ProGen: Language Modeling for Protein Generation

8 March 2020

Papers citing "ProGen: Language Modeling for Protein Generation"

49 / 99 papers shown

Title
Plug & Play Directed Evolution of Proteins with Gradient-based Discrete MCMC Patrick Emami Aidan Perreault Jeffrey N. Law David J. Biagioni Peter C. St. John 18 13 0 20 Dec 2022
Unsupervised language models for disease variant prediction Allan Zhou Nicholas C. Landolfi Daniel C. O’Neill 22 0 0 07 Dec 2022
Protein Language Models and Structure Prediction: Connection and Progression Bozhen Hu Jun-Xiong Xia Jiangbin Zheng Cheng Tan Yufei Huang Yongjie Xu Stan Z. Li 19 40 0 30 Nov 2022
Training self-supervised peptide sequence models on artificially chopped proteins Gil Sadeh Zichen Wang J. Grewal Huzefa Rangwala Layne Price 19 2 0 09 Nov 2022
Learning the shape of protein micro-environments with a holographic convolutional neural network Michael N. Pun Andrew Ivanov Quinn Bellamy Zachary Montague Colin H. LaMont P. Bradley J. Otwinowski Armita Nourmohammad 11 12 0 05 Nov 2022
Mega: Moving Average Equipped Gated Attention Xuezhe Ma Chunting Zhou Xiang Kong Junxian He Liangke Gui Graham Neubig Jonathan May Luke Zettlemoyer 14 182 0 21 Sep 2022
Materials Transformers Language Models for Generative Materials Design: a benchmark study Nihang Fu Lai Wei Yuqi Song Qinyang Li Rui Xin Sadman Sadeed Omee Rongzhi Dong Edirisuriya M Dilanga Siriwardane Jianjun Hu 14 2 0 27 Jun 2022
ProGen2: Exploring the Boundaries of Protein Language Models Erik Nijkamp Jeffrey A. Ruffolo Eli N. Weinstein Nikhil Naik Ali Madani AI4TS 22 283 0 27 Jun 2022
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models N. Anand Tudor Achim DiffM 187 173 0 26 May 2022
RITA: a Study on Scaling Up Generative Protein Sequence Models Daniel Hesslow Niccoló Zanichelli Pascal Notin Iacopo Poli D. Marks 18 90 0 11 May 2022
Multi-segment preserving sampling for deep manifold sampler Daniel Berenberg Jae Hyeon Lee S. Kelow Ji Won Park Andrew Watkins Vladimir Gligorijević Richard Bonneau Stephen Ra Kyunghyun Cho MedIm 19 5 0 09 May 2022
Crystal Transformer: Self-learning neural language model for Generative and Tinkering Design of Materials Lai Wei Qinyang Li Yuqi Song Stanislav Stefanov Edirisuriya M Dilanga Siriwardane Fanglin Chen Jianjun Hu AI4CE 20 9 0 25 Apr 2022
Generative De Novo Protein Design with Global Context Cheng Tan Zhangyang Gao Jun-Xiong Xia Bozhen Hu Stan Z. Li 9 7 0 21 Apr 2022
Generative power of a protein language model trained on multiple sequence alignments Damiano Sgarbossa Umberto Lupo Anne-Florence Bitbol 19 32 0 14 Apr 2022
SNP2Vec: Scalable Self-Supervised Pre-Training for Genome-Wide Association Study Samuel Cahyawijaya Tiezheng Yu Zihan Liu Tiffany Mak Xiaopu Zhou N. Ip Pascale Fung 11 8 0 14 Apr 2022
Few Shot Protein Generation Soumya Ram Tristan Bepler 26 6 0 03 Apr 2022
Protein language models trained on multiple sequence alignments learn phylogenetic relationships Umberto Lupo Damiano Sgarbossa Anne-Florence Bitbol 24 34 0 29 Mar 2022
Improving Molecular Representation Learning with Metric Learning-enhanced Optimal Transport Fang Wu Nicolas Courty Shuting Jin Stan Z. Li OOD OT 18 8 0 13 Feb 2022
Compute Trends Across Three Eras of Machine Learning J. Sevilla Lennart Heim A. Ho T. Besiroglu Marius Hobbhahn Pablo Villalobos 20 269 0 11 Feb 2022
Regression Transformer: Concurrent sequence regression and generation for molecular language modeling Jannis Born Matteo Manica 13 91 0 01 Feb 2022
Pre-training Co-evolutionary Protein Representation via A Pairwise Masked Language Model Liang He Shizhuo Zhang Lijun Wu Huanhuan Xia Fusong Ju ... Jianwei Zhu Pan Deng Bin Shao Tao Qin Tie-Yan Liu 26 31 0 29 Oct 2021
