ProGen: Language Modeling for Protein Generation

8 March 2020

Papers citing "ProGen: Language Modeling for Protein Generation"

50 / 99 papers shown

Title
Aligning Large Language Models with Healthcare Stakeholders: A Pathway to Trustworthy AI Integration Kexin Ding Mu Zhou Akshay Chaudhari Shaoting Zhang Dimitris N. Metaxas LM&MA 43 0 0 02 May 2025
An All-Atom Generative Model for Designing Protein Complexes Ruizhe Chen Dongyu Xue Xiangxin Zhou Zaixiang Zheng Xiangxiang Zeng Quanquan Gu 19 0 0 17 Apr 2025
BioMaze: Benchmarking and Enhancing Large Language Models for Biological Pathway Reasoning Haiteng Zhao Chang Ma FangZhi Xu Lingpeng Kong Zhi-Hong Deng LRM 44 2 0 23 Feb 2025
Towards More Accurate Full-Atom Antibody Co-Design Jiayang Wu Xingyi Zhang Xiangyu Dong Kun Xie Ziqi Liu Wensheng Gan Sibo Wang Le Song 39 0 0 11 Feb 2025
A Comprehensive Survey of Foundation Models in Medicine Wasif Khan Seowung Leem Kyle B. See Joshua K. Wong Shaoting Zhang R. Fang AI4CE LM&MA VLM 102 18 0 17 Jan 2025
Open-Source Protein Language Models for Function Prediction and Protein Design Shivasankaran Vanaja Pandi Bharath Ramsundar AI4CE 68 0 0 18 Dec 2024
DrugGen: Advancing Drug Discovery with Large Language Models and Reinforcement Learning Feedback Mahsa Sheikholeslami Navid Mazrouei Yousof Gheisari Afshin Fasihi Matin Irajpour Ali Motahharynia MedIm LM&MA 62 2 0 20 Nov 2024
Concept Bottleneck Language Models For protein design Aya Abdelsalam Ismail Tuomas Oikarinen Amy Wang Julius Adebayo Samuel Stanton ... J. Kleinhenz Allen Goodman H. C. Bravo Kyunghyun Cho Nathan C. Frey 34 4 0 09 Nov 2024
Training Compute-Optimal Protein Language Models Xingyi Cheng Bo Chen Pan Li Jing Gong Jie Tang Le Song 81 13 0 04 Nov 2024
SFM-Protein: Integrative Co-evolutionary Pre-training for Advanced Protein Sequence Representation Liang He Peiran Jin Yaosen Min Shufang Xie Lijun Wu Tao Qin Xiaozhuan Liang Kaiyuan Gao Yuliang Jiang Tie-Yan Liu AI4TS 23 1 0 31 Oct 2024
MutaPLM: Protein Language Modeling for Mutation Explanation and Engineering Yizhen Luo Zikun Nie Massimo Hong Suyuan Zhao Hao Zhou Zaiqing Nie 33 0 0 30 Oct 2024
Discrete Modeling via Boundary Conditional Diffusion Processes Yuxuan Gu Xiaocheng Feng Lei Huang Yingsheng Wu Zekun Zhou Weihong Zhong Kun Zhu Bing Qin DiffM 28 0 0 29 Oct 2024
MAMMAL -- Molecular Aligned Multi-Modal Architecture and Language Yoel Shoshan Moshiko Raboh Michal Ozery-Flato Vadim Ratner Alex Golts ... Sharon Kurant Joseph A. Morrone Parthasarathy Suryanarayanan Michal Rosen-Zvi Efrat Hexter 26 1 0 28 Oct 2024
Metalic: Meta-Learning In-Context with Protein Language Models Jacob Beck Shikha Surana Manus McAuliffe Oliver Bent Thomas D. Barrett Juan Jose Garau Luis Paul Duckworth AI4CE 28 0 0 10 Oct 2024
Computational design of target-specific linear peptide binders with TransformerBeta Haowen Zhao Francesco A. Aprile Barbara Bravi 29 0 0 07 Oct 2024
Large Language Models in Drug Discovery and Development: From Disease Mechanisms to Clinical Trials Yizhen Zheng Huan Yee Koh M. Yang Li Li Lauren T. May Geoffrey I. Webb Shirui Pan George Church LM&MA 42 9 0 06 Sep 2024
Wavelet GPT: Wavelet Inspired Large Language Models Prateek Verma AI4TS 18 0 0 04 Sep 2024
Design Proteins Using Large Language Models: Enhancements and Comparative Analyses Kamyar Zeinalipour Neda Jamshidi Monica Bianchini Marco Maggini Marco Gori 19 0 0 12 Aug 2024
Towards Signal Processing In Large Language Models Prateek Verma Mert Pilanci 42 3 0 10 Jun 2024
Full-Atom Peptide Design based on Multi-modal Flow Matching Jiahan Li Chaoran Cheng Zuofan Wu Ruihan Guo Shitong Luo Zhizhou Ren Jian-wei Peng Jianzhu Ma 40 15 0 02 Jun 2024
ProtAgents: Protein discovery via large language model multi-agent collaborations combining physics and machine learning Alireza Ghafarollahi Markus J. Buehler LLMAG AI4CE 13 23 0 27 Jan 2024
ESM-NBR: fast and accurate nucleic acid-binding residue prediction via protein language model feature representation and multi-task learning Wenwu Zeng Dafeng Lv Wenjuan Liu Shaoliang Peng 14 4 0 01 Dec 2023
