Evaluating Protein Transfer Learning with TAPE

19 June 2019

Roshan Rao

Nicholas Bhattacharya

Pieter Abbeel

Papers citing "Evaluating Protein Transfer Learning with TAPE"

32 / 182 papers shown

Title
Structure Inducing Pre-Training Matthew B. A. McDermott Brendan Yap Peter Szolovits Marinka Zitnik 40 18 0 18 Mar 2021
Pretrained Transformers as Universal Computation Engines Kevin Lu Aditya Grover Pieter Abbeel Igor Mordatch 28 217 0 09 Mar 2021
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development Kexin Huang Tianfan Fu Wenhao Gao Yue Zhao Yusuf Roohani J. Leskovec Connor W. Coley Cao Xiao Jimeng Sun Marinka Zitnik OOD LM&MA 33 261 0 18 Feb 2021
Adversarial Contrastive Pre-training for Protein Sequences Matthew B. A. McDermott Brendan Yap Harry Hsu Di Jin Peter Szolovits AAML 12 9 0 31 Jan 2021
Evolution Is All You Need: Phylogenetic Augmentation for Contrastive Learning Amy X. Lu Alex X. Lu Alan M. Moses SSL 25 13 0 25 Dec 2020
Noise-Robust End-to-End Quantum Control using Deep Autoregressive Policy Networks Jiahao Yao Paul Köttering Hans Gundlach Lin Lin Marin Bukov 18 14 0 12 Dec 2020
Utilising Graph Machine Learning within Drug Discovery and Development Thomas Gaudelet Ben Day Arian R. Jamasb Jyothish Soman Cristian Regep ... Jian Tang D. Roblin Tom L. Blundell M. Bronstein J. Taylor-King AI4CE 27 36 0 09 Dec 2020
ATOM3D: Tasks On Molecules in Three Dimensions Raphael J. L. Townshend M. Vögele Patricia Suriana Alexander Derry Alexander Powers ... Brandon M. Anderson Stephan Eismann Risi Kondor Russ Altman R. Dror AI4CE 19 118 0 07 Dec 2020
Align-gram : Rethinking the Skip-gram Model for Protein Sequence Analysis Nabil Ibtehaz S. Sourav Md. Shamsuzzoha Bayzid M. S. Rahman 19 2 0 06 Dec 2020
Pre-training Protein Language Models with Label-Agnostic Binding Pairs Enhances Performance in Downstream Tasks Modestas Filipavicius Matteo Manica Joris Cadow María Rodríguez Martínez 10 13 0 05 Dec 2020
Generative Capacity of Probabilistic Protein Sequence Models Francisco McGee Quentin Novinger R. Levy Vincenzo Carnevale A. Haldane 27 34 0 03 Dec 2020
Modifying Memories in Transformer Models Chen Zhu A. S. Rawat Manzil Zaheer Srinadh Bhojanapalli Daliang Li Felix X. Yu Sanjiv Kumar KELM 18 190 0 01 Dec 2020
Profile Prediction: An Alignment-Based Pre-Training Task for Protein Sequence Models Pascal Sturmfels Jesse Vig Ali Madani Nazneen Rajani 13 24 0 01 Dec 2020
What is a meaningful representation of protein sequences? N. Detlefsen Søren Hauberg Wouter Boomsma 10 111 0 28 Nov 2020
Is Transfer Learning Necessary for Protein Landscape Prediction? Amir Shanehsazzadeh David Belanger David Dohan SSL 12 61 0 31 Oct 2020
Fixed-Length Protein Embeddings using Contextual Lenses Amir Shanehsazzadeh David Belanger David Dohan 10 1 0 15 Oct 2020
Combination of digital signal processing and assembled predictive models facilitates the rational design of proteins David Medina-Ortiz Sebastián Contreras Juan Amado-Hinojosa Jorge Torres-Almonacid J. Asenjo Marcelo A. Navarrete Á. Olivera-Nappa 6 8 0 07 Oct 2020
AdaLead: A simple and robust adaptive greedy search algorithm for sequence design Sam Sinai Richard Wang Alexander Whatley Stewart Slocum Elina Locane Eric D. Kelsic 25 77 0 05 Oct 2020
A primer on model-guided exploration of fitness landscapes for biological sequence design Sam Sinai Eric D. Kelsic 32 28 0 04 Oct 2020
GEFA: Early Fusion Approach in Drug-Target Affinity Prediction T. Nguyen Thin Nguyen T. Le T. Tran GNN 9 59 0 25 Sep 2020
Transfer Learning for Protein Structure Classification at Low Resolution Alexander Hudson S. Gong 17 1 0 11 Aug 2020
Deep Learning in Protein Structural Modeling and Design Wenhao Gao S. Mahajan Jeremias Sulam Jeffrey J. Gray 29 159 0 16 Jul 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 20 917 0 13 Jul 2020
Variable Skipping for Autoregressive Range Density Estimation Eric Liang Zongheng Yang Ion Stoica Pieter Abbeel Yan Duan Xi Chen 14 4 0 10 Jul 2020
BERTology Meets Biology: Interpreting Attention in Protein Language Models Jesse Vig Ali Madani L. Varshney Caiming Xiong R. Socher Nazneen Rajani 29 288 0 26 Jun 2020
Enforcing Predictive Invariance across Structured Biomedical Domains Wengong Jin Regina Barzilay Tommi Jaakkola OOD 24 27 0 06 Jun 2020
$PaccMann$^{RL}$ on SARS-CoV-2: Designing antiviral candidates with conditional generative models$ PaccMann $^{RL}$ on SARS-CoV-2: Designing antiviral candidates with conditional generative models Jannis Born Matteo Manica Joris Cadow Greta Markert N. Mill Modestas Filipavicius María Rodríguez Martínez 21 4 0 27 May 2020
Telling BERT's full story: from Local Attention to Global Aggregation Damian Pascual Gino Brunner Roger Wattenhofer 20 19 0 10 Apr 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 26 275 0 08 Mar 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 6 62 0 25 Nov 2019
Blockwise Self-Attention for Long Document Understanding J. Qiu Hao Ma Omer Levy Scott Yih Sinong Wang Jie Tang 11 251 0 07 Nov 2019
GLUE: A Multi-Task Benchmark and Analysis Platform for Natural Language Understanding Alex Jinpeng Wang Amanpreet Singh Julian Michael Felix Hill Omer Levy Samuel R. Bowman ELM 297 6,959 0 20 Apr 2018