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RNAs are essential molecules that carry genetic information vital for life, with profound implications for drug development and biotechnology.
Mixed precision training, 2018
Paulius Micikevicius, Sharan Narang, Jonah Alben, Gregory Diamos, Erich Elsen, David Garcia, Boris Ginsburg, Michael Houston, Oleksii Kuchaiev, Ganesh Venkatesh, and Hao Wu · 2018
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Decoupled weight decay regularization, 2019
Ilya Loshchilov and Frank Hutter · 2019
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Transformer protein language models are unsupervised structure learners
Roshan Rao, Joshua Meier, Tom Sercu, Sergey Ovchinnikov, and Alexander Rives · 2020
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Rnacentral 2021: secondary structure integration, improved sequence search and new member databases
Blake A Sweeney, Anton I Petrov, Carlos E Ribas, Robert D Finn, Alex Bateman, Maciej Szymanski, Wojciech M Karlowski, Stefan E Seemann, Jan Gorodkin, Jamie J Cannone, Robin R Gutell, Simon Kay, Steven Marygold, Gil dos Santos, Adam Frankish, Jonathan M Mudge, Ruth Barshir, Simon Fishilevich, Patricia P Chan, Todd M Lowe, Ruth Seal, Elspeth Bruford, Simona Panni, Pablo Porras, Dimitra Karagkouni, Artemis G Hatzigeorgiou, Lina Ma, Zhang Zhang, Pieter-Jan Volders, Pieter Mestdagh, Sam Griffiths-Jones, Bastian Fromm, Kevin J Peterson, Ioanna Kalvari, Eric P Nawrocki, Anton S Petrov, Shuai Weng, Philia Bouchard-Bourelle, Michelle Scott, Lauren M Lui, David Hoksza, Ruth C Lovering, Barbara Kramarz, Prita Mani, Sridhar Ramachandran, and Zasha Weinberg · 2020
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Language models enable zero-shot prediction of the effects of mutations on protein function
Joshua Meier, Roshan Rao, Robert Verkuil, Jason Liu, Tom Sercu, and Alex Rives · 2021
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Prottrans: Toward understanding the language of life through self-supervised learning
Ahmed Elnaggar, Michael Heinzinger, Christian Dallago, Ghalia Rehawi, Yu Wang, Llion Jones, Tom Gibbs, Tamas Feher, Christoph Angerer, Martin Steinegger, et al · 2021
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Modeling protein using large-scale pretrain language model
Yijia Xiao, Jiezhong Qiu, Ziang Li, Chang-Yu Hsieh, and Jie Tang · 2021
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Inner monologue: Embodied reasoning through planning with language models, 2022
Wenlong Huang, Fei Xia, Ted Xiao, Harris Chan, Jacky Liang, Pete Florence, Andy Zeng, Jonathan Tompson, Igor Mordatch, Yevgen Chebotar, Pierre Sermanet, Noah Brown, Tomas Jackson, Linda Luu, Sergey Levine, Karol Hausman, and Brian Ichter · 2022
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Interpretable rna foundation model from unannotated data for highly accurate rna structure and function predictions, 2022
Jiayang Chen, Zhihang Hu, Siqi Sun, Qingxiong Tan, Yixuan Wang, Qinze Yu, Licheng Zong, Liang Hong, Jin Xiao, Tao Shen, Irwin King, and Yu Li · 2022
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Evolutionary-scale prediction of atomic-level protein structure with a language model
Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Nikita Smetanin, Robert Verkuil, Ori Kabeli, Yaniv Shmueli, et al · 2023
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Protst: Multi-modality learning of protein sequences and biomedical texts, 2023
Minghao Xu, Xinyu Yuan, Santiago Miret, and Jian Tang · 2023
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Han Guo, Mingjia Huo, and Pengtao Xie · 2023
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Zeyuan Wang, Qiang Zhang, Keyan Ding, Ming Qin, Xiang Zhuang, Xiaotong Li, and Huajun Chen · 2023
Proteingpt: Multimodal llm for protein property prediction and structure understanding, 2024
Yijia Xiao, Edward Sun, Yiqiao Jin, Qifan Wang, and Wei Wang · 2024
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Rinalmo: General-purpose rna language models can generalize well on structure prediction tasks, 2024
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Proteinclip: enhancing protein language models with natural language
Kevin E Wu, Howard Chang, and James Zou · 2024
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Protllm: An interleaved protein-language llm with protein-as-word pre-training, 2024
Le Zhuo, Zewen Chi, Minghao Xu, Heyan Huang, Heqi Zheng, Conghui He, Xian-Ling Mao, and Wentao Zhang · 2024
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Rna language models predict mutations that improve rna function
Yekaterina Shulgina, Marena I. Trinidad, Conner J. Langeberg, Hunter Nisonoff, Seyone Chithrananda, Petr Skopintsev, Amos J. Nissley, Jaymin Patel, Ron S. Boger, Honglue Shi, Peter H. Yoon, Erin E. Doherty, Tara Pande, Aditya M. Iyer, Jennifer A. Doudna, and Jamie H. D. Cate · 2024
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Chaoqun He, Renjie Luo, Yuzhuo Bai, Shengding Hu, Zhen Leng Thai, Junhao Shen, Jinyi Hu, Xu Han, Yujie Huang, Yuxiang Zhang, Jie Liu, Lei Qi, Zhiyuan Liu, and Maosong Sun · 2024
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The llama 3 herd of models, 2024
Abhimanyu Dubey, Abhinav Jauhri, Abhinav Pandey, Abhishek Kadian, Ahmad Al-Dahle, Aiesha Letman, Akhil Mathur, Alan Schelten, Amy Yang, Angela Fan, Anirudh Goyal, Anthony Hartshorn, Aobo Yang, Archi Mitra, Archie Sravankumar, Artem Korenev, Arthur Hinsvark, Arun Rao, Aston Zhang, Aurelien Rodriguez, Austen Gregerson, Ava Spataru, Baptiste Roziere, Bethany Biron, Binh Tang, Bobbie Chern, Charlotte Caucheteux, Chaya Nayak, Chloe Bi, Chris Marra, Chris McConnell, Christian Keller, Christophe Touret, Chunyang Wu, Corinne Wong, Cristian Canton Ferrer, Cyrus Nikolaidis, Damien Allonsius, Daniel Song, Danielle Pintz, Danny Livshits, David Esiobu, Dhruv Choudhary, Dhruv Mahajan, Diego Garcia-Olano, Diego Perino, Dieuwke Hupkes, Egor Lakomkin, Ehab AlBadawy, Elina Lobanova, Emily Dinan, Eric Michael Smith, Filip Radenovic, Frank Zhang, Gabriel Synnaeve, Gabrielle Lee, Georgia Lewis Anderson, Graeme Nail, Gregoire Mialon, Guan Pang, Guillem Cucurell, Hailey Nguyen, Hannah Korevaar, Hu Xu, Hugo 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Chatnt: A multimodal conversational agent for dna, rna and protein tasks
Guillaume Richard, Bernardo P de Almeida, Hugo Dalla-Torre, Christopher Blum, Lorenz Hexemer, Priyanka Pandey, Stefan Laurent, Marie P Lopez, Alexander Laterre, Maren Lang, Ugur Sahin, Karim Beguir, and Thomas Pierrot · 2024
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