Motif-based Graph Self-Supervised Learning for Molecular Property Prediction

3 October 2021

Qi Liu

Papers citing "Motif-based Graph Self-Supervised Learning for Molecular Property Prediction"

50 / 125 papers shown

Title
Improving Self-supervised Molecular Representation Learning using Persistent Homology Yuankai Luo Lei Shi Veronika Thost SSL 34 8 0 29 Nov 2023
GlycoNMR: Dataset and benchmarks for NMR chemical shift prediction of carbohydrates with graph neural networks Zizhang Chen R. P. Badman Lachele Foley Robert Woods Pengyu Hong 51 0 0 28 Nov 2023
MultiModal-Learning for Predicting Molecular Properties: A Framework Based on Image and Graph Structures Zhuoyuan Wang Jiacong Mi Shan Lu Jieyue He 27 2 0 28 Nov 2023
Generalized Graph Prompt: Toward a Unification of Pre-Training and Downstream Tasks on Graphs Xingtong Yu Zhenghao Liu Yuan Fang Zemin Liu Sihong Chen Xinming Zhang 43 24 0 26 Nov 2023
Advancing Drug Discovery with Enhanced Chemical Understanding via Asymmetric Contrastive Multimodal Learning Hao Xu Yifei Wang Yunrui Li Pengyu Hong Pengyu Hong 33 3 0 11 Nov 2023
Protein-ligand binding representation learning from fine-grained interactions Shikun Feng Minghao Li Yinjun Jia Wei-Ying Ma Yanyan Lan SSL AI4CE 29 8 0 09 Nov 2023
Identifying Semantic Component for Robust Molecular Property Prediction Zijian Li Zunhong Xu Ruichu Cai Zhenhui Yang Yuguang Yan Zhifeng Hao Guan-Hong Chen Kun Zhang 25 9 0 08 Nov 2023
GPT-ST: Generative Pre-Training of Spatio-Temporal Graph Neural Networks Zhonghang Li Lianghao Xia Yong-mei Xu Chao Huang AI4TS AI4CE 93 25 0 07 Nov 2023
Better with Less: A Data-Active Perspective on Pre-Training Graph Neural Networks Jiarong Xu Renhong Huang Xin Jiang Yuxuan Cao Carl Yang Chunping Wang Yang Yang AI4CE 36 14 0 02 Nov 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 39 36 0 23 Oct 2023
UniMAP: Universal SMILES-Graph Representation Learning Shikun Feng Lixin Yang Wei-Ying Ma Yanyan Lan OffRL 19 6 0 22 Oct 2023
SGOOD: Substructure-enhanced Graph-Level Out-of-Distribution Detection Zhihao Ding Jieming Shi Shiqi Shen Xuequn Shang Jiannong Cao Zhipeng Wang Zhi Gong OODD OOD 42 4 0 16 Oct 2023
AdaptSSR: Pre-training User Model with Augmentation-Adaptive Self-Supervised Ranking Yang Yu Qi Liu Kai Zhang Yuren Zhang Chao Song Min Hou Yuqing Yuan Zhihao Ye Zaixin Zhang Sanshi Lei Yu 35 2 0 15 Oct 2023
Atom-Motif Contrastive Transformer for Molecular Property Prediction Wentao Yu Shuo Chen Chen Gong Gang Niu Masashi Sugiyama ViT 45 2 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 36 62 0 11 Oct 2023
Fragment-based Pretraining and Finetuning on Molecular Graphs Kha-Dinh Luong Ambuj Singh AI4CE 35 12 0 05 Oct 2023
GraphPatcher: Mitigating Degree Bias for Graph Neural Networks via Test-time Augmentation Mingxuan Ju Tong Zhao Wenhao Yu Neil Shah Yanfang Ye 31 13 0 01 Oct 2023
Deep Prompt Tuning for Graph Transformers Reza Shirkavand Heng-Chiao Huang 23 7 0 18 Sep 2023
Motif-aware Attribute Masking for Molecular Graph Pre-training Eric Inae Gang Liu Meng Jiang AI4CE 48 14 0 08 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 43 1 0 08 Sep 2023
Hierarchical Grammar-Induced Geometry for Data-Efficient Molecular Property Prediction Minghao Guo Veronika Thost Samuel W Song A. Balachandran Payel Das Jie Chen Wojciech Matusik AI4CE 34 0 0 04 Sep 2023
Geometry-aware Line Graph Transformer Pre-training for Molecular Property Prediction Peizhen Bai Xianyuan Liu Haiping Lu ViT AI4CE 41 2 0 01 Sep 2023
Search to Fine-tune Pre-trained Graph Neural Networks for Graph-level Tasks Zhili Wang Shimin Di Lei Chen Xiaofang Zhou 50 10 0 14 Aug 2023
Fractional Denoising for 3D Molecular Pre-training Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 52 25 0 20 Jul 2023
DiffDTM: A conditional structure-free framework for bioactive molecules generation targeted for dual proteins Lei Huang Zheng Yuan Huihui Yan Rong Sheng Linjing Liu ... Nanjun Chen Fei Huang Songfang Huang Ka-Chun Wong Yaoyun Zhang 30 0 0 24 Jun 2023