A Hierarchical Training Paradigm for Antibody Structure-sequence Co-design Fang Wu Stan Z. Li 27 17 0 30 Oct 2023
Functional Geometry Guided Protein Sequence and Backbone Structure Co-Design Justin Dumouchelle Yunlong Zhao Wenxian Shi Yang Yang Lei Li 26 2 0 06 Oct 2023
Joint Design of Protein Sequence and Structure based on Motifs Zhenqiao Song Yunlong Zhao Yufei Song Wenxian Shi Yang Yang Lei Li 3DV DiffM 25 3 0 04 Oct 2023
Mixup-Augmented Meta-Learning for Sample-Efficient Fine-Tuning of Protein Simulators Jingbang Chen Yian Wang Xingwei Qu Shuangjia Zheng Yao-Chun Yang Hao Dong Jie Fu 15 0 0 29 Aug 2023
Generative Language Models on Nucleotide Sequences of Human Genes M. Ihtiyar Arzucan Özgür 13 0 0 20 Jul 2023
Conformer LLMs -- Convolution Augmented Large Language Models Prateek Verma 23 1 0 02 Jul 2023
Beyond the Hype: Assessing the Performance, Trustworthiness, and Clinical Suitability of GPT3.5 Salmonn Talebi E. Tong M. Mofrad LM&MA 6 5 0 28 Jun 2023
A Systematic Survey in Geometric Deep Learning for Structure-based Drug Design Zaixin Zhang Jiaxian Yan Qi Liu Enhong Chen Marinka Zitnik 32 1 0 20 Jun 2023
Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials Shengchao Liu Weitao Du Yanjing Li Zhuoxinran Li Zhiling Zheng ... Anima Anandkumar C. Borgs J. Chayes Hongyu Guo Jian Tang AI4CE 33 19 0 15 Jun 2023
Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequences Minsu Kim Federico Berto Sungsoo Ahn Jinkyoo Park DD 27 18 0 05 Jun 2023
Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation Le Zhang Jiayang Chen Tao Shen Yu-Hu Li S. Sun 11 5 0 02 Jun 2023
Is novelty predictable? Clara Fannjiang Jennifer Listgarten AI4CE 17 14 0 01 Jun 2023
ChatGPT-powered Conversational Drug Editing Using Retrieval and Domain Feedback Shengchao Liu Jiong Wang Yijin Yang Chengpeng Wang Ling Liu Hongyu Guo Chaowei Xiao LM&MA KELM AI4MH 28 39 0 29 May 2023
Scaling Data-Constrained Language Models Niklas Muennighoff Alexander M. Rush Boaz Barak Teven Le Scao Aleksandra Piktus Nouamane Tazi S. Pyysalo Thomas Wolf Colin Raffel ALM 21 197 0 25 May 2023
A Latent Diffusion Model for Protein Structure Generation Cong Fu Keqiang Yan Limei Wang Wing Yee Au Michael McThrow Tao Komikado Koji Maruhashi Kanji Uchino Xiaoning Qian Shuiwang Ji DiffM 18 31 0 06 May 2023
Exploring the Protein Sequence Space with Global Generative Models S. Romero-Romero Sebastian Lindner Noelia Ferruz 27 5 0 03 May 2023
Importance Weighted Expectation-Maximization for Protein Sequence Design Zhenqiao Song Lei Li 24 17 0 30 Apr 2023
Improving Autoregressive NLP Tasks via Modular Linearized Attention Victor Agostinelli Lizhong Chen 22 1 0 17 Apr 2023
ProtFIM: Fill-in-Middle Protein Sequence Design via Protein Language Models Youhan Lee Hasun Yu 6 3 0 29 Mar 2023
Large AI Models in Health Informatics: Applications, Challenges, and the Future Jianing Qiu Lin Li Jiankai Sun Jiachuan Peng Peilun Shi ... Bo Xiao Wu Yuan Ningli Wang Dong Xu Benny P. L. Lo AI4MH LM&MA 40 127 0 21 Mar 2023
Architext: Language-Driven Generative Architecture Design Theodoros Galanos Antonios Liapis Georgios N. Yannakakis VLM AI4CE 26 6 0 13 Mar 2023
Extrapolative Controlled Sequence Generation via Iterative Refinement Vishakh Padmakumar Richard Yuanzhe Pang He He Ankur P. Parikh 21 9 0 08 Mar 2023
Protein Representation Learning via Knowledge Enhanced Primary Structure Modeling Hong-Yu Zhou Yunxiang Fu Zhicheng Zhang Cheng Bian Yizhou Yu 22 8 0 30 Jan 2023
On Pre-trained Language Models for Antibody Danqing Wang Fei Ye Zhou Hao 33 10 0 28 Jan 2023
ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts Minghao Xu Xinyu Yuan Santiago Miret Jian Tang AI4TS 27 94 0 28 Jan 2023
Ankh: Optimized Protein Language Model Unlocks General-Purpose Modelling Ahmed Elnaggar Hazem Essam Wafaa Salah-Eldin Walid Moustafa Mohamed Elkerdawy Charlotte Rochereau B. Rost 153 86 0 16 Jan 2023
Generative Antibody Design for Complementary Chain Pairing Sequences through Encoder-Decoder Language Model S. K. Chu K. Wei AI4CE 19 7 0 06 Jan 2023
A Survey on Protein Representation Learning: Retrospect and Prospect Lirong Wu Yu-Feng Huang H. Lin Stan Z. Li AI4TS 26 12 0 31 Dec 2022