Beyond Sequence: Impact of Geometric Context for RNA Property Prediction

15 October 2024

Papers citing "Beyond Sequence: Impact of Geometric Context for RNA Property Prediction"

34 / 34 papers shown

Title
Geometric Hyena Networks for Large-scale Equivariant Learning Artem Moskalev Mangal Prakash Junjie Xu Tianyu Cui Rui Liao Tommaso Mansi 26 1 0 28 May 2025
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
HELM: Hierarchical Encoding for mRNA Language Modeling Mehdi Yazdani-Jahromi Mangal Prakash Tommaso Mansi Artem Moskalev Rui Liao 119 3 0 13 Mar 2025
Specialized Foundation Models Struggle to Beat Supervised Baselines Zongzhe Xu Ritvik Gupta Wenduo Cheng Alexander Shen Junhong Shen Ameet Talwalkar M. Khodak AI4CE 83 8 0 05 Nov 2024
Are High-Degree Representations Really Unnecessary in Equivariant Graph Neural Networks? Jiacheng Cen Anyi Li Ning Lin Yuxiang Ren Zihe Wang Wenbing Huang 76 4 0 15 Oct 2024
SE(3)-Hyena Operator for Scalable Equivariant Learning Artem Moskalev Mangal Prakash Rui Liao Tommaso Mansi 72 2 0 01 Jul 2024
RiNALMo: General-Purpose RNA Language Models Can Generalize Well on Structure Prediction Tasks Rafael Josip Penić Tin Vlasic Roland G. Huber Yue Wan M. Šikić AI4CE 34 31 0 29 Feb 2024
Shape-aware Graph Spectral Learning Junjie Xu Enyan Dai Dongsheng Luo Xiang Zhang Suhang Wang 50 3 0 16 Oct 2023
FAENet: Frame Averaging Equivariant GNN for Materials Modeling Alexandre Duval Victor Schmidt A. Garcia Santiago Miret Fragkiskos D. Malliaros Yoshua Bengio David Rolnick 67 60 0 28 Apr 2023
A Survey on Spectral Graph Neural Networks Deyu Bo Xiao Wang Yang Liu Yuan Fang Yawen Li Chuan Shi 66 27 0 11 Feb 2023
On the Expressive Power of Geometric Graph Neural Networks Chaitanya K. Joshi Cristian Bodnar Simon Mathis Taco Cohen Pietro Liò 76 90 0 23 Jan 2023
MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields Ilyes Batatia D. P. Kovács G. Simm Christoph Ortner Gábor Csányi 66 476 0 15 Jun 2022
KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction Han Li Dan Zhao Jianyang Zeng 43 64 0 02 Jun 2022
Probabilistic Transformer: Modelling Ambiguities and Distributions for RNA Folding and Molecule Design Jörg Franke Frederic Runge Frank Hutter 41 14 0 27 May 2022
Recipe for a General, Powerful, Scalable Graph Transformer Ladislav Rampášek Mikhail Galkin Vijay Prakash Dwivedi Anh Tuan Luu Guy Wolf Dominique Beaini 106 563 0 25 May 2022
How Powerful are Spectral Graph Neural Networks Xiyuan Wang Muhan Zhang 99 195 0 23 May 2022
Deep learning models for predicting RNA degradation via dual crowdsourcing H. Wayment-Steele W. Kladwang Andrew Watkins Do Soon Kim Bojan Tunguz ... Emin Öztürk K. Amer Mohamed Fares Eterna Participants Rhiju Das 42 19 0 14 Oct 2021
E(n) Equivariant Graph Neural Networks Victor Garcia Satorras Emiel Hoogeboom Max Welling 83 1,015 0 19 Feb 2021
E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials Simon L. Batzner Albert Musaelian Lixin Sun Mario Geiger J. Mailoa M. Kornbluth N. Molinari Tess E. Smidt Boris Kozinsky 275 1,283 0 08 Jan 2021
Masked Label Prediction: Unified Message Passing Model for Semi-Supervised Classification Yunsheng Shi Zhengjie Huang Shikun Feng Hui Zhong Wenjin Wang Yu Sun AI4CE 73 780 0 08 Sep 2020
Learning from Protein Structure with Geometric Vector Perceptrons Bowen Jing Stephan Eismann Patricia Suriana Raphael J. L. Townshend R. Dror GNN 3DV 62 480 0 03 Sep 2020
Directional Message Passing for Molecular Graphs Johannes Klicpera Janek Groß Stephan Günnemann 114 869 0 06 Mar 2020
RNA Secondary Structure Prediction By Learning Unrolled Algorithms Xinshi Chen Yu Li Ramzan Umarov Xin Gao Le Song SyDa AI4TS 44 118 0 13 Feb 2020
SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery Shion Honda Shoi Shi H. Ueda MedIm 65 174 0 12 Nov 2019
Optuna: A Next-generation Hyperparameter Optimization Framework Takuya Akiba Shotaro Sano Toshihiko Yanase Takeru Ohta Masanori Koyama 541 5,769 0 25 Jul 2019
Fast Graph Representation Learning with PyTorch Geometric Matthias Fey J. E. Lenssen 3DH GNN 3DPC 200 4,334 0 06 Mar 2019
Spectral Multigraph Networks for Discovering and Fusing Relationships in Molecules Boris Knyazev Xiao Lin Mohamed R. Amer Graham W. Taylor GNN 47 31 0 23 Nov 2018
How Powerful are Graph Neural Networks? Keyulu Xu Weihua Hu J. Leskovec Stefanie Jegelka GNN 216 7,623 0 01 Oct 2018
Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds Nathaniel Thomas Tess E. Smidt S. Kearnes Lusann Yang Li Li Kai Kohlhoff Patrick F. Riley 3DPC 82 966 0 22 Feb 2018
Graph Attention Networks Petar Velickovic Guillem Cucurull Arantxa Casanova Adriana Romero Pietro Lio Yoshua Bengio GNN 428 20,089 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 137 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 636 130,942 0 12 Jun 2017
Semi-Supervised Classification with Graph Convolutional Networks Thomas Kipf Max Welling GNN SSL 579 28,999 0 09 Sep 2016
Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering M. Defferrard Xavier Bresson P. Vandergheynst GNN 312 7,646 0 30 Jun 2016