On Learning the Transformer Kernel Sankalan Pal Chowdhury Adamos Solomou Kumar Avinava Dubey Mrinmaya Sachan ViT 44 14 0 15 Oct 2021
Pre-trained Language Models in Biomedical Domain: A Systematic Survey Benyou Wang Qianqian Xie Jiahuan Pei Zhihong Chen Prayag Tiwari Zhao Li Jie Fu LM&MA AI4CE 37 163 0 11 Oct 2021
Cross-lingual Transfer of Monolingual Models Evangelia Gogoulou Ariel Ekgren T. Isbister Magnus Sahlgren 27 17 0 15 Sep 2021
Deep Generative Modeling for Protein Design Alexey Strokach Philip M. Kim AI4CE 179 90 0 31 Aug 2021
Combiner: Full Attention Transformer with Sparse Computation Cost Hongyu Ren H. Dai Zihang Dai Mengjiao Yang J. Leskovec Dale Schuurmans Bo Dai 73 77 0 12 Jul 2021
Deep Extrapolation for Attribute-Enhanced Generation Alvin Chan Ali Madani Ben Krause Nikhil Naik 19 24 0 07 Jul 2021
A Generative Model for Raw Audio Using Transformer Architectures Prateek Verma C. Chafe 10 28 0 30 Jun 2021
Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design Yue Cao Payel Das Vijil Chenthamarakshan Pin-Yu Chen Igor Melnyk Yang Shen 24 45 0 24 Jun 2021
Adaptive machine learning for protein engineering B. Hie Kevin Kaichuang Yang 6 80 0 10 Jun 2021
Question Generation for Adaptive Education Megha Srivastava Noah D. Goodman AI4Ed 11 39 0 08 Jun 2021
On the Expressive Power of Self-Attention Matrices Valerii Likhosherstov K. Choromanski Adrian Weller 35 33 0 07 Jun 2021
Luna: Linear Unified Nested Attention Xuezhe Ma Xiang Kong Sinong Wang Chunting Zhou Jonathan May Hao Ma Luke Zettlemoyer 23 114 0 03 Jun 2021
Ten Quick Tips for Deep Learning in Biology Benjamin D. Lee A. Gitter Casey S. Greene S. Raschka F. Maguire ... Alexandr A Kalinin T. Triche Benjamin J. Lengerich Timothy J. Triche Jr S. Boca OOD 16 26 0 29 May 2021
Protein sequence-to-structure learning: Is this the end(-to-end revolution)? É. Laine Stephan Eismann A. Elofsson Sergei Grudinin OOD 3DV 17 34 0 16 May 2021
Protein sequence design with deep generative models Zachary Wu Kadina E. Johnston F. Arnold Kevin Kaichuang Yang 16 134 0 09 Apr 2021
Artificial Intelligence Advances for De Novo Molecular Structure Modeling in Cryo-EM Dong Si Andrew Nakamura Runbang Tang Haowen Guan Jie Hou Ammaar Firozi Renzhi Cao Kyle Hippe Minglei Zhao 16 6 0 11 Feb 2021
Evolution Is All You Need: Phylogenetic Augmentation for Contrastive Learning Amy X. Lu Alex X. Lu Alan M. Moses SSL 17 13 0 25 Dec 2020
Generative Capacity of Probabilistic Protein Sequence Models Francisco McGee Quentin Novinger R. Levy Vincenzo Carnevale A. Haldane 22 34 0 03 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 8 111 0 28 Nov 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
Rethinking Attention with Performers K. Choromanski Valerii Likhosherstov David Dohan Xingyou Song Andreea Gane ... Afroz Mohiuddin Lukasz Kaiser David Belanger Lucy J. Colwell Adrian Weller 8 1,517 0 30 Sep 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 12 915 0 13 Jul 2020
BERTology Meets Biology: Interpreting Attention in Protein Language Models Jesse Vig Ali Madani L. Varshney Caiming Xiong R. Socher Nazneen Rajani 20 288 0 26 Jun 2020
Masked Language Modeling for Proteins via Linearly Scalable Long-Context Transformers K. Choromanski Valerii Likhosherstov David Dohan Xingyou Song Andreea Gane ... Peter Hawkins Jared Davis David Belanger Lucy J. Colwell Adrian Weller 28 84 0 05 Jun 2020
A Survey of Deep Learning for Scientific Discovery M. Raghu Erica Schmidt OOD AI4CE 35 120 0 26 Mar 2020
Megatron-LM: Training Multi-Billion Parameter Language Models Using Model Parallelism M. Shoeybi M. Patwary Raul Puri P. LeGresley Jared Casper Bryan Catanzaro MoE 245 1,817 0 17 Sep 2019