Learning the Language of Protein Structure

8 January 2025

Papers citing "Learning the Language of Protein Structure"

34 / 34 papers shown

Title
Bio2Token: All-atom tokenization of any biomolecular structure with Mamba Andrew Liu Axel Elaldi Nathan Russell Olivia Viessmann Mamba 99 3 0 24 Oct 2024
Advancing Multimodal Medical Capabilities of Gemini Lin Yang Shawn Xu Andrew Sellergren Timo Kohlberger Yuchen Zhou ... David Steiner Rory Pilgrim Christopher J. Kelly Shekoofeh Azizi Daniel Golden MedIm 72 66 0 06 May 2024
Me LLaMA: Foundation Large Language Models for Medical Applications Qianqian Xie Qingyu Chen Aokun Chen C.A.I. Peng Yan Hu ... Huan He Lucila Ohno-Machido Yonghui Wu Hua Xu Jiang Bian LM&MA AI4MH 113 4 0 20 Feb 2024
Masked Audio Generation using a Single Non-Autoregressive Transformer Alon Ziv Itai Gat Gaël Le Lan Tal Remez Felix Kreuk Alexandre Défossez Jade Copet Gabriel Synnaeve Yossi Adi 86 40 0 09 Jan 2024
HQ-VAE: Hierarchical Discrete Representation Learning with Variational Bayes Yuhta Takida Yukara Ikemiya Takashi Shibuya Kazuki Shimada Woosung Choi ... Naoki Murata Toshimitsu Uesaka Kengo Uchida Wei-Hsiang Liao Yuki Mitsufuji BDL 86 12 0 31 Dec 2023
SE(3)-Stochastic Flow Matching for Protein Backbone Generation A. Bose Tara Akhound-Sadegh Guillaume Huguet Kilian Fatras Jarrid Rector-Brooks Cheng-Hao Liu A. Nica Maksym Korablyov Michael M. Bronstein Alexander Tong DiffM 72 84 0 03 Oct 2023
Finite Scalar Quantization: VQ-VAE Made Simple Fabian Mentzer David C. Minnen E. Agustsson Michael Tschannen 94 183 0 27 Sep 2023
VQGraph: Rethinking Graph Representation Space for Bridging GNNs and MLPs Ling Yang Ye Tian Minkai Xu Zhongyi Liu Shenda Hong Wei Qu Wentao Zhang Tengjiao Wang Muhan Zhang J. Leskovec 61 14 0 04 Aug 2023
Towards Generalist Biomedical AI Tao Tu Shekoofeh Azizi Danny Driess M. Schaekermann Mohamed Amin ... Yossi Matias K. Singhal Peter R. Florence Alan Karthikesalingam Vivek Natarajan LM&MA MedIm AI4MH 96 271 0 26 Jul 2023
PASTA: Pretrained Action-State Transformer Agents Raphael Boige Yannis Flet-Berliac Arthur Flajolet Guillaume Richard Thomas Pierrot LM&Ro OffRL 87 5 0 20 Jul 2023
Discrete Graph Auto-Encoder Yoann Boget Magda Gregorova Alexandros Kalousis 28 4 0 13 Jun 2023
Simple and Controllable Music Generation Jade Copet Felix Kreuk Itai Gat Tal Remez David Kant Gabriel Synnaeve Yossi Adi Alexandre Défossez MGen 116 369 0 08 Jun 2023
Straightening Out the Straight-Through Estimator: Overcoming Optimization Challenges in Vector Quantized Networks Minyoung Huh Brian Cheung Pulkit Agrawal Phillip Isola MQ 45 54 0 15 May 2023
Visual Instruction Tuning Haotian Liu Chunyuan Li Qingyang Wu Yong Jae Lee SyDa VLM MLLM 560 4,861 0 17 Apr 2023
SE(3) diffusion model with application to protein backbone generation Jason Yim Brian L. Trippe Valentin De Bortoli Emile Mathieu Arnaud Doucet Regina Barzilay Tommi Jaakkola DiffM 65 207 0 05 Feb 2023
Muse: Text-To-Image Generation via Masked Generative Transformers Huiwen Chang Han Zhang Jarred Barber AJ Maschinot José Lezama ... Kevin Patrick Murphy William T. Freeman Michael Rubinstein Yuanzhen Li Dilip Krishnan DiffM 260 553 0 02 Jan 2023
