v1v2 (latest)

Beyond Sequence: Impact of Geometric Context for RNA Property Prediction

International Conference on Learning Representations (ICLR), 2024

15 October 2024

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

37 / 37 papers shown

Title
HyperHELM: Hyperbolic Hierarchy Encoding for mRNA Language Modeling Max van Spengler Artem Moskalev Tommaso Mansi Mangal Prakash Rui Liao 84 0 0 29 Sep 2025
Property-Isometric Variational Autoencoders for Sequence Modeling and Design Elham Sadeghi Xianqi Deng I-Hsin Lin Stacy M. Copp Petko Bogdanov 100 0 0 16 Sep 2025
Equi-mRNA: Protein Translation Equivariant Encoding for mRNA Language Models Mehdi Yazdani-Jahromi Ali Khodabandeh Yalabadi O. Garibay 52 1 0 20 Aug 2025
Geometric Hyena Networks for Large-scale Equivariant Learning Artem Moskalev Mangal Prakash Junjie Xu Tianyu Cui Rui Liao Tommaso Mansi 134 4 0 28 May 2025
A Comprehensive Benchmark for RNA 3D Structure-Function Modeling Luis Wyss Vincent Mallet Wissam Karroucha Karsten Borgwardt Carlos Oliver 293 2 0 27 Mar 2025
HELM: Hierarchical Encoding for mRNA Language ModelingInternational Conference on Learning Representations (ICLR), 2024 Mehdi Yazdani-Jahromi Mangal Prakash Tommaso Mansi Artem Moskalev Rui Liao 248 9 0 13 Mar 2025
Specialized Foundation Models Struggle to Beat Supervised BaselinesInternational Conference on Learning Representations (ICLR), 2024 Zongzhe Xu Ritvik Gupta Wenduo Cheng Alexander Shen Junhong Shen Ameet Talwalkar M. Khodak AI4CE 261 21 0 05 Nov 2024
Are High-Degree Representations Really Unnecessary in Equivariant Graph Neural Networks?Neural Information Processing Systems (NeurIPS), 2024 Jiacheng Cen Anyi Li Ning Lin Yuxiang Ren Zihe Wang Wenbing Huang 347 16 0 15 Oct 2024
SE(3)-Hyena Operator for Scalable Equivariant Learning Artem Moskalev Mangal Prakash Rui Liao Tommaso Mansi 227 5 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 131 62 0 29 Feb 2024
Shape-aware Graph Spectral Learning Junjie Xu Enyan Dai Dongsheng Luo Xiang Zhang Suhang Wang 210 4 0 16 Oct 2023
FAENet: Frame Averaging Equivariant GNN for Materials ModelingInternational Conference on Machine Learning (ICML), 2023 Alexandre Duval Victor Schmidt A. Garcia Santiago Miret Fragkiskos D. Malliaros Yoshua Bengio David Rolnick 222 84 0 28 Apr 2023
A Survey on Spectral Graph Neural Networks Deyu Bo Xiao Wang Yang Liu Yuan Fang Yawen Li Chuan Shi 212 36 0 11 Feb 2023
On the Expressive Power of Geometric Graph Neural NetworksInternational Conference on Machine Learning (ICML), 2023 Chaitanya K. Joshi Cristian Bodnar Simon Mathis Taco Cohen Pietro Liò 355 113 0 23 Jan 2023
MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force FieldsNeural Information Processing Systems (NeurIPS), 2022 Ilyes Batatia D. P. Kovács G. Simm Christoph Ortner Gábor Csányi 241 701 0 15 Jun 2022
KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property PredictionKnowledge Discovery and Data Mining (KDD), 2022 Han Li Dan Zhao Jianyang Zeng 142 68 0 02 Jun 2022
Probabilistic Transformer: Modelling Ambiguities and Distributions for RNA Folding and Molecule DesignNeural Information Processing Systems (NeurIPS), 2022 Jörg Franke Frederic Runge Katharina Eggensperger 182 16 0 27 May 2022
