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
Multi-Modal Molecular Representation Learning via Structure Awareness Rong Yin Ruyue Liu Xiaoshuai Hao Xingrui Zhou Y. Liu Can Ma Weiping Wang 29 0 0 09 May 2025
Unified Molecule Generation and Property Prediction Adam Izdebski Jan Olszewski Pankhil Gawade Krzysztof Koras Serra Korkmaz Valentin Rauscher Jakub M. Tomczak E. Szczurek 31 0 0 23 Apr 2025
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 30 0 0 10 Apr 2025
NaFM: Pre-training a Foundation Model for Small-Molecule Natural Products Yuheng Ding Yusong Wang Bo Qiang Jie Yu Qi Li Yiran Zhou Zhenmin Liu 153 0 0 22 Mar 2025
Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling Shuqi Lu Xiaohong Ji Bohang Zhang Lin Yao Siyuan Liu Zhifeng Gao Linfeng Zhang Guolin Ke AI4CE 46 1 0 13 Mar 2025
GraphT5: Unified Molecular Graph-Language Modeling via Multi-Modal Cross-Token Attention Sangyeup Kim Nayeon Kim Yinhua Piao Sun Kim 36 0 0 07 Mar 2025
A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery Yiheng Zhu Mingyang Li Junlong Liu Kun Fu J. Wu Q. Li Mingze Yin Jieping Ye Jian Wu Z. Wang 60 0 0 06 Mar 2025
Pre-training Graph Neural Networks with Structural Fingerprints for Materials Discovery Shuyi Jia Shitij Govil Manav Ramprasad Victor Fung AI4CE 64 1 0 03 Mar 2025
MV-CLAM: Multi-View Molecular Interpretation with Cross-Modal Projection via Language Model Sumin Ha Jun Hyeong Kim Yinhua Piao Sun Kim 44 0 0 23 Feb 2025
RAG-Enhanced Collaborative LLM Agents for Drug Discovery Namkyeong Lee Edward De Brouwer Ehsan Hajiramezanali Tommaso Biancalani Chanyoung Park Gabriele Scalia 36 0 0 22 Feb 2025
MolSpectra: Pre-training 3D Molecular Representation with Multi-modal Energy Spectra Liang Wang Shaozhen Liu Yu Rong Deli Zhao Qiang Liu Shu Wu Liang Wang MedIm 66 2 0 22 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 100 3 0 18 Feb 2025
Membership Inference Risks in Quantized Models: A Theoretical and Empirical Study Eric Aubinais Philippe Formont Pablo Piantanida Elisabeth Gassiat 38 0 0 10 Feb 2025
Enhancing Graph Self-Supervised Learning with Graph Interplay Xinjian Zhao Wei Pang Xiangru Jian Yaoyao Xu Chaolong Ying Tianshu Yu 45 0 0 17 Jan 2025
Graph Generative Pre-trained Transformer Xiaohui Chen Yinkai Wang Jiaxing He Yuanqi Du S. Hassoun Xiaolin Xu Li Liu 41 1 0 03 Jan 2025
MOL-Mamba: Enhancing Molecular Representation with Structural & Electronic Insights Jingjing Hu D. Guo Zhan Si Deguang Liu Yunfeng Diao J. Zhang Jinxing Zhou Meng Wang Mamba 98 1 0 21 Dec 2024
Pre-training Graph Neural Networks on Molecules by Using Subgraph-Conditioned Graph Information Bottleneck Van Thuy Hoang O-Joun Lee AI4CE 80 1 0 20 Dec 2024
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 70 1 0 07 Dec 2024
3D Interaction Geometric Pre-training for Molecular Relational Learning Namkyeong Lee Yunhak Oh Heewoong Noh Gyoung S. Na Minkai Xu Hanchen Wang Tianfan Fu Chanyoung Park AI4CE 69 0 0 04 Dec 2024
MolParser: End-to-end Visual Recognition of Molecule Structures in the Wild Xi Fang Jiankun Wang X. Cai Shangqian Chen Shuwen Yang Lin Yao Linfeng Zhang Guolin Ke Linfeng Zhang Guolin Ke 50 1 0 17 Nov 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 46 0 0 07 Nov 2024
Two-Stage Pretraining for Molecular Property Prediction in the Wild Kevin Tirta Wijaya Minghao Guo Michael Sun Hans-Peter Seidel Wojciech Matusik Vahid Babaei AI4CE 27 0 0 05 Nov 2024
Exploring Consistency in Graph Representations:from Graph Kernels to Graph Neural Networks Xuyuan Liu Yinghao Cai Qihui Yang Yujun Yan 31 0 0 31 Oct 2024
Multi-view biomedical foundation models for molecule-target and property prediction Parthasarathy Suryanarayanan Yunguang Qiu Shreyans Sethi Diwakar Mahajan Hongyang Li ... Bum Chul Kwon Pablo Meyer Feixiong Cheng Jianying Hu Joseph A. Morrone AI4CE 33 0 0 25 Oct 2024
