Molecule Attention Transformer

19 February 2020

Stanislaw Jastrzebski

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Papers citing "Molecule Attention Transformer"

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Title
A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery Yiheng Zhu Mingyang Li Junlong Liu Kun Fu Jiangxu Wu Q. Li Mingze Yin Jieping Ye Jian Wu Zhi Wang 62 0 0 06 Mar 2025
A Survey of Graph Transformers: Architectures, Theories and Applications Chaohao Yuan Kangfei Zhao Ercan Engin Kuruoglu Liang Wang Tingyang Xu Wenbing Huang Deli Zhao Hong Cheng Yu Rong 57 4 0 23 Feb 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
GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers Guoguo Ai Guansong Pang Hezhe Qiao Yuan Gao Hui Yan 67 0 0 26 Nov 2024
Contextual Representation Anchor Network to Alleviate Selection Bias in Few-Shot Drug Discovery Ruifeng Li Wei Liu Xiangxin Zhou Mingqian Li Qiang Zhang Hongyang Chen Xuemin Lin 44 0 0 28 Oct 2024
KA-GNN: Kolmogorov-Arnold Graph Neural Networks for Molecular Property Prediction Longlong Li Yipeng Zhang Guanghui Wang Kelin Xia 31 3 0 15 Oct 2024
REBIND: Enhancing ground-state molecular conformation via force-based graph rewiring Taewon Kim Hyunjin Seo Sungsoo Ahn Eunho Yang AI4CE 32 1 0 04 Oct 2024
EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics Chenqing Hua Yong Liu Dinghuai Zhang Odin Zhang Sitao Luan Kevin K. Yang Guy Wolf Doina Precup Shuangjia Zheng 33 5 0 01 Oct 2024
Reactzyme: A Benchmark for Enzyme-Reaction Prediction Chenqing Hua Bozitao Zhong Sitao Luan Liang Hong Guy Wolf Doina Precup Shuangjia Zheng 39 5 0 24 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
SPIN: SE(3)-Invariant Physics Informed Network for Binding Affinity Prediction Seungyeon Choi Sangmin Seo Sanghyun Park 32 0 0 10 Jul 2024
Benchmark on Drug Target Interaction Modeling from a Structure Perspective Xinnan Zhang Jialin Wu Junyi Xie Tianlong Chen Kaixiong Zhou 23 0 0 04 Jul 2024
Knowledge-Aware Parsimony Learning: A Perspective from Relational Graphs Quanming Yao Yongqi Zhang Yaqing Wang Nan Yin James Kwok Qiang Yang 31 0 0 29 Jun 2024
A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery Yu Zhang Xiusi Chen Bowen Jin Sheng Wang Shuiwang Ji Wei Wang Jiawei Han 44 27 0 16 Jun 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
Molecular Property Prediction Based on Graph Structure Learning Bangyi Zhao Weixia Xu Jihong Guan Shuigeng Zhou 19 7 0 28 Dec 2023
A Universal Framework for Accurate and Efficient Geometric Deep Learning of Molecular Systems Shuo-feng Zhang Yang Liu Lei Xie AI4CE GNN PINN 31 10 0 19 Nov 2023
Natural Language Processing for Financial Regulation I. Achitouv Dragos Gorduza Antoine Jacquier AILaw 15 2 0 14 Nov 2023
In-Context Learning for Few-Shot Molecular Property Prediction Christopher Fifty J. Leskovec Sebastian Thrun 36 5 0 13 Oct 2023
Atom-Motif Contrastive Transformer for Molecular Property Prediction Wentao Yu Shuo Chen Chen Gong Gang Niu Masashi Sugiyama ViT 39 2 0 11 Oct 2023
PACIA: Parameter-Efficient Adapter for Few-Shot Molecular Property Prediction Shiguang Wu Yaqing Wang Quanming Yao 19 4 0 01 Oct 2023
3D-Mol: A Novel Contrastive Learning Framework for Molecular Property Prediction with 3D Information Taojie Kuang Yiming Ren Zhixiang Ren 25 7 0 28 Sep 2023
CTAGE: Curvature-Based Topology-Aware Graph Embedding for Learning Molecular Representations Yili Chen Zhengyu Li Zheng Wan Hui Yu Xian Wei 23 0 0 25 Jul 2023
ChiENN: Embracing Molecular Chirality with Graph Neural Networks Piotr Gaiñski Michał Koziarski Jacek Tabor Marek Śmieja GNN 34 3 0 05 Jul 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 35 11 0 08 Jun 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 23 60 0 28 May 2023
