MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction
Prediction via Microenvironment-Aware Protein Embedding

MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding

22 February 2024

Lirong Wu

Siyuan Li

Nitesh V. Chawla

Stan Z. Li

Papers citing "MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding"

18 / 18 papers shown

Title
SCOPE-DTI: Semi-Inductive Dataset Construction and Framework Optimization for Practical Usability Enhancement in Deep Learning-Based Drug Target Interaction Prediction Y. Chen Xiang Ji Ziyue Zhang Yuming Zhou Yang-Chi-Dung Lin ... Yixian Huang Shidong Cui Shih-Chung Yen Ariel Warshel Hsien-Da Huang 64 0 0 12 Mar 2025
MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction Cheng Tan Zhenxiao Cao Zhangyang Gao Lirong Wu Siyuan Li Yufei Huang Jun-Xiong Xia Bozhen Hu Stan Z. Li 43 0 0 04 Nov 2024
Learning to Model Graph Structural Information on MLPs via Graph Structure Self-Contrasting Lirong Wu Haitao Lin Guojiang Zhao Cheng Tan Stan Z. Li 28 0 0 09 Sep 2024
Reactzyme: A Benchmark for Enzyme-Reaction Prediction Chenqing Hua Bozitao Zhong Sitao Luan Liang Hong Guy Wolf Doina Precup Shuangjia Zheng 39 5 0 24 Aug 2024
Multi-level Interaction Modeling for Protein Mutational Effect Prediction Yuanle Mo Xin Hong Bowen Gao Yinjun Jia Yanyan Lan AI4CE 24 2 0 28 May 2024
Learning to Predict Mutation Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning Lirong Wu Yijun Tian Haitao Lin Yufei Huang Siyuan Li Nitesh V. Chawla Stan Z. Li 42 4 0 16 May 2024
VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling Siyuan Li Zedong Wang Zicheng Liu Di Wu Cheng Tan Jiangbin Zheng Yufei Huang Stan Z. Li 40 7 0 13 May 2024
ProLLM: Protein Chain-of-Thoughts Enhanced LLM for Protein-Protein Interaction Prediction Mingyu Jin Haochen Xue Zhenting Wang Boming Kang Ruosong Ye Kaixiong Zhou Mengnan Du Yongfeng Zhang LLMAG 35 10 0 30 Mar 2024
A Teacher-Free Graph Knowledge Distillation Framework with Dual Self-Distillation Lirong Wu Haitao Lin Zhangyang Gao Guojiang Zhao Stan Z. Li 40 8 0 06 Mar 2024
PPFlow: Target-aware Peptide Design with Torsional Flow Matching Haitao Lin Odin Zhang Huifeng Zhao Dejun Jiang Lirong Wu Zicheng Liu Yufei Huang Stan Z. Li 54 12 0 05 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
Effective Protein-Protein Interaction Exploration with PPIretrieval Chenqing Hua Connor W. Coley Guy Wolf Doina Precup Shuangjia Zheng 30 3 0 06 Feb 2024
A Graph is Worth $K$ Words: Euclideanizing Graph using Pure Transformer Zhangyang Gao Daize Dong Cheng Tan Jun-Xiong Xia Bozhen Hu Stan Z. Li 46 6 0 04 Feb 2024
Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction Yufei Huang Siyuan Li Jin Su Lirong Wu Odin Zhang ... Zihan Liu Zhangyang Gao Yuyang Liu Jiangbin Zheng Stan. ZQ. Li 3DV 38 13 0 14 Oct 2023
Knowledge Distillation on Graphs: A Survey Yijun Tian Shichao Pei Xiangliang Zhang Chuxu Zhang Nitesh V. Chawla 18 28 0 01 Feb 2023
Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook Matching Perspective Cheng Tan Zhangyang Gao Hanqun Cao Xingran Chen Ge Wang Lirong Wu Jun-Xiong Xia Jiangbin Zheng Stan Z. Li 27 1 0 02 Dec 2022
Adversarial Masking for Self-Supervised Learning Yuge Shi N. Siddharth Philip H. S. Torr Adam R. Kosiorek SSL 56 82 0 31 Jan 2022
Masked Autoencoders Are Scalable Vision Learners Kaiming He Xinlei Chen Saining Xie Yanghao Li Piotr Dollár Ross B. Girshick ViT TPM 305 7,443 0 11 Nov 2021