Ankh: Optimized Protein Language Model Unlocks General-Purpose Modelling

16 January 2023

Papers citing "Ankh: Optimized Protein Language Model Unlocks General-Purpose Modelling"

26 / 26 papers shown

Title
VenusFactory: A Unified Platform for Protein Engineering Data Retrieval and Language Model Fine-Tuning Y. Tan Chen Liu Jingyuan Gao Banghao Wu Mingchen Li ... Lingrong Zhang Huiqun Yu Guisheng Fan Liang Hong Bingxin Zhou 44 0 0 19 Mar 2025
evoBPE: Evolutionary Protein Sequence Tokenization Burak Suyunu Özdeniz Dolu Arzucan Özgür 56 0 0 11 Mar 2025
Protein Large Language Models: A Comprehensive Survey Yijia Xiao Wanjia Zhao Junkai Zhang Yiqiao Jin Han Zhang ... Xiao Luo Yu-Jie Zhang James Y. Zou Y. Sun Wei Wang LM&MA AI4CE 47 3 0 21 Feb 2025
Linguistic Laws Meet Protein Sequences: A Comparative Analysis of Subword Tokenization Methods Burak Suyunu Enes Taylan Arzucan Özgür 62 1 0 26 Nov 2024
SeqProFT: Applying LoRA Finetuning for Sequence-only Protein Property Predictions Shuo Zhang Jian K. Liu 54 0 0 18 Nov 2024
Training Compute-Optimal Protein Language Models Xingyi Cheng Bo Chen Pan Li Jing Gong Jie Tang Le Song 74 12 0 04 Nov 2024
Training on test proteins improves fitness, structure, and function prediction Anton Bushuiev Roman Bushuiev Nikola Zadorozhny Raman Samusevich Hannes Stärk Jiri Sedlar Tomáš Pluskal Josef Sivic 23 0 0 04 Nov 2024
Immunogenicity Prediction with Dual Attention Enables Vaccine Target Selection Song-bo Li Yang Tan Song Ke Liang Hong Bingxin Zhou 23 2 0 03 Oct 2024
Large-Scale Multi-omic Biosequence Transformers for Modeling Protein-Nucleic Acid Interactions Sully F. Chen Robert J. Steele Beakal Lemeneh S. Lad Eric Oermann Eric K. Oermann AI4CE 33 0 0 29 Aug 2024
Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance? Y. Tan Lirong Zheng Bozitao Zhong Liang Hong Bingxin Zhou 35 4 0 28 Jun 2024
A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery Yu Zhang Xiusi Chen Bowen Jin Sheng Wang Shuiwang Ji Wei Wang Jiawei Han 40 27 0 16 Jun 2024
Are Protein Language Models Compute Optimal? Yaiza Serrano Álvaro Ciudad Alexis Molina 27 7 0 11 Jun 2024
Contrastive learning of T cell receptor representations Yuta Nagano Andrew Pyo Martina Milighetti James Henderson John Shawe-Taylor Benny Chain Andreas Tiffeau-Mayer 28 4 0 10 Jun 2024
Simple, Efficient and Scalable Structure-aware Adapter Boosts Protein Language Models Yang Tan Mingchen Li Bingxin Zhou Bozitao Zhong Lirong Zheng P. Tan Ziyi Zhou Huiqun Yu Guisheng Fan Liang Hong 18 8 0 23 Apr 2024
Efficiently Predicting Mutational Effect on Homologous Proteins by Evolution Encoding Zhiqiang Zhong Davide Mottin 26 1 0 20 Feb 2024
ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation Zuobai Zhang Jiarui Lu Vijil Chenthamarakshan Aurélie C. Lozano Payel Das Jian Tang 21 1 0 10 Feb 2024
Structure-Informed Protein Language Model Zuobai Zhang Jiarui Lu Vijil Chenthamarakshan Aurélie C. Lozano Payel Das Jian Tang 13 7 0 07 Feb 2024
Endowing Protein Language Models with Structural Knowledge Dexiong Chen Philip Hartout Paolo Pellizzoni Carlos G. Oliver Karsten Borgwardt 35 12 0 26 Jan 2024
xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein Bo Chen Xingyi Cheng Pan Li Yangli-ao Geng Jing Gong ... Chiming Liu Aohan Zeng Yuxiao Dong Jie Tang Leo T. Song 29 98 0 11 Jan 2024
Stable Online and Offline Reinforcement Learning for Antibody CDRH3 Design Yannick Vogt Mehdi Naouar M. Kalweit Christoph Cornelius Miething Justus Duyster Roland Mertelsmann Gabriel Kalweit Joschka Boedecker OffRL OnRL 19 0 0 29 Nov 2023
PETA: Evaluating the Impact of Protein Transfer Learning with Sub-word Tokenization on Downstream Applications Yang Tan Mingchen Li P. Tan Ziyi Zhou Huiqun Yu Guisheng Fan Liang Hong 13 0 0 26 Oct 2023
Ophiuchus: Scalable Modeling of Protein Structures through Hierarchical Coarse-graining SO(3)-Equivariant Autoencoders Allan dos Santos Costa Ilan Mitnikov Mario Geiger Manvitha Ponnapati Tess E. Smidt Joseph Jacobson DiffM 10 3 0 04 Oct 2023
Exploring the Protein Sequence Space with Global Generative Models S. Romero-Romero Sebastian Lindner Noelia Ferruz 22 4 0 03 May 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 38 123 0 21 Mar 2023
A Systematic Study of Joint Representation Learning on Protein Sequences and Structures Zuobai Zhang Chuanrui Wang Minghao Xu Vijil Chenthamarakshan A. Lozano Payel Das Jian Tang 19 28 0 11 Mar 2023
Review and Comparison of Commonly Used Activation Functions for Deep Neural Networks Tomasz Szandała 54 269 0 15 Oct 2020