Explainability Techniques for Chemical Language Models Stefan Hödl William Robinson Yoram Bachrach Wilhelm Huck Tal Kachman 24 5 0 25 May 2023
G-Adapter: Towards Structure-Aware Parameter-Efficient Transfer Learning for Graph Transformer Networks Anchun Gui Jinqiang Ye Han Xiao 22 19 0 17 May 2023
Are VAEs Bad at Reconstructing Molecular Graphs? Hagen Muenkler Hubert Misztela Michał Pikusa Marwin H. S. Segler Nadine Schneider Krzysztof Maziarz DRL 25 2 0 04 May 2023
Context-enriched molecule representations improve few-shot drug discovery Johannes Schimunek Philipp Seidl Lukas Friedrich Daniel Kuhn F. Rippmann Sepp Hochreiter G. Klambauer 47 26 0 24 Apr 2023
Bayesian Optimization of Catalysis With In-Context Learning M. C. Ramos Shane S. Michtavy Marc D. Porosoff Andrew D. White BDL 44 30 0 11 Apr 2023
Difficulty in chirality recognition for Transformer architectures learning chemical structures from string Yasuhiro Yoshikai T. Mizuno Shumpei Nemoto Hiroyuki Kusuhara 22 16 0 21 Mar 2023
Automated patent extraction powers generative modeling in focused chemical spaces Akshay Subramanian Kevin P. Greenman Alexis Gervaix Tzuhsiung Yang Rafael Gómez-Bombarelli 33 6 0 14 Mar 2023
Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language Philipp Seidl Andreu Vall Sepp Hochreiter G. Klambauer 59 37 0 06 Mar 2023
Are More Layers Beneficial to Graph Transformers? Haiteng Zhao Shuming Ma Dongdong Zhang Zhi-Hong Deng Furu Wei 27 12 0 01 Mar 2023
Deep Learning Methods for Small Molecule Drug Discovery: A Survey Wenhao Hu Yingying Liu Xuanyu Chen Wenhao Chai Hangyue Chen Hongwei Wang Gaoang Wang 63 10 0 01 Mar 2023
Activity Cliff Prediction: Dataset and Benchmark Ziqiao Zhang Bangyi Zhao Ailin Xie Yatao Bian Shuigeng Zhou 17 10 0 15 Feb 2023
Implicit Geometry and Interaction Embeddings Improve Few-Shot Molecular Property Prediction Christopher Fifty Joseph M. Paggi Ehsan Amid J. Leskovec R. Dror AI4CE 20 0 0 04 Feb 2023
Predicting Protein-Ligand Binding Affinity with Equivariant Line Graph Network Yi Yi Xu Wan Kangfei Zhao Ou-Yang Le Pei-Ying Zhao 21 1 0 27 Oct 2022
Investigation of chemical structure recognition by encoder-decoder models in learning progress Katsuhisa Morita T. Mizuno Hiroyuki Kusuhara 19 8 0 24 Oct 2022
Substructure-Atom Cross Attention for Molecular Representation Learning Jiye G. Kim Seungbeom Lee Dongwoo Kim Sungsoo Ahn Jaesik Park 11 4 0 15 Oct 2022
ProGReST: Prototypical Graph Regression Soft Trees for Molecular Property Prediction Dawid Rymarczyk D. Dobrowolski Tomasz Danel 35 3 0 07 Oct 2022
Can Pre-trained Models Really Learn Better Molecular Representations for AI-aided Drug Discovery? Ziqiao Zhang Yatao Bian Ailin Xie Peng Han Long-Kai Huang Shuigeng Zhou 27 5 0 21 Aug 2022
From Static to Dynamic Structures: Improving Binding Affinity Prediction with a Graph-Based Deep Learning Model Yaosen Min Ye Wei Peizhuo Wang Xiao-tong Wang Han Li ... Yu Shi Yingheng Wang Ji Wu Dan Zhao Jianyang Zeng AI4CE 13 2 0 19 Aug 2022
Expressing Multivariate Time Series as Graphs with Time Series Attention Transformer W. Ng K. Siu Albert C. Cheung Michael K. Ng AI4TS 16 7 0 19 Aug 2022
GEM-2: Next Generation Molecular Property Prediction Network by Modeling Full-range Many-body Interactions Lihang Liu Donglong He Xiaomin Fang Shanzhuo Zhang Fan Wang Jingzhou He Hua-Hong Wu 19 3 0 11 Aug 2022
Graph neural networks for materials science and chemistry Patrick Reiser Marlen Neubert André Eberhard Luca Torresi Chen Zhou ... Houssam Metni Clint van Hoesel Henrik Schopmans T. Sommer Pascal Friederich GNN AI4CE 50 373 0 05 Aug 2022
Pre-training Transformers for Molecular Property Prediction Using Reaction Prediction J. Broberg Maria Bånkestad Erik Ylipää AI4CE 13 5 0 06 Jul 2022
KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction Han Li Dan Zhao Jianyang Zeng 27 61 0 02 Jun 2022