming Qian Yuting Song Fei Gao Hai Jin Chen Yu Xia Xie 43 0 0 31 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
ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling Kangjie Zheng Siyu Long Tianyu Lu Junwei Yang Xinyu Dai Ming Zhang Zaiqing Nie Wei-Ying Ma Hao Zhou 41 5 0 05 Mar 2024
Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks Tianyu Fan Lirong Wu Yufei Huang Haitao Lin Cheng Tan Zhangyang Gao Stan Z. Li 34 3 0 03 Mar 2024
A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications Jiaqi Han Jiacheng Cen Liming Wu Zongzhao Li Xiangzhe Kong ... Zhewei Wei Deli Zhao Yu Rong Wenbing Huang Wenbing Huang AI4CE 34 20 0 01 Mar 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
Pretraining Strategy for Neural Potentials Zehua Zhang Zijie Li A. Farimani AI4CE 44 0 0 24 Feb 2024
Contextual Molecule Representation Learning from Chemical Reaction Knowledge Han Tang Shikun Feng Bicheng Lin Yuyan Ni Jingjing Liu Wei-Ying Ma Yanyan Lan 27 2 0 21 Feb 2024
Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic Survey Taojie Kuang Pengfei Liu Zhixiang Ren AI4CE 47 1 0 11 Feb 2024
Triplet Interaction Improves Graph Transformers: Accurate Molecular Graph Learning with Triplet Graph Transformers Md Shamim Hussain Mohammed J. Zaki D. Subramanian ViT 33 5 0 07 Feb 2024
A Graph is Worth $K$ Words: Euclideanizing Graph using Pure Transformer Zhangyang Gao Daize Dong Cheng Tan Jun-Xiong Xia Bozhen Hu Stan Z. Li 46 6 0 04 Feb 2024
Structure-Aware E(3)-Invariant Molecular Conformer Aggregation Networks D. M. Nguyen Nina Lukashina Tai Nguyen An T. Le TrungTin Nguyen Nhat Ho Jan Peters Daniel Sonntag Viktor Zaverkin Mathias Niepert 33 5 0 03 Feb 2024
Graph Multi-Similarity Learning for Molecular Property Prediction Hao Xu Zhengyang Zhou Pengyu Hong 38 1 0 31 Jan 2024
Unsupervised Discovery of Steerable Factors When Graph Deep Generative Models Are Entangled Shengchao Liu Chengpeng Wang Jiarui Lu Weili Nie Hanchen Wang Zhuoxinran Li Bolei Zhou Jian Tang 35 3 0 29 Jan 2024
Enhancing Molecular Property Prediction with Auxiliary Learning and Task-Specific Adaptation Vishal Dey Xia Ning AAML AI4CE 21 0 0 29 Jan 2024
Towards 3D Molecule-Text Interpretation in Language Models Sihang Li Zhiyuan Liu Yancheng Luo Xiang Wang Xiangnan He Kenji Kawaguchi Tat-Seng Chua Qi Tian AI4CE 33 42 0 25 Jan 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
PepHarmony: A Multi-View Contrastive Learning Framework for Integrated Sequence and Structure-Based Peptide Encoding Ruochi Zhang Haoran Wu Chang Liu Hua-Wang Li Yuqian Wu ... Yifan Wang Yifan Deng Jiahui Chen Fengfeng Zhou Xin Gao AI4TS 37 2 0 21 Jan 2024
Multi-Modal Representation Learning for Molecular Property Prediction: Sequence, Graph, Geometry Zeyu Wang Tianyi Jiang Jinhuan Wang Qi Xuan AI4CE 27 8 0 07 Jan 2024
Pre-training of Molecular GNNs via Conditional Boltzmann Generator Daiki Koge N. Ono Shigehiko Kanaya AI4CE 14 0 0 20 Dec 2023
Molecule Joint Auto-Encoding: Trajectory Pretraining with 2D and 3D Diffusion Weitao Du Jiujiu Chen Xuecang Zhang Zhiming Ma Shengchao Liu DiffM 27 9 0 06 Dec 2023
Improving Self-supervised Molecular Representation Learning using Persistent Homology Yuankai Luo Lei Shi Veronika Thost SSL 34 8 0 29 Nov 2023
MultiModal-Learning for Predicting Molecular Properties: A Framework Based on Image and Graph Structures Zhuoyuan Wang Jiacong Mi Shan Lu Jieyue He 19 2 0 28 Nov 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 25 58 0 27 Nov 2023