Recipe for a General, Powerful, Scalable Graph TransformerNeural Information Processing Systems (NeurIPS), 2022 Ladislav Rampášek Mikhail Galkin Vijay Prakash Dwivedi Anh Tuan Luu Guy Wolf Dominique Beaini 369 799 0 25 May 2022
How Powerful are Spectral Graph Neural NetworksInternational Conference on Machine Learning (ICML), 2022 Xiyuan Wang Muhan Zhang 292 275 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 158 28 0 14 Oct 2021
E(n) Equivariant Graph Neural NetworksInternational Conference on Machine Learning (ICML), 2021 Victor Garcia Satorras Emiel Hoogeboom Max Welling 410 1,262 0 19 Feb 2021
E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic PotentialsNature Communications (Nat Commun), 2021 Simon L. Batzner Albert Musaelian Lixin Sun Mario Geiger J. Mailoa M. Kornbluth N. Molinari Tess E. Smidt Boris Kozinsky 689 1,649 0 08 Jan 2021
Masked Label Prediction: Unified Message Passing Model for Semi-Supervised ClassificationInternational Joint Conference on Artificial Intelligence (IJCAI), 2020 Yunsheng Shi Zhengjie Huang Shikun Feng Hui Zhong Wenjin Wang Yu Sun AI4CE 489 945 0 08 Sep 2020
Learning from Protein Structure with Geometric Vector PerceptronsInternational Conference on Learning Representations (ICLR), 2020 Bowen Jing Stephan Eismann Patricia Suriana Raphael J. L. Townshend R. Dror GNN 3DV 346 569 0 03 Sep 2020
Directional Message Passing for Molecular GraphsInternational Conference on Learning Representations (ICLR), 2020 Johannes Klicpera Janek Groß Stephan Günnemann 494 988 0 06 Mar 2020
RNA Secondary Structure Prediction By Learning Unrolled AlgorithmsInternational Conference on Learning Representations (ICLR), 2020 Xinshi Chen Yu Li Ramzan Umarov Xin Gao Le Song SyDa AI4TS 104 129 0 13 Feb 2020
SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery Shion Honda Shoi Shi H. Ueda MedIm 158 214 0 12 Nov 2019
Optuna: A Next-generation Hyperparameter Optimization FrameworkKnowledge Discovery and Data Mining (KDD), 2019 Takuya Akiba Shotaro Sano Toshihiko Yanase Takeru Ohta Masanori Koyama 809 7,675 0 25 Jul 2019
Fast Graph Representation Learning with PyTorch Geometric Matthias Fey J. E. Lenssen 3DH GNN 3DPC 1.1K 4,934 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 118 31 0 23 Nov 2018
How Powerful are Graph Neural Networks? Keyulu Xu Weihua Hu J. Leskovec Stefanie Jegelka GNN 762 8,863 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 266 1,085 0 22 Feb 2018
Graph Attention NetworksInternational Conference on Learning Representations (ICLR), 2017 Petar Velickovic Guillem Cucurull Arantxa Casanova Adriana Romero Pietro Lio Yoshua Bengio GNN 1.9K 23,539 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 579 1,243 0 26 Jun 2017
Attention Is All You NeedNeural Information Processing Systems (NeurIPS), 2017 Ashish Vaswani Noam M. Shazeer Niki Parmar Jakob Uszkoreit Llion Jones Aidan Gomez Lukasz Kaiser Illia Polosukhin 3DV 2.4K 157,232 0 12 Jun 2017
Semi-Supervised Classification with Graph Convolutional Networks Thomas Kipf Max Welling GNN SSL 1.6K 32,393 0 09 Sep 2016
Convolutional Neural Networks on Graphs with Fast Localized Spectral FilteringNeural Information Processing Systems (NeurIPS), 2016 M. Defferrard Xavier Bresson P. Vandergheynst GNN 801 8,175 0 30 Jun 2016