PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence
Understanding

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PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding

5 June 2022

Jian Tang

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Papers citing "PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding"

19 / 19 papers shown

Title
PFMBench: Protein Foundation Model Benchmark Zhangyang Gao Hao Wang Cheng Tan Chenrui Xu Mengdi Liu Bozhen Hu Linlin Chao Xiaoming Zhang Stan Z. Li 17 0 0 01 Jun 2025
Rethinking Text-based Protein Understanding: Retrieval or LLM? Juntong Wu Zijing Liu He Cao Hao Li Bin Feng Zishan Shu Ke Yu Li Yuan Yu-Feng Li 83 1 0 26 May 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 135 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 72 1 0 06 Apr 2025
Protein Structure Tokenization: Benchmarking and New Recipe Xinyu Yuan Zichen Wang Marcus Collins Huzefa Rangwala 62 1 0 28 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 207 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 Zhang James Zou Yizhou Sun Wei Wang LM&MA AI4CE 145 4 0 21 Feb 2025
Leveraging Large Language Models to Predict Antibody Biological Activity Against Influenza A Hemagglutinin Ella Barkan Ibrahim Siddiqui Kevin J. Cheng Alex Golts Yoel Shoshan J. Weber Yailin Campos Mota Michal Ozery-Flato Giuseppe A. Sautto AI4CE 96 0 0 02 Feb 2025
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 119 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 83 1 0 10 Oct 2024
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning Jiaqing Xie Yue Zhao 134 1 0 02 Oct 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 79 2 0 02 Apr 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 60 2 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 168 25 0 01 Mar 2024
Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction Zuobai Zhang Minghao Xu A. Lozano Vijil Chenthamarakshan Payel Das Jian Tang DiffM 88 21 0 28 Jan 2023
ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts Minghao Xu Xinyu Yuan Santiago Miret Jian Tang AI4TS 104 106 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 238 102 0 16 Jan 2023
Protein Language Models and Structure Prediction: Connection and Progression Bozhen Hu Jun Xia Jiangbin Zheng Cheng Tan Yufei Huang Yongjie Xu Stan Z. Li 70 41 0 30 Nov 2022
ImmunoLingo: Linguistics-based formalization of the antibody language Mai Ha Vu Philippe A. Robert Rahmad Akbar B. Swiatczak G. K. Sandve Dag Trygve Tryslew Haug Victor Greiff AI4CE 99 8 0 26 Sep 2022

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