Neural Atoms: Propagating Long-range Interaction in Molecular Graphs through Efficient Communication Channel Xuan Li Zhanke Zhou Jiangchao Yao Yu Rong Lu Zhang Bo Han 37 3 0 02 Nov 2023
From Molecules to Materials: Pre-training Large Generalizable Models for Atomic Property Prediction Nima Shoghi Adeesh Kolluru John R. Kitchin Zachary W. Ulissi C. L. Zitnick Brandon M. Wood AI4CE 24 32 0 25 Oct 2023
Rethinking Tokenizer and Decoder in Masked Graph Modeling for Molecules Zhiyuan Liu Yaorui Shi An Zhang Enzhi Zhang Kenji Kawaguchi Xiang Wang Tat-Seng Chua AI4CE 36 36 0 23 Oct 2023
UniMAP: Universal SMILES-Graph Representation Learning Shikun Feng Lixin Yang Wei-Ying Ma Yanyan Lan OffRL 16 6 0 22 Oct 2023
Improving Molecular Properties Prediction Through Latent Space Fusion Eduardo Soares Akihiro Kishimoto E. V. Brazil Seiji Takeda Hiroshi Kajino Renato F. G. Cerqueira BDL AI4CE 18 2 0 20 Oct 2023
Large Language Models for Scientific Synthesis, Inference and Explanation Yizhen Zheng Huan Yee Koh Jiaxin Ju A. T. Nguyen Lauren T. May Geoffrey I. Webb Shirui Pan ELM 51 31 0 12 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 30 61 0 11 Oct 2023
Fragment-based Pretraining and Finetuning on Molecular Graphs Kha-Dinh Luong Ambuj Singh AI4CE 25 12 0 05 Oct 2023
Augment to Interpret: Unsupervised and Inherently Interpretable Graph Embeddings Gregory Scafarto Madalina Ciortan Simon Tihon Quentin Ferre 17 2 0 28 Sep 2023
MHG-GNN: Combination of Molecular Hypergraph Grammar with Graph Neural Network Akihiro Kishimoto Hiroshi Kajino Masataka Hirose Junta Fuchiwaki Indra Priyadarsini Lisa Hamada Hajime Shinohara D. Nakano Seiji Takeda AI4CE 31 4 0 28 Sep 2023
3D-Mol: A Novel Contrastive Learning Framework for Molecular Property Prediction with 3D Information Taojie Kuang Yiming Ren Zhixiang Ren 27 7 0 28 Sep 2023
Uncovering Neural Scaling Laws in Molecular Representation Learning Dingshuo Chen Yanqiao Zhu Jieyu Zhang Yuanqi Du Zhixun Li Qiang Liu Shu Wu Liang Wang 32 16 0 15 Sep 2023
3D Denoisers are Good 2D Teachers: Molecular Pretraining via Denoising and Cross-Modal Distillation Sungjun Cho Dae-Woong Jeong Sung Moon Ko Jinwoo Kim Sehui Han Seunghoon Hong Honglak Lee Moontae Lee AI4CE DiffM 30 1 0 08 Sep 2023
Geometry-aware Line Graph Transformer Pre-training for Molecular Property Prediction Peizhen Bai Xianyuan Liu Haiping Lu ViT AI4CE 34 2 0 01 Sep 2023
On Data Imbalance in Molecular Property Prediction with Pre-training Limin Wang Masatoshi Hanai Toyotaro Suzumura Shun Takashige Kenjiro Taura AI4CE 30 0 0 17 Aug 2023
Search to Fine-tune Pre-trained Graph Neural Networks for Graph-level Tasks Zhili Wang Shimin Di Lei Chen Xiaofang Zhou 43 10 0 14 Aug 2023
GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text Peng Liu Yiming Ren Jun Tao Zhixiang Ren AI4CE 30 79 0 14 Aug 2023
Fractional Denoising for 3D Molecular Pre-training Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 47 25 0 20 Jul 2023
Can Large Language Models Empower Molecular Property Prediction? Chao Qian Huayi Tang Zhi-Jiang Yang Hongsi Liang Y. Liu AI4CE 36 38 0 14 Jul 2023
Artificial Intelligence for Drug Discovery: Are We There Yet? C. Hasselgren Tudor I. Oprea 13 62 0 13 Jul 2023
Multimodal Molecular Pretraining via Modality Blending Qiying Yu Yudi Zhang Yuyan Ni Shi Feng Yanyan Lan Hao Zhou Jingjing Liu 21 13 0 12 Jul 2023