Molecule Attention Transformer

19 February 2020

Stanislaw Jastrzebski

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Papers citing "Molecule Attention Transformer"

28 / 78 papers shown

Title
Meta-learning Adaptive Deep Kernel Gaussian Processes for Molecular Property Prediction Wenlin Chen Austin Tripp José Miguel Hernández-Lobato 14 23 0 05 May 2022
Graph Masked Autoencoders with Transformers Sixiao Zhang Hongxu Chen Haoran Yang Xiangguo Sun Philip S. Yu Guandong Xu 21 18 0 17 Feb 2022
XAI for Transformers: Better Explanations through Conservative Propagation Ameen Ali Thomas Schnake Oliver Eberle G. Montavon Klaus-Robert Muller Lior Wolf FAtt 15 89 0 15 Feb 2022
Efficient Softmax Approximation for Deep Neural Networks with Attention Mechanism Ihor Vasyltsov Wooseok Chang 25 12 0 21 Nov 2021
MassFormer: Tandem Mass Spectrum Prediction for Small Molecules using Graph Transformers A. Young Bo Wang Hannes L. Röst 21 5 0 08 Nov 2021
Geometric Transformer for End-to-End Molecule Properties Prediction Yoni Choukroun Lior Wolf AI4CE ViT 25 16 0 26 Oct 2021
Permutation invariant graph-to-sequence model for template-free retrosynthesis and reaction prediction Zhengkai Tu Connor W. Coley 30 90 0 19 Oct 2021
Attentive Walk-Aggregating Graph Neural Networks M. F. Demirel Shengchao Liu Siddhant Garg Zhenmei Shi Yingyu Liang 87 9 0 06 Oct 2021
Molformer: Motif-based Transformer on 3D Heterogeneous Molecular Graphs Fang Wu Dragomir R. Radev Huabin Xing ViT 36 54 0 04 Oct 2021
GeomGCL: Geometric Graph Contrastive Learning for Molecular Property Prediction Shuangli Li Jingbo Zhou Tong Xu Dejing Dou Hui Xiong AI4CE 28 118 0 24 Sep 2021
Structure-aware Interactive Graph Neural Networks for the Prediction of Protein-Ligand Binding Affinity Shuangli Li Jingbo Zhou Tong Xu Liang Huang Fan Wang Haoyi Xiong Weili Huang Dejing Dou Hui Xiong MLAU 27 165 0 21 Jul 2021
Learning Attributed Graph Representations with Communicative Message Passing Transformer Jianwen Chen Shuangjia Zheng Ying Song Jiahua Rao Yuedong Yang 22 46 0 19 Jul 2021
GeoT: A Geometry-aware Transformer for Reliable Molecular Property Prediction and Chemically Interpretable Representation Learning Bumju Kwak J. Park Taewon Kang Jeonghee Jo Byunghan Lee Sungroh Yoon AI4CE 23 6 0 29 Jun 2021
Dual-view Molecule Pre-training Jinhua Zhu Yingce Xia Tao Qin Wen-gang Zhou Houqiang Li Tie-Yan Liu AI4CE 27 51 0 17 Jun 2021
ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction Xiaomin Fang Lihang Liu Jieqiong Lei Donglong He Shanzhuo Zhang Jingbo Zhou Fan Wang Hua-Hong Wu Haifeng Wang AI4CE 16 431 0 11 Jun 2021
Do Transformers Really Perform Bad for Graph Representation? Chengxuan Ying Tianle Cai Shengjie Luo Shuxin Zheng Guolin Ke Di He Yanming Shen Tie-Yan Liu GNN 28 433 0 09 Jun 2021
Predicting times of waiting on red signals using BERT Witold Szejgis Anna Warno P. Góra 21 1 0 20 Feb 2021
Factor Graph Molecule Network for Structure Elucidation Hieu Le Trung Yiqing Xu Wee Sun Lee GNN 11 0 0 10 Dec 2020
Directed Graph Attention Neural Network Utilizing 3D Coordinates for Molecular Property Prediction Chao Qian Yunhai Xiong Xiang Chen 6 13 0 01 Dec 2020
Molecular representation learning with language models and domain-relevant auxiliary tasks Benedek Fabian T. Edlich H. Gaspar Marwin H. S. Segler Joshua Meyers Marco Fiscato Mohamed Ahmed 13 124 0 26 Nov 2020
Comparison of Atom Representations in Graph Neural Networks for Molecular Property Prediction Agnieszka Pocha Tomasz Danel Lukasz Maziarka GNN 32 7 0 23 Nov 2020
ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction Seyone Chithrananda Gabriel Grand Bharath Ramsundar AI4CE 20 388 0 19 Oct 2020
Distance Encoding: Design Provably More Powerful Neural Networks for Graph Representation Learning Pan Li Yanbang Wang Hongwei Wang J. Leskovec GNN 23 12 0 31 Aug 2020
Making Neural Networks Interpretable with Attribution: Application to Implicit Signals Prediction Darius Afchar Romain Hennequin FAtt XAI 36 16 0 26 Aug 2020
Data Movement Is All You Need: A Case Study on Optimizing Transformers A. Ivanov Nikoli Dryden Tal Ben-Nun Shigang Li Torsten Hoefler 28 130 0 30 Jun 2020
GEOM: Energy-annotated molecular conformations for property prediction and molecular generation Simon Axelrod Rafael Gómez-Bombarelli 3DV AI4CE 28 205 0 09 Jun 2020
Graph-Aware Transformer: Is Attention All Graphs Need? Sang-yong Yoo Young-Seok Kim Kang Lee Kuhwan Jeong Junhwi Choi Hoshik Lee Y. S. Choi GNN 19 11 0 09 Jun 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 172 1,778 0 02 Mar 2017