Multi-task Bioassay Pre-training for Protein-ligand Binding Affinity Prediction Jiaxian Yan Zhaofeng Ye Ziyi Yang Chengqiang Lu Shengyu Zhang Qi Liu J. Qiu 45 11 0 08 Jun 2023
Bi-level Contrastive Learning for Knowledge-Enhanced Molecule Representations Pengcheng Jiang Cao Xiao Tianfan Fu Jimeng Sun 50 3 0 02 Jun 2023
There is more to graphs than meets the eye: Learning universal features with self-supervision L. Das Sai Munikoti M. Halappanavar SSL OOD 33 1 0 31 May 2023
GIMLET: A Unified Graph-Text Model for Instruction-Based Molecule Zero-Shot Learning Haiteng Zhao Shengchao Liu Chang Ma Hannan Xu Jie Fu Zhihong Deng Lingpeng Kong Qi Liu 31 61 0 28 May 2023
Learning Subpocket Prototypes for Generalizable Structure-based Drug Design Zaixin Zhang Qi Liu 40 34 0 22 May 2023
Atomic and Subgraph-aware Bilateral Aggregation for Molecular Representation Learning Jiahao Chen Yurou Liu Jiangmeng Li Bing-Huang Su Jirong Wen 29 0 0 22 May 2023
MolXPT: Wrapping Molecules with Text for Generative Pre-training Zequn Liu Wei Zhang Yingce Xia Lijun Wu Shufang Xie Tao Qin M. Zhang Tie-Yan Liu 28 67 0 18 May 2023
G-Adapter: Towards Structure-Aware Parameter-Efficient Transfer Learning for Graph Transformer Networks Anchun Gui Jinqiang Ye Han Xiao 27 19 0 17 May 2023
Capturing Fine-grained Semantics in Contrastive Graph Representation Learning Lin Shu Chuan Chen Zibin Zheng 21 0 0 23 Apr 2023
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design Zaixin Zhang Qi Liu Cheekong Lee Chang-Yu Hsieh Enhong Chen 29 18 0 12 Apr 2023
A Comprehensive Survey on Deep Graph Representation Learning Wei Ju Zheng Fang Yiyang Gu Zequn Liu Qingqing Long ... Jingyang Yuan Yusheng Zhao Yifan Wang Xiao Luo Ming Zhang GNN AI4TS 72 141 0 11 Apr 2023
InstructBio: A Large-scale Semi-supervised Learning Paradigm for Biochemical Problems Fang Wu Huiling Qin Siyuan Li Stan Z. Li Xianyuan Zhan Jinbo Xu 24 5 0 08 Apr 2023
When to Pre-Train Graph Neural Networks? From Data Generation Perspective! Yu Cao Jiarong Xu Carl Yang Jiaan Wang Yunchao Zhang Chunping Wang Lei Chen Yang Yang 18 16 0 29 Mar 2023
Data-Centric Learning from Unlabeled Graphs with Diffusion Model Gang Liu Eric Inae Tong Zhao Jiaxin Xu Te Luo Meng Jiang DiffM 31 23 0 17 Mar 2023
Backdoor Defense via Deconfounded Representation Learning Zaixin Zhang Qi Liu Zhicai Wang Zepu Lu Qingyong Hu AAML 57 40 0 13 Mar 2023
Denoise Pretraining on Nonequilibrium Molecules for Accurate and Transferable Neural Potentials Yuyang Wang Chang Xu Zijie Li A. Farimani AAML AI4CE 29 21 0 03 Mar 2023
De Novo Molecular Generation via Connection-aware Motif Mining Zijie Geng Shufang Xie Yingce Xia Lijun Wu Tao Qin Jie Wang Yongdong Zhang Feng Wu Tie-Yan Liu 27 32 0 02 Feb 2023
t-SMILES: A Scalable Fragment-based Molecular Representation Framework for De Novo Molecule Generation Juan-Ni Wu Tong Wang Yue (Eleanor) Chen Li-Juan Tang Hai-Long Wu Ru-Qin Yu 27 0 0 04 Jan 2023
MolCPT: Molecule Continuous Prompt Tuning to Generalize Molecular Representation Learning Cameron Diao Kaixiong Zhou Zirui Liu Xiao Huang Xia Hu 36 14 0 20 Dec 2022
Latent Graph Inference using Product Manifolds Haitz Sáez de Ocáriz Borde Anees Kazi Federico Barbero Pietro Lio BDL 42 19 0 26 Nov 2022
A Systematic Survey of Chemical Pre-trained Models Jun Xia Yanqiao Zhu Yuanqi Du Stan Z.Li AI4CE 58 51 0 29 Oct 2022
Substructure-Atom Cross Attention for Molecular Representation Learning Jiye G. Kim Seungbeom Lee Dongwoo Kim Sungsoo Ahn Jaesik Park 19 4 0 15 Oct 2022
Hierarchical Graph Transformer with Adaptive Node Sampling Zaixin Zhang Qi Liu Qingyong Hu Cheekong Lee 78 82 0 08 Oct 2022
Multi-task Self-supervised Graph Neural Networks Enable Stronger Task Generalization Mingxuan Ju Tong Zhao Qianlong Wen Wenhao Yu Neil Shah Yanfang Ye Chuxu Zhang SSL 21 34 0 05 Oct 2022
Universal Prompt Tuning for Graph Neural Networks Taoran Fang Yunchao Zhang Yang Yang Chunping Wang Lei Chen 36 49 0 30 Sep 2022