OntoProtein: Protein Pretraining With Gene Ontology Embedding

OntoProtein: Protein Pretraining With Gene Ontology Embedding

23 January 2022

Ningyu Zhang

Xiaozhuan Liang

Shumin Deng

Huajun Chen

Papers citing "OntoProtein: Protein Pretraining With Gene Ontology Embedding"

15 / 15 papers shown

Title
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
ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding Yijia Xiao Edward Sun Yiqiao Jin Qifan Wang Wei Wang 47 9 0 21 Aug 2024
GOProteinGNN: Leveraging Protein Knowledge Graphs for Protein Representation Learning Dan Kalifa Uriel Singer Kira Radinsky 42 1 0 31 Jul 2024
Ontology Embedding: A Survey of Methods, Applications and Resources Jiaoyan Chen Olga Mashkova Fernando Zhapa-Camacho R. Hoehndorf Yuan He Ian Horrocks 47 4 0 16 Jun 2024
ProtChatGPT: Towards Understanding Proteins with Large Language Models Chao Wang Hehe Fan Ruijie Quan Yi Yang 26 12 0 15 Feb 2024
xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data Jing Gong Minsheng Hao Xingyi Cheng Xin Zeng Chiming Liu Jianzhu Ma Xuegong Zhang Taifeng Wang Leo T. Song 23 17 0 26 Nov 2023
Multi-level Protein Representation Learning for Blind Mutational Effect Prediction Y. Tan Bingxin Zhou Yuanhong Jiang Yu Wang Liang Hong 21 2 0 08 Jun 2023
Knowledge-Design: Pushing the Limit of Protein Design via Knowledge Refinement Zhangyang Gao Cheng Tan Stan Z. Li 21 15 0 20 May 2023
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey from Precision to Interpretability Zhiqiang Zhong A. Barkova Davide Mottin 22 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 60 61 0 09 Feb 2023
ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts Minghao Xu Xinyu Yuan Santiago Miret Jian Tang AI4TS 25 94 0 28 Jan 2023
Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design Kaiyuan Gao Lijun Wu Jinhua Zhu Tianbo Peng Yingce Xia ... Shufang Xie Tao Qin Haiguang Liu Kun He Tie-Yan Liu 22 9 0 26 Oct 2022
Relphormer: Relational Graph Transformer for Knowledge Graph Representations Zhen Bi Shuyang Cheng Jing Chen Xiaozhuan Liang Feiyu Xiong Ningyu Zhang 29 37 0 22 May 2022
K-BERT: Enabling Language Representation with Knowledge Graph Weijie Liu Peng Zhou Zhe Zhao Zhiruo Wang Qi Ju Haotang Deng Ping Wang 229 778 0 17 Sep 2019
Knowledge Enhanced Contextual Word Representations Matthew E. Peters Mark Neumann IV RobertL.Logan Roy Schwartz Vidur Joshi Sameer Singh Noah A. Smith 226 656 0 09 Sep 2019