Evaluating Protein Transfer Learning with TAPE

19 June 2019

Roshan Rao

Nicholas Bhattacharya

Pieter Abbeel

Papers citing "Evaluating Protein Transfer Learning with TAPE"

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Title
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation Xiangru Tang Howard Dai Elizabeth Knight Fang Wu Yunyang Li Tianxiao Li Mark B. Gerstein 24 25 0 13 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 26 1 0 10 Feb 2024
Structure-Informed Protein Language Model Zuobai Zhang Jiarui Lu Vijil Chenthamarakshan Aurélie C. Lozano Payel Das Jian Tang 21 8 0 07 Feb 2024
Endowing Protein Language Models with Structural Knowledge Dexiong Chen Philip Hartout Paolo Pellizzoni Carlos G. Oliver Karsten Borgwardt 43 12 0 26 Jan 2024
Deep Manifold Transformation for Protein Representation Learning Bozhen Hu Z. Zang Cheng Tan Stan Z. Li 16 1 0 12 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 42 101 0 11 Jan 2024
Tree Search-Based Evolutionary Bandits for Protein Sequence Optimization Jiahao Qiu Hui Yuan Jinghong Zhang Wentao Chen Huazheng Wang Mengdi Wang 24 1 0 08 Jan 2024
Masked Modeling for Self-supervised Representation Learning on Vision and Beyond Siyuan Li Luyuan Zhang Zedong Wang Di Wu Lirong Wu ... Jun-Xiong Xia Cheng Tan Yang Liu Baigui Sun Stan Z. Li SSL 36 14 0 31 Dec 2023
BEND: Benchmarking DNA Language Models on biologically meaningful tasks Frederikke Isa Marin Felix Teufel Marc Horlacher Dennis Madsen Dennis Pultz Ole Winther Wouter Boomsma 22 34 0 21 Nov 2023
Protein-ligand binding representation learning from fine-grained interactions Shikun Feng Minghao Li Yinjun Jia Wei-Ying Ma Yanyan Lan SSL AI4CE 24 8 0 09 Nov 2023
Graph Neural Networks for Road Safety Modeling: Datasets and Evaluations for Accident Analysis Abhinav Nippani Dongyue Li Haotian Ju Haris N. Koutsopoulos Hongyang R. Zhang GNN 46 6 0 31 Oct 2023
Exploring Post-Training Quantization of Protein Language Models Shuang Peng Fei Yang Ning Sun Sheng Chen Yanfeng Jiang Aimin Pan MQ 21 0 0 30 Oct 2023
A Hierarchical Training Paradigm for Antibody Structure-sequence Co-design Fang Wu Stan Z. Li 33 17 0 30 Oct 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 26 0 0 26 Oct 2023
Pre-Training on Large-Scale Generated Docking Conformations with HelixDock to Unlock the Potential of Protein-ligand Structure Prediction Models Lihang Liu Shanzhuo Zhang Donglong He Xianbin Ye Jingbo Zhou ... Fan Wang Jingzhou He Liang Zheng Yonghui Li Xiaomin Fang AI4CE 22 8 0 21 Oct 2023
ProFSA: Self-supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment Bowen Gao Yinjun Jia Yuanle Mo Yuyan Ni Wei-Ying Ma Zhiming Ma Yanyan Lan 22 7 0 11 Oct 2023
InstructProtein: Aligning Human and Protein Language via Knowledge Instruction Zeyuan Wang Qiang Zhang Keyan Ding Ming Qin Zhuang Xiang Xiaotong Li Huajun Chen 22 28 0 05 Oct 2023
pLMFPPred: a novel approach for accurate prediction of functional peptides integrating embedding from pre-trained protein language model and imbalanced learning Zebin Ma Yongli Zou Xiaobin Huang Wenjin Yan Hao Xu Jie-jin Yang Ying Zhang Jinqi Huang 12 4 0 25 Sep 2023
Insights Into the Inner Workings of Transformer Models for Protein Function Prediction M. Wenzel Erik Grüner Nils Strodthoff ViT 27 7 0 07 Sep 2023
Improving Protein Optimization with Smoothed Fitness Landscapes Andrew Kirjner Jason Yim Raman Samusevich Shahar Bracha Tommi Jaakkola Regina Barzilay Ila Fiete 13 16 0 02 Jul 2023
Otter-Knowledge: benchmarks of multimodal knowledge graph representation learning from different sources for drug discovery Hoang Thanh Lam M. Sbodio Marcos Martínez Galindo Mykhaylo Zayats Raúl Fernández-Díaz Víctor Valls Gabriele Picco Cesar Berrospi Ramis V. López 16 8 0 22 Jun 2023
Investigating Pre-trained Language Models on Cross-Domain Datasets, a Step Closer to General AI Mohamad Ballout U. Krumnack Gunther Heidemann Kai-Uwe Kühnberger 18 3 0 21 Jun 2023
