Protein Representation Learning by Geometric Structure Pretraining

11 March 2022

Zuobai Zhang

Minghao Xu

Arian R. Jamasb

Vijil Chenthamarakshan

Jian Tang

Papers citing "Protein Representation Learning by Geometric Structure Pretraining"

49 / 49 papers shown

Title
A Comprehensive Benchmark for RNA 3D Structure-Function Modeling Luis Wyss Vincent Mallet Wissam Karroucha Karsten Borgwardt Carlos Oliver 68 0 0 27 Mar 2025
UniZyme: A Unified Protein Cleavage Site Predictor Enhanced with Enzyme Active-Site Knowledge Chenao Li Shuo Yan Enyan Dai 75 0 0 10 Feb 2025
Structure-Enhanced Protein Instruction Tuning: Towards General-Purpose Protein Understanding with LLMs Wei Wu Chao Wang L. Chen Mingze Yin Yiheng Zhu Kun Fu Jieping Ye Hui Xiong Zheng Wang 57 1 0 04 Oct 2024
EditRoom: LLM-parameterized Graph Diffusion for Composable 3D Room Layout Editing Kaizhi Zheng Xiaotong Chen Xuehai He Jing Gu Linjie Li Zhengyuan Yang Kevin Qinghong Lin Jianfeng Wang Lijuan Wang Xin Eric Wang KELM DiffM 72 0 0 03 Oct 2024
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning Jiaqing Xie Yue Zhao 87 1 0 02 Oct 2024
ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding Yijia Xiao Edward Sun Yiqiao Jin Qifan Wang Wei Wang 63 14 0 21 Aug 2024
E(n) Equivariant Topological Neural Networks Claudio Battiloro Ege Karaismailoglu Mauricio Tec George Dasoulas Michelle Audirac Francesca Dominici 84 9 0 24 May 2024
A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications Jiaqi Han Jiacheng Cen Liming Wu Zongzhao Li Xiangzhe Kong ... Zhewei Wei Deli Zhao Yu Rong Wenbing Huang Wenbing Huang AI4CE 106 23 0 01 Mar 2024
Understanding Oversmoothing in Diffusion-Based GNNs From the Perspective of Operator Semigroup Theory Weichen Zhao Chenguang Wang Xinyan Wang Congying Han Tiande Guo Tianshu Yu 95 0 0 23 Feb 2024
ProtChatGPT: Towards Understanding Proteins with Large Language Models Chao Wang Hehe Fan Ruijie Quan Yi Yang 64 14 0 15 Feb 2024
Contrastive Representation Learning for 3D Protein Structures Pedro Hermosilla Timo Ropinski 3DV 81 51 0 31 May 2022
Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval Pascal Notin M. Dias J. Frazer Javier Marchena-Hurtado Aidan Gomez D. Marks Y. Gal 87 186 0 27 May 2022
Structure-aware Protein Self-supervised Learning Can Chen Jingbo Zhou Fan Wang Xue Liu Dejing Dou SSL 65 66 0 06 Apr 2022
Multi-Scale Representation Learning on Proteins Vignesh Ram Somnath Charlotte Bunne Andreas Krause 60 95 0 04 Apr 2022
TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery Zhaocheng Zhu Chence Shi Zuobai Zhang Shengchao Liu Minghao Xu ... Chang Ma Runcheng Liu Louis-Pascal Xhonneux Meng Qu Jian Tang OOD VLM MedIm 24 72 0 16 Feb 2022
Pre-training Co-evolutionary Protein Representation via A Pairwise Masked Language Model Liang He Shizhuo Zhang Lijun Wu Huanhuan Xia Fusong Ju ... Jianwei Zhu Pan Deng Jia Zhang Tao Qin Tie-Yan Liu 87 31 0 29 Oct 2021
Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design Yue Cao Payel Das Vijil Chenthamarakshan Pin-Yu Chen Igor Melnyk Yang Shen 49 46 0 24 Jun 2021
Self-supervised Graph-level Representation Learning with Local and Global Structure Minghao Xu Hang Wang Bingbing Ni Hongyu Guo Jian Tang SSL 32 209 0 08 Jun 2021
GemNet: Universal Directional Graph Neural Networks for Molecules Johannes Klicpera Florian Becker Stephan Günnemann AI4CE 74 456 0 02 Jun 2021
E(n) Equivariant Graph Neural Networks Victor Garcia Satorras Emiel Hoogeboom Max Welling 81 997 0 19 Feb 2021
Is Transfer Learning Necessary for Protein Landscape Prediction? Amir Shanehsazzadeh David Belanger David Dohan SSL 91 62 0 31 Oct 2020
Learning from Protein Structure with Geometric Vector Perceptrons Bowen Jing Stephan Eismann Patricia Suriana Raphael J. L. Townshend R. Dror GNN 3DV 59 479 0 03 Sep 2020
ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing Ahmed Elnaggar M. Heinzinger Christian Dallago Ghalia Rehawi Yu Wang ... Tamas B. Fehér Christoph Angerer Martin Steinegger D. Bhowmik B. Rost DRL 52 935 0 13 Jul 2020