FragNet: A Graph Neural Network for Molecular Property Prediction with Four Layers of Interpretability G. Panapitiya Peiyuan Gao C Mark Maupin Emily Saldanha AI4CE 33 1 0 16 Oct 2024
Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction Yasir Ghunaim Robert Hoehndorf AI4CE 19 0 0 15 Oct 2024
KA-GNN: Kolmogorov-Arnold Graph Neural Networks for Molecular Property Prediction Longlong Li Yipeng Zhang Guanghui Wang Kelin Xia 29 3 0 15 Oct 2024
UniGEM: A Unified Approach to Generation and Property Prediction for Molecules Shikun Feng Yuyan Ni Yan Lu Zhi-Ming Ma Wei-Ying Ma Yanyan Lan 38 5 0 14 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 31 6 0 04 Oct 2024
FARM: Functional Group-Aware Representations for Small Molecules Thao Nguyen Kuan-Hao Huang Ge Liu Martin Burke Ying Diao Heng Ji 20 0 0 02 Oct 2024
Polyatomic Complexes: A topologically-informed learning representation for atomistic systems Rahul Khorana Marcus Noack Jin Qian AI4CE 26 0 0 23 Sep 2024
Learning to Model Graph Structural Information on MLPs via Graph Structure Self-Contrasting Lirong Wu Haitao Lin Guojiang Zhao Cheng Tan Stan Z. Li 28 0 0 09 Sep 2024
MaskMol: Knowledge-guided Molecular Image Pre-Training Framework for Activity Cliffs Zhixiang Cheng Hongxin Xiang Pengsen Ma Li Zeng Xin Jin ... Yang Deng Bosheng Song Xinxin Feng Changhui Deng Xiangxiang Zeng 28 0 0 02 Sep 2024
Cross-Modal Learning for Chemistry Property Prediction: Large Language Models Meet Graph Machine Learning Sakhinana Sagar Srinivas Venkataramana Runkana AI4CE 33 1 0 27 Aug 2024
Molecular Graph Representation Learning Integrating Large Language Models with Domain-specific Small Models Tianyu Zhang Yuxiang Ren Chengbin Hou Hairong Lv Xuegong Zhang AI4CE 34 1 0 19 Aug 2024
Advancements in Molecular Property Prediction: A Survey of Single and Multimodal Approaches Tanya Liyaqat T. Ahmad Chandni Saxena 32 2 0 18 Aug 2024
UniMoT: Unified Molecule-Text Language Model with Discrete Token Representation Jiayuan Zhu Yunli Qi Yongqiang Chen Quanming Yao 29 7 0 01 Aug 2024
A Large Encoder-Decoder Family of Foundation Models For Chemical Language Eduardo Soares Victor Shirasuna E. V. Brazil Renato F. G. Cerqueira Dmitry Zubarev Kristin Schmidt AI4CE 27 7 0 24 Jul 2024
Molecular Topological Profile (MOLTOP) -- Simple and Strong Baseline for Molecular Graph Classification Jakub Adamczyk Wojciech Czech 42 2 0 16 Jul 2024
Pre-training with Fractional Denoising to Enhance Molecular Property Prediction Yuyan Ni Shikun Feng Xin Hong Yuancheng Sun Wei-Ying Ma Zhiming Ma Qiwei Ye Yanyan Lan AI4CE 36 10 0 14 Jul 2024
MolTRES: Improving Chemical Language Representation Learning for Molecular Property Prediction Jun-Hyung Park Yeachan Kim Mingyu Lee Hyuntae Park SangKeun Lee 30 0 0 09 Jul 2024
Uni-Mol2: Exploring Molecular Pretraining Model at Scale Xiaohong Ji Zhen Wang Zhifeng Gao Hang Zheng Linfeng Zhang Guolin Ke Weinan E AI4CE 38 6 0 21 Jun 2024
HIGHT: Hierarchical Graph Tokenization for Graph-Language Alignment Yongqiang Chen Quanming Yao Juzheng Zhang James Cheng Yatao Bian 32 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 33 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 34 6 0 18 Jun 2024
MoleculeCLA: Rethinking Molecular Benchmark via Computational Ligand-Target Binding Analysis Shikun Feng Jiaxin Zheng Yinjun Jia Yanwen Huang Fengfeng Zhou Wei-Ying Ma Yanyan Lan 32 0 0 13 Jun 2024
Medication Recommendation via Dual Molecular Modalities and Multi-Substructure Enhancement Shizhuo Mu Shunpan Liang Xiang Li 32 0 0 30 May 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 24 0 0 23 May 2024
UniCorn: A Unified Contrastive Learning Approach for Multi-view Molecular Representation Learning Shikun Feng Yuyan Ni Minghao Li Yanwen Huang Zhiming Ma Wei-Ying Ma Yanyan Lan SSL 41 7 0 15 May 2024