High Fidelity Neural Audio Compression Alexandre Défossez Jade Copet Gabriel Synnaeve Yossi Adi 91 660 0 24 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 90 201 0 30 Sep 2022
Scaling Autoregressive Models for Content-Rich Text-to-Image Generation Jiahui Yu Yuanzhong Xu Jing Yu Koh Thang Luong Gunjan Baid ... Zarana Parekh Xin Li Han Zhang Jason Baldridge Yonghui Wu EGVM 192 1,129 0 22 Jun 2022
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem Brian L. Trippe Jason Yim D. Tischer D. Baker Tamara Broderick Regina Barzilay Tommi Jaakkola DiffM 74 239 0 08 Jun 2022
Flamingo: a Visual Language Model for Few-Shot Learning Jean-Baptiste Alayrac Jeff Donahue Pauline Luc Antoine Miech Iain Barr ... Mikolaj Binkowski Ricardo Barreira Oriol Vinyals Andrew Zisserman Karen Simonyan MLLM VLM 418 3,585 0 29 Apr 2022
MaskGIT: Masked Generative Image Transformer Huiwen Chang Han Zhang Lu Jiang Ce Liu William T. Freeman ViT 153 678 0 08 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 89 154 0 15 Nov 2021
Vector-quantized Image Modeling with Improved VQGAN Jiahui Yu Xin Li Jing Yu Koh Han Zhang Ruoming Pang James Qin Alexander Ku Yuanzhong Xu Jason Baldridge Yonghui Wu ViT VLM DRL 117 519 0 09 Oct 2021
Decision Transformer: Reinforcement Learning via Sequence Modeling Lili Chen Kevin Lu Aravind Rajeswaran Kimin Lee Aditya Grover Michael Laskin Pieter Abbeel A. Srinivas Igor Mordatch OffRL 136 1,656 0 02 Jun 2021
Learning Transferable Visual Models From Natural Language Supervision Alec Radford Jong Wook Kim Chris Hallacy Aditya A. Ramesh Gabriel Goh ... Amanda Askell Pamela Mishkin Jack Clark Gretchen Krueger Ilya Sutskever CLIP VLM 967 29,731 0 26 Feb 2021
Learning from Protein Structure with Geometric Vector Perceptrons Bowen Jing Stephan Eismann Patricia Suriana Raphael J. L. Townshend R. Dror GNN 3DV 69 488 0 03 Sep 2020
Self-Supervised MultiModal Versatile Networks Jean-Baptiste Alayrac Adrià Recasens R. Schneider Relja Arandjelović Jason Ramapuram J. Fauw Lucas Smaira Sander Dieleman Andrew Zisserman SSL 134 374 0 29 Jun 2020
Generating Diverse High-Fidelity Images with VQ-VAE-2 Ali Razavi Aaron van den Oord Oriol Vinyals DRL BDL 147 1,823 0 02 Jun 2019
The Curious Case of Neural Text Degeneration Ari Holtzman Jan Buys Li Du Maxwell Forbes Yejin Choi 190 3,201 0 22 Apr 2019
BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding Jacob Devlin Ming-Wei Chang Kenton Lee Kristina Toutanova VLM SSL SSeg 1.8K 95,114 0 11 Oct 2018
Neural Discrete Representation Learning Aaron van den Oord Oriol Vinyals Koray Kavukcuoglu BDL SSL OCL 228 5,061 0 02 Nov 2017
Attention Is All You Need Ashish Vaswani Noam M. Shazeer Niki Parmar Jakob Uszkoreit Llion Jones Aidan Gomez Lukasz Kaiser Illia Polosukhin 3DV 728 132,199 0 12 Jun 2017
Improving Variational Inference with Inverse Autoregressive Flow Diederik P. Kingma Tim Salimans Rafal Jozefowicz Xi Chen Ilya Sutskever Max Welling BDL DRL 142 1,823 0 15 Jun 2016