GCC: Graph Contrastive Coding for Graph Neural Network Pre-Training J. Qiu Qibin Chen Yuxiao Dong Jing Zhang Hongxia Yang Ming Ding Kuansan Wang Jie Tang SSL 190 951 0 17 Jun 2020
Contrastive Multi-View Representation Learning on Graphs Kaveh Hassani Amir Hosein Khas Ahmadi SSL 208 1,299 0 10 Jun 2020
Language Models are Few-Shot Learners Tom B. Brown Benjamin Mann Nick Ryder Melanie Subbiah Jared Kaplan ... Christopher Berner Sam McCandlish Alec Radford Ilya Sutskever Dario Amodei BDL 560 41,706 0 28 May 2020
Directional Message Passing for Molecular Graphs Johannes Klicpera Janek Groß Stephan Günnemann 110 869 0 06 Mar 2020
A Simple Framework for Contrastive Learning of Visual Representations Ting-Li Chen Simon Kornblith Mohammad Norouzi Geoffrey E. Hinton SSL 297 18,686 0 13 Feb 2020
Momentum Contrast for Unsupervised Visual Representation Learning Kaiming He Haoqi Fan Yuxin Wu Saining Xie Ross B. Girshick SSL 149 12,050 0 13 Nov 2019
Evaluating Protein Transfer Learning with TAPE Roshan Rao Nicholas Bhattacharya Neil Thomas Yan Duan Xi Chen John F. Canny Pieter Abbeel Yun S. Song SSL 83 796 0 19 Jun 2019
Strategies for Pre-training Graph Neural Networks Weihua Hu Bowen Liu Joseph Gomes Marinka Zitnik Percy Liang Vijay S. Pande J. Leskovec SSL AI4CE 96 1,396 0 29 May 2019
PullNet: Open Domain Question Answering with Iterative Retrieval on Knowledge Bases and Text Haitian Sun Tania Bedrax-Weiss William W. Cohen RALM ReLM 61 349 0 21 Apr 2019
Learning protein sequence embeddings using information from structure Tristan Bepler Bonnie Berger 59 289 0 22 Feb 2019
BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding Jacob Devlin Ming-Wei Chang Kenton Lee Kristina Toutanova VLM SSL SSeg 1.3K 94,479 0 11 Oct 2018
Representation Learning with Contrastive Predictive Coding Aaron van den Oord Yazhe Li Oriol Vinyals DRL SSL 269 10,245 0 10 Jul 2018
Neural Message Passing with Edge Updates for Predicting Properties of Molecules and Materials Peter Bjørn Jørgensen K. Jacobsen Mikkel N. Schmidt 56 82 0 08 Jun 2018
UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction Leland McInnes John Healy James Melville 148 9,383 0 09 Feb 2018
Graph Attention Networks Petar Velickovic Guillem Cucurull Arantxa Casanova Adriana Romero Pietro Lio Yoshua Bengio GNN 403 20,061 0 30 Oct 2017
SchNet: A continuous-filter convolutional neural network for modeling quantum interactions Kristof T. Schütt Pieter-Jan Kindermans Huziel Enoc Sauceda Felix Stefan Chmiela A. Tkatchenko K. Müller 129 1,074 0 26 Jun 2017
Attention Is All You Need Ashish Vaswani Noam M. Shazeer Niki Parmar Jakob Uszkoreit Llion Jones Aidan Gomez Lukasz Kaiser Illia Polosukhin 3DV 547 130,873 0 12 Jun 2017
Inductive Representation Learning on Large Graphs William L. Hamilton Z. Ying J. Leskovec 440 15,174 0 07 Jun 2017
DeepSF: deep convolutional neural network for mapping protein sequences to folds Jie Hou B. Adhikari Jianlin Cheng 46 199 0 04 Jun 2017
Neural Message Passing for Quantum Chemistry Justin Gilmer S. Schoenholz Patrick F. Riley Oriol Vinyals George E. Dahl 403 7,430 0 04 Apr 2017
Modeling Relational Data with Graph Convolutional Networks Michael Schlichtkrull Thomas Kipf Peter Bloem Rianne van den Berg Ivan Titov Max Welling GNN 172 4,807 0 17 Mar 2017
Axiomatic Attribution for Deep Networks Mukund Sundararajan Ankur Taly Qiqi Yan OOD FAtt 158 5,963 0 04 Mar 2017
Variational Graph Auto-Encoders Thomas Kipf Max Welling GNN BDL SSL CML 132 3,573 0 21 Nov 2016
Semi-Supervised Classification with Graph Convolutional Networks Thomas Kipf Max Welling GNN SSL 552 28,964 0 09 Sep 2016
Gaussian Error Linear Units (GELUs) Dan Hendrycks Kevin Gimpel 163 4,984 0 27 Jun 2016
ImageNet Large Scale Visual Recognition Challenge Olga Russakovsky Jia Deng Hao Su J. Krause S. Satheesh ... A. Karpathy A. Khosla Michael S. Bernstein Alexander C. Berg Li Fei-Fei VLM ObjD 1.3K 39,468 0 01 Sep 2014