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
Elucidating the Design Space of Multimodal Protein Language Models Cheng-Yen Hsieh Qing Guo Daiheng Zhang Dongyu Xue Fei Ye Shujian Huang Zaixiang Zheng Quanquan Gu 31 1 0 15 Apr 2025
Leveraging State Space Models in Long Range Genomics Matvei Popov Aymen Kallala Anirudha Ramesh Narimane Hennouni Shivesh Khaitan Rick Gentry Alain-Sam Cohen Mamba 62 0 0 07 Apr 2025
Prot42: a Novel Family of Protein Language Models for Target-aware Protein Binder Generation Mohammad Amaan Sayeed Engin Tekin Maryam Nadeem Nancy A. ElNaker A. Singh Natalia Vassilieva Boulbaba Ben Amor 26 0 0 06 Apr 2025
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 50 0 0 19 Mar 2025
Protein Structure Tokenization: Benchmarking and New Recipe Xinyu Yuan Zichen Wang Marcus Collins Huzefa Rangwala 36 0 0 28 Feb 2025
Overconfident Oracles: Limitations of In Silico Sequence Design Benchmarking Shikha Surana Nathan Grinsztajn Timothy Atkinson Paul Duckworth Thomas D. Barrett 41 2 0 24 Feb 2025
A Survey of Graph Transformers: Architectures, Theories and Applications Chaohao Yuan Kangfei Zhao Ercan Engin Kuruoglu Liang Wang Tingyang Xu Wenbing Huang Deli Zhao Hong Cheng Yu Rong 57 4 0 23 Feb 2025
Protein Large Language Models: A Comprehensive Survey Yijia Xiao Wanjia Zhao Junkai Zhang Yiqiao Jin Han Zhang ... Xiao Luo Yu-Jie Zhang James Zou Yizhou Sun Wei Wang LM&MA AI4CE 61 3 0 21 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 105 18 0 17 Jan 2025
Open-Source Protein Language Models for Function Prediction and Protein Design Shivasankaran Vanaja Pandi Bharath Ramsundar AI4CE 70 0 0 18 Dec 2024
SeqProFT: Applying LoRA Finetuning for Sequence-only Protein Property Predictions Shuo Zhang Jian K. Liu 67 0 0 18 Nov 2024
Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences Niklas Schmidinger Lisa Schneckenreiter Philipp Seidl Johannes Schimunek Pieter-Jan Hoedt Johannes Brandstetter Andreas Mayr Sohvi Luukkonen Sepp Hochreiter G. Klambauer MedIm 61 4 0 06 Nov 2024
Training Compute-Optimal Protein Language Models Xingyi Cheng Bo Chen Pan Li Jing Gong Jie Tang Le Song 84 13 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 31 0 0 04 Nov 2024
Comprehensive benchmarking of large language models for RNA secondary structure prediction L. I. Zablocki L. A. Bugnon M. Gerard L. Di Persia G. Stegmayer D. H. Milone AI4TS 28 3 0 21 Oct 2024
DPLM-2: A Multimodal Diffusion Protein Language Model Qing Guo Zaixiang Zheng Fei Ye Dongyu Xue Shujian Huang Quanquan Gu 28 13 0 17 Oct 2024
Position Specific Scoring Is All You Need? Revisiting Protein Sequence Classification Tasks Sarwan Ali Taslim Murad Prakash Chourasia Haris Mansoor I. Khan Pin-Yu Chen Murray Patterson 31 1 0 16 Oct 2024
BSM: Small but Powerful Biological Sequence Model for Genes and Proteins Weixi Xiang Xueting Han Xiujuan Chai Jing Bai 26 1 0 15 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
U-net based prediction of cerebrospinal fluid distribution and ventricular reflux grading Melanie Rieff Fabian Holzberger Oksana Lapina Geir Ringstad Lars Magnus Valnes Bogna Warsza Kent-Andre Mardal Per Kristian Eide Barbara Wohlmuth 41 0 0 06 Oct 2024
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning Jiaqing Xie Yue Zhao 33 0 0 02 Oct 2024
Nearest Neighbor CCP-Based Molecular Sequence Analysis Sarwan Ali Prakash Chourasia Bipin Koirala Murray Patterson 39 1 0 07 Sep 2024
Protein sequence classification using natural language processing techniques Huma Perveen Julie Weeds 18 0 0 06 Sep 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 44 9 0 06 Sep 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 41 0 0 29 Aug 2024
Design Proteins Using Large Language Models: Enhancements and Comparative Analyses Kamyar Zeinalipour Neda Jamshidi Monica Bianchini Marco Maggini Marco Gori 24 0 0 12 Aug 2024