PoET: A generative model of protein families as sequences-of-sequences Timothy F. Truong Tristan Bepler SLR 19 38 0 09 Jun 2023
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 22 13 0 02 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 30 39 0 29 May 2023
Exploring the Protein Sequence Space with Global Generative Models S. Romero-Romero Sebastian Lindner Noelia Ferruz 29 5 0 03 May 2023
Importance Weighted Expectation-Maximization for Protein Sequence Design Zhenqiao Song Lei Li 26 17 0 30 Apr 2023
InstructBio: A Large-scale Semi-supervised Learning Paradigm for Biochemical Problems Fang Wu Huiling Qin Siyuan Li Stan Z. Li Xianyuan Zhan Jinbo Xu 24 5 0 08 Apr 2023
Biological Sequence Kernels with Guaranteed Flexibility Alan N. Amin Eli N. Weinstein D. Marks 27 4 0 06 Apr 2023
Lightweight Contrastive Protein Structure-Sequence Transformation Jiangbin Zheng Ge Wang Yufei Huang Bozhen Hu Siyuan Li Cheng Tan Xinwen Fan Stan Z. Li 22 6 0 19 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 27 30 0 11 Mar 2023
Sparsity May Cry: Let Us Fail (Current) Sparse Neural Networks Together! Shiwei Liu Tianlong Chen Zhenyu (Allen) Zhang Xuxi Chen Tianjin Huang Ajay Jaiswal Zhangyang Wang 32 29 0 03 Mar 2023
Retrieved Sequence Augmentation for Protein Representation Learning Chang Ma Haiteng Zhao Lin Zheng Jiayi Xin Qintong Li Lijun Wu Zhihong Deng Yang Lu Qi Liu Lingpeng Kong AI4TS 27 9 0 24 Feb 2023
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey from Precision to Interpretability Zhiqiang Zhong A. Barkova Davide Mottin 24 8 0 16 Feb 2023
A Text-guided Protein Design Framework Shengchao Liu Yanjing Li Zhuoxinran Li A. Gitter Yutao Zhu ... Arvind Ramanathan Chaowei Xiao Jian Tang Hongyu Guo Anima Anandkumar 70 61 0 09 Feb 2023
Data-Efficient Protein 3D Geometric Pretraining via Refinement of Diffused Protein Structure Decoy Yufei Huang Lirong Wu Haitao Lin Jiangbin Zheng Ge Wang Stan Z. Li DiffM 31 14 0 05 Feb 2023
Structure-informed Language Models Are Protein Designers Zaixiang Zheng Yifan Deng Dongyu Xue Yi Zhou YE Fei Quanquan Gu 29 87 0 03 Feb 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
LEXTREME: A Multi-Lingual and Multi-Task Benchmark for the Legal Domain Joel Niklaus Veton Matoshi Pooja Rani Andrea Galassi Matthias Sturmer Ilias Chalkidis ELM AILaw 19 55 0 30 Jan 2023
On Pre-trained Language Models for Antibody Danqing Wang Fei Ye Zhou Hao 33 10 0 28 Jan 2023
Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction Zuobai Zhang Minghao Xu A. Lozano Vijil Chenthamarakshan Payel Das Jian Tang DiffM 19 19 0 28 Jan 2023
ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts Minghao Xu Xinyu Yuan Santiago Miret Jian Tang AI4TS 27 95 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 167 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
Reprogramming Pretrained Language Models for Protein Sequence Representation Learning R. Vinod Pin-Yu Chen Payel Das 93 12 0 05 Jan 2023
A Survey on Protein Representation Learning: Retrospect and Prospect Lirong Wu Yu-Feng Huang H. Lin Stan Z. Li AI4TS 33 12 0 31 Dec 2022
SESNet: sequence-structure feature-integrated deep learning method for data-efficient protein engineering Mingchen Li Liqi Kang Y. Xiong Yu Wang Guisheng Fan P. Tan Liang Hong 16 22 0 29 Dec 2022
Integration of Pre-trained Protein Language Models into Geometric Deep Learning Networks Fang Wu Yujun Tao Dragomir R. Radev Jinbo Xu Stan Z. Li AI4CE 30 32 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 21 40 0 30 Nov 2022
Probabilistic thermal stability prediction through sparsity promoting transformer representation Yevgen Zainchkovskyy J. Ferkinghoff-Borg Anja Bennett T. Egebjerg Nikolai Lorenzen Per Greisen Søren Hauberg Carsten Stahlhut AI4CE 13 0 0 10 Nov 2022