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What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much?

12 August 2024

Rafał Karczewski

Papers citing "What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much?"

48 / 48 papers shown

Title
DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design Jiaqi Guan Xiangxin Zhou Yuwei Yang Yu Bao Jian-wei Peng Jianzhu Ma Qiang Liu Liang Wang Quanquan Gu 78 75 0 26 Feb 2024
Going beyond persistent homology using persistent homology Johanna Immonen Amauri H. Souza Vikas Garg 67 13 0 10 Nov 2023
Genetic algorithms are strong baselines for molecule generation Austin Tripp José Miguel Hernández-Lobato 69 19 0 13 Oct 2023
Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation Tuan Le Julian Cremer Frank Noé Djork-Arné Clevert Kristof T. Schütt DiffM 101 31 0 29 Sep 2023
AbODE: Ab Initio Antibody Design using Conjoined ODEs Yogesh Verma Markus Heinonen Vikas Garg 97 19 0 31 May 2023
Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration Haitao Lin Yufei Huang Haotian Zhang Lirong Wu Siyuan Li Zhiyuan Chen Stan Z. Li DiffM 74 27 0 30 May 2023
Learning Subpocket Prototypes for Generalizable Structure-based Drug Design Zaixin Zhang Qi Liu 64 37 0 22 May 2023
3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction Jiaqi Guan Wesley Wei Qian Xingang Peng Yufeng Su Jian-wei Peng Jianzhu Ma DiffM 97 177 0 06 Mar 2023
Equivariant Polynomials for Graph Neural Networks Omri Puny Derek Lim B. Kiani Haggai Maron Y. Lipman 71 33 0 22 Feb 2023
On the Expressive Power of Geometric Graph Neural Networks Chaitanya K. Joshi Cristian Bodnar Simon Mathis Taco Cohen Pietro Liò 112 91 0 23 Jan 2023
Reinforced Genetic Algorithm for Structure-based Drug Design Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 88 55 0 28 Nov 2022
Structure-based Drug Design with Equivariant Diffusion Models Arne Schneuing Yuanqi Du Charles Harris Arian R. Jamasb Ilia Igashov ... Pietro Lio Carla P. Gomes Max Welling Michael M. Bronstein B. Correia DiffM 133 225 0 24 Oct 2022
Protein Sequence and Structure Co-Design with Equivariant Translation Chence Shi Chuanrui Wang Jiarui Lu Bozitao Zhong Jian Tang DiffM 54 48 0 17 Oct 2022
Modular Flows: Differential Molecular Generation Yogesh Verma Samuel Kaski Markus Heinonen Vikas Garg 72 14 0 12 Oct 2022
Equivariant 3D-Conditional Diffusion Models for Molecular Linker Design Ilia Igashov Hannes Stärk Clément Vignac Victor Garcia Satorras P. Frossard Max Welling Michael M. Bronstein B. Correia DiffM 86 85 0 11 Oct 2022
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 237 444 0 04 Oct 2022
Protein structure generation via folding diffusion Kevin E. Wu Kevin Kaichuang Yang Rianne van den Berg James Zou Alex X. Lu Ava P. Amini DiffM 93 203 0 30 Sep 2022
How Powerful are Spectral Graph Neural Networks Xiyuan Wang Muhan Zhang 126 201 0 23 May 2022
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets Xingang Peng Shitong Luo Jiaqi Guan Qi Xie Jian-wei Peng Jianzhu Ma 85 190 0 15 May 2022
Theory of Graph Neural Networks: Representation and Learning Stefanie Jegelka GNN AI4CE 83 70 0 16 Apr 2022
Equivariant Diffusion for Molecule Generation in 3D Emiel Hoogeboom Victor Garcia Satorras Clément Vignac Max Welling DiffM 133 622 0 31 Mar 2022
A 3D Generative Model for Structure-Based Drug Design Shitong Luo Jiaqi Guan Jianzhu Ma Jian-wei Peng DiffM 140 186 0 20 Mar 2022
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction Hannes Stärk O. Ganea L. Pattanaik Regina Barzilay Tommi Jaakkola 102 270 0 07 Feb 2022
Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking O. Ganea Xinyuan Huang Charlotte Bunne Yatao Bian Regina Barzilay Tommi Jaakkola Andreas Krause 98 154 0 15 Nov 2021
Generating 3D Molecules Conditional on Receptor Binding Sites with Deep Generative Models Matthew Ragoza Tomohide Masuda D. Koes DiffM 64 117 0 28 Oct 2021
3D Infomax improves GNNs for Molecular Property Prediction Hannes Stärk Dominique Beaini Gabriele Corso Prudencio Tossou Christian Dallago Stephan Günnemann Pietro Lio AI4CE 92 208 0 08 Oct 2021
Learning to design drug-like molecules in three-dimensional space using deep generative models Yibo Li Jianfeng Pei L. Lai DiffM 87 113 0 17 Apr 2021
E(n) Equivariant Graph Neural Networks Victor Garcia Satorras Emiel Hoogeboom Max Welling 113 1,035 0 19 Feb 2021
GraphDF: A Discrete Flow Model for Molecular Graph Generation Youzhi Luo Keqiang Yan Shuiwang Ji DRL 251 200 0 01 Feb 2021
Building powerful and equivariant graph neural networks with structural message-passing Clément Vignac Andreas Loukas P. Frossard 68 123 0 26 Jun 2020
We Should at Least Be Able to Design Molecules That Dock Well Tobiasz Ciepliński Tomasz Danel Sabina Podlewska Stanislaw Jastrzebski 44 30 0 20 Jun 2020
MoFlow: An Invertible Flow Model for Generating Molecular Graphs Chengxi Zang Fei Wang BDL 131 295 0 17 Jun 2020
Improving Graph Neural Network Expressivity via Subgraph Isomorphism Counting Giorgos Bouritsas Fabrizio Frasca Stefanos Zafeiriou M. Bronstein 136 438 0 16 Jun 2020
A Survey on The Expressive Power of Graph Neural Networks Ryoma Sato 348 173 0 09 Mar 2020
Generalization and Representational Limits of Graph Neural Networks Vikas Garg Stefanie Jegelka Tommi Jaakkola GNN 108 314 0 14 Feb 2020
GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation Chence Shi Minkai Xu Zhaocheng Zhu Weinan Zhang Ming Zhang Jian Tang 179 438 0 26 Jan 2020
PyTorch: An Imperative Style, High-Performance Deep Learning Library Adam Paszke Sam Gross Francisco Massa Adam Lerer James Bradbury ... Sasank Chilamkurthy Benoit Steiner Lu Fang Junjie Bai Soumith Chintala ODL 553 42,639 0 03 Dec 2019
Provably Powerful Graph Networks Haggai Maron Heli Ben-Hamu Hadar Serviansky Y. Lipman 133 582 0 27 May 2019
Learning Multimodal Graph-to-Graph Translation for Molecular Optimization Wengong Jin Kevin Kaichuang Yang Regina Barzilay Tommi Jaakkola 97 231 0 03 Dec 2018
Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networks Christopher Morris Martin Ritzert Matthias Fey William L. Hamilton J. E. Lenssen Gaurav Rattan Martin Grohe GNN 194 1,645 0 04 Oct 2018
How Powerful are Graph Neural Networks? Keyulu Xu Weihua Hu J. Leskovec Stefanie Jegelka GNN 257 7,705 0 01 Oct 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 359 1,371 0 12 Feb 2018
Graph Attention Networks Petar Velickovic Guillem Cucurull Arantxa Casanova Adriana Romero Pietro Lio Yoshua Bengio GNN 484 20,265 0 30 Oct 2017
Inductive Representation Learning on Large Graphs William L. Hamilton Z. Ying J. Leskovec 516 15,331 0 07 Jun 2017
Automatic chemical design using a data-driven continuous representation of molecules Rafael Gómez-Bombarelli Jennifer N. Wei David Duvenaud José Miguel Hernández-Lobato Benjamín Sánchez-Lengeling Dennis Sheberla J. Aguilera-Iparraguirre Timothy D. Hirzel Ryan P. Adams Alán Aspuru-Guzik 3DV 176 2,939 0 07 Oct 2016
Semi-Supervised Classification with Graph Convolutional Networks Thomas Kipf Max Welling GNN SSL 677 29,183 0 09 Sep 2016
Gaussian Error Linear Units (GELUs) Dan Hendrycks Kevin Gimpel 174 5,049 0 27 Jun 2016
Adam: A Method for Stochastic Optimization Diederik P. Kingma Jimmy Ba ODL 2.1K 150,364 0 22 Dec 2014