Multi-Modal CLIP-Informed Protein Editing Mingze Yin Hanjing Zhou Yiheng Zhu Miao Lin YiXuan Wu ... Hongxia Xu Chang-Yu Hsieh Tingjun Hou Jintai Chen Jian Wu 45 7 0 27 Jul 2024
Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors Qizhi Pei Lijun Wu Zhenyu He Jinhua Zhu Yingce Xia Shufang Xie Rui Yan 29 0 0 21 Jul 2024
Repurformer: Transformers for Repurposing-Aware Molecule Generation Changhun Lee Gyumin Lee 49 0 0 16 Jul 2024
Pre-training with Fractional Denoising to Enhance Molecular Property Prediction Yuyan Ni Shikun Feng Xin Hong Yuancheng Sun Wei-Ying Ma Zhiming Ma Qiwei Ye Yanyan Lan AI4CE 36 10 0 14 Jul 2024
Closed-Form Test Functions for Biophysical Sequence Optimization Algorithms Samuel Stanton R. Alberstein Nathan C. Frey Andrew Watkins Kyunghyun Cho 37 4 0 28 Jun 2024
Evaluating representation learning on the protein structure universe Arian R. Jamasb Alex Morehead Chaitanya K. Joshi Zuobai Zhang Kieran Didi ... Charles Harris Jian Tang Jianlin Cheng Pietro Lio Tom L. Blundell SSL 48 12 0 19 Jun 2024
BEACON: Benchmark for Comprehensive RNA Tasks and Language Models Yuchen Ren Zhiyuan Chen Lifeng Qiao Hongtai Jing Yuchen Cai ... Siqi Sun Hongliang Yan Dong Yuan Wanli Ouyang Xihui Liu 44 9 0 14 Jun 2024
Robust Optimization in Protein Fitness Landscapes Using Reinforcement Learning in Latent Space Minji Lee L. Vecchietti Hyunkyu Jung Hyun Joo Ro Meeyoung Cha Ho Min Kim 32 5 0 29 May 2024
Boosting Protein Language Models with Negative Sample Mining Yaoyao Xu Xinjian Zhao Xiaozhuang Song Benyou Wang Tianshu Yu 38 0 0 28 May 2024
GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning Minghao Xu Yunteng Geng Yihang Zhang Ling Yang Jian Tang Wentao Zhang 40 2 0 25 May 2024
Could Chemical LLMs benefit from Message Passing Jiaqing Xie Ziheng Chi 38 0 0 14 May 2024
Offline Model-Based Optimization via Policy-Guided Gradient Search Yassine Chemingui Aryan Deshwal Trong Nghia Hoang J. Doppa OffRL 45 9 0 08 May 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 26 8 0 23 Apr 2024
Functional Protein Design with Local Domain Alignment Chaohao Yuan Songyou Li Geyan Ye Yikun Zhang Long-Kai Huang Wenbing Huang Wei Liu Jianhua Yao Yu Rong 29 2 0 18 Apr 2024
Kermut: Composite kernel regression for protein variant effects Peter Mørch Groth Mads Herbert Kerrn Lars Olsen Jesper Salomon Wouter Boomsma 39 2 0 09 Apr 2024
HeMeNet: Heterogeneous Multichannel Equivariant Network for Protein Multitask Learning Rong Han Wenbing Huang Lingxiao Luo Xinyan Han Jiaming Shen Qing Cui Jun Zhou Ting Chen 47 2 0 02 Apr 2024
Clustering for Protein Representation Learning Ruijie Quan Wenguan Wang Fan Ma Hehe Fan Yi Yang 29 5 0 30 Mar 2024
Transfer Learning for T-Cell Response Prediction Josua Stadelmaier Brandon Malone Ralf Eggeling 26 0 0 18 Mar 2024
ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling Kangjie Zheng Siyu Long Tianyu Lu Junwei Yang Xinyu Dai Ming Zhang Zaiqing Nie Wei-Ying Ma Hao Zhou 41 5 0 05 Mar 2024
Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey Qizhi Pei Lijun Wu Kaiyuan Gao Jinhua Zhu Yue Wang Zun Wang Tao Qin Rui Yan AI4CE 49 19 0 03 Mar 2024
Enhancing Protein Predictive Models via Proteins Data Augmentation: A Benchmark and New Directions Rui Sun Lirong Wu Haitao Lin Yufei Huang Stan Z. Li 30 1 0 01 Mar 2024
A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications Jiaqi Han Jiacheng Cen Liming Wu Zongzhao Li Xiangzhe Kong ... Zhewei Wei Deli Zhao Yu Rong Wenbing Huang Wenbing Huang AI4CE 34 20 0 01 Mar 2024
Self-Guided Masked Autoencoders for Domain-Agnostic Self-Supervised Learning Johnathan Xie Yoonho Lee Annie S. Chen Chelsea Finn 25 3 0 22 Feb 2024
Efficiently Predicting Mutational Effect on Homologous Proteins by Evolution Encoding Zhiqiang Zhong Davide Mottin 29 1 0 20 Feb 2024