What is a meaningful representation of protein sequences?

28 November 2020

Papers citing "What is a meaningful representation of protein sequences?"

25 / 25 papers shown

Title
Interpreting Equivariant Representations Andreas Abildtrup Hansen Anna Calissano Aasa Feragen 93 1 0 23 Jan 2024
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 62 947 0 13 Jul 2020
BERTology Meets Biology: Interpreting Attention in Protein Language Models Jesse Vig Ali Madani Lav Varshney Caiming Xiong R. Socher Nazneen Rajani 71 293 0 26 Jun 2020
ProGen: Language Modeling for Protein Generation Ali Madani Bryan McCann Nikhil Naik N. Keskar N. Anand Raphael R. Eguchi Po-Ssu Huang R. Socher 66 283 0 08 Mar 2020
Variational Autoencoders with Riemannian Brownian Motion Priors Dimitris Kalatzis David Eklund Georgios Arvanitidis Søren Hauberg BDL DRL 117 49 0 12 Feb 2020
Pre-Training of Deep Bidirectional Protein Sequence Representations with Structural Information Seonwoo Min Seunghyun Park Siwon Kim Hyun-Soo Choi Byunghan Lee Sungroh Yoon SSL 46 62 0 25 Nov 2019
RoBERTa: A Robustly Optimized BERT Pretraining Approach Yinhan Liu Myle Ott Naman Goyal Jingfei Du Mandar Joshi Danqi Chen Omer Levy M. Lewis Luke Zettlemoyer Veselin Stoyanov AIMat 653 24,464 0 26 Jul 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 91 796 0 19 Jun 2019
Reliable training and estimation of variance networks N. Detlefsen Martin Jørgensen Søren Hauberg UQCV 89 89 0 04 Jun 2019
Learning protein sequence embeddings using information from structure Tristan Bepler Bonnie Berger 73 290 0 22 Feb 2019
Continuous Hierarchical Representations with Poincaré Variational Auto-Encoders Emile Mathieu Charline Le Lan Chris J. Maddison Ryota Tomioka Yee Whye Teh BDL DRL 74 178 0 17 Jan 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 94,891 0 11 Oct 2018
Explorations in Homeomorphic Variational Auto-Encoding Luca Falorsi P. D. Haan Tim R. Davidson Nicola De Cao Maurice Weiler Patrick Forré Taco S. Cohen BDL DRL 96 116 0 12 Jul 2018
3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data Maurice Weiler Mario Geiger Max Welling Wouter Boomsma Taco S. Cohen 3DPC 108 505 0 06 Jul 2018
Only Bayes should learn a manifold (on the estimation of differential geometric structure from data) Søren Hauberg 55 33 0 13 Jun 2018
Hyperspherical Variational Auto-Encoders Tim R. Davidson Luca Falorsi Nicola De Cao Thomas Kipf Jakub M. Tomczak DRL BDL 104 385 0 03 Apr 2018
Intertwiners between Induced Representations (with Applications to the Theory of Equivariant Neural Networks) Taco S. Cohen Mario Geiger Maurice Weiler 60 47 0 28 Mar 2018
Latent Space Oddity: on the Curvature of Deep Generative Models Georgios Arvanitidis Lars Kai Hansen Søren Hauberg DRL 107 270 0 31 Oct 2017
Attention Is All You Need Ashish Vaswani Noam M. Shazeer Niki Parmar Jakob Uszkoreit Llion Jones Aidan Gomez Lukasz Kaiser Illia Polosukhin 3DV 701 131,652 0 12 Jun 2017
DeepSF: deep convolutional neural network for mapping protein sequences to folds Jie Hou B. Adhikari Jianlin Cheng 63 200 0 04 Jun 2017
Dilated Residual Networks Feng Yu V. Koltun Thomas Funkhouser MedIm 121 1,617 0 28 May 2017
Deep Residual Learning for Image Recognition Kaiming He Xinming Zhang Shaoqing Ren Jian Sun MedIm 2.2K 194,020 0 10 Dec 2015
Metrics for Probabilistic Geometries A. Tosi Søren Hauberg A. Vellido Neil D. Lawrence 79 62 0 27 Nov 2014
Efficient Estimation of Word Representations in Vector Space Tomas Mikolov Kai Chen G. Corrado J. Dean 3DV 677 31,512 0 16 Jan 2013
Representation Learning: A Review and New Perspectives Yoshua Bengio Aaron Courville Pascal Vincent OOD SSL 261 12,439 0 24 Jun 2012