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Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D…

Effective protein representation learning is crucial for predicting protein functions. Traditional methods often pretrain protein language models on large, unlabeled amino acid sequences, followed by finetuning on labeled data. While…

Biomolecules · Quantitative Biology 2024-09-05 Jiangbin Zheng , Stan Z. Li

Geometric deep learning (GDL) has demonstrated huge power and enormous potential in molecular data analysis. However, a great challenge still remains for highly efficient molecular representations. Currently, covalent-bond-based molecular…

Computational Physics · Physics 2023-06-28 Cong Shen , Jiawei Luo , Kelin Xia

Graph-level representations (and clustering/classification based on these representations) are required in a variety of applications. Examples include identifying malicious network traffic, prediction of protein properties, and many others.…

Machine Learning · Computer Science 2024-11-20 Xiang Li , Gagan Agrawal , Rajiv Ramnath , Ruoming Jin

Heterogeneous graphs can well describe the complex entity relationships in the real world. For example, online shopping networks contain multiple physical types of consumers and products, as well as multiple relationship types such as…

Machine Learning · Computer Science 2024-07-02 Jing Zhang , Xiaoqian Jiang , Yingjie Xie , Cangqi Zhou

Contrastive learning has achieved great success in self-supervised visual representation learning, but existing approaches mostly ignored spatial information which is often crucial for visual representation. This paper presents…

Computer Vision and Pattern Recognition · Computer Science 2020-11-20 Xinyue Huo , Lingxi Xie , Longhui Wei , Xiaopeng Zhang , Hao Li , Zijie Yang , Wengang Zhou , Houqiang Li , Qi Tian

Data augmentation is a crucial component in unsupervised contrastive learning (CL). It determines how positive samples are defined and, ultimately, the quality of the learned representation. In this work, we open the door to new…

Computer Vision and Pattern Recognition · Computer Science 2023-05-31 Benoit Dufumier , Carlo Alberto Barbano , Robin Louiset , Edouard Duchesnay , Pietro Gori

Graph Contrastive Learning (GCL), learning the node representations by augmenting graphs, has attracted considerable attentions. Despite the proliferation of various graph augmentation strategies, some fundamental questions still remain…

Machine Learning · Computer Science 2022-10-06 Nian Liu , Xiao Wang , Deyu Bo , Chuan Shi , Jian Pei

Recent years, graph contrastive learning (GCL), which aims to learn representations from unlabeled graphs, has made great progress. However, the existing GCL methods mostly adopt human-designed graph augmentations, which are sensitive to…

Social and Information Networks · Computer Science 2023-06-30 Xiao Shen , Dewang Sun , Shirui Pan , Xi Zhou , Laurence T. Yang

Graph contrastive learning (GCL) has garnered significant attention recently since it learns complex structural information from graphs through self-supervised learning manner. However, prevalent GCL models may suffer from performance…

Machine Learning · Computer Science 2025-04-28 Xiaofan Wei , Binyan Zhang

Graphs model complex relationships between entities, with nodes and edges capturing intricate connections. Node representation learning involves transforming nodes into low-dimensional embeddings. These embeddings are typically used as…

Machine Learning · Computer Science 2024-11-04 Ying-Chun Lin , Jennifer Neville

The electronic map plays a crucial role in geographic information systems, serving various urban managerial scenarios and daily life services. Developing effective Map Entity Representation Learning (MERL) methods is crucial to extracting…

Machine Learning · Computer Science 2024-02-12 Jiawei Jiang , Yifan Yang , Jingyuan Wang , Junjie Wu

Link prediction tasks focus on predicting possible future connections. Most existing researches measure the likelihood of links by different similarity scores on node pairs and predict links between nodes. However, the similarity-based…

Machine Learning · Computer Science 2023-03-09 Zehua Zhang , Shilin Sun , Guixiang Ma , Caiming Zhong

Molecule representation learning (MRL) methods aim to embed molecules into a real vector space. However, existing SMILES-based (Simplified Molecular-Input Line-Entry System) or GNN-based (Graph Neural Networks) MRL methods either take…

Machine Learning · Computer Science 2021-09-23 Hongwei Wang , Weijiang Li , Xiaomeng Jin , Kyunghyun Cho , Heng Ji , Jiawei Han , Martin D. Burke

Molecular property prediction refers to the task of labeling molecules with some biochemical properties, playing a pivotal role in the drug discovery and design process. Recently, with the advancement of machine learning, deep…

Molecular Networks · Quantitative Biology 2024-01-10 Zeyu Wang , Tianyi Jiang , Jinhuan Wang , Qi Xuan

Recent studies show that graph neural networks (GNNs) are prevalent to model high-order relationships for collaborative filtering (CF). Towards this research line, graph contrastive learning (GCL) has exhibited powerful performance in…

Information Retrieval · Computer Science 2024-02-27 Xubin Ren , Lianghao Xia , Jiashu Zhao , Dawei Yin , Chao Huang

In this work, we aim to consider the application of contrastive learning in the scenario of the recommendation system adequately, making it more suitable for recommendation task. We propose a learning paradigm called supervised contrastive…

Information Retrieval · Computer Science 2022-04-20 Chun Yang

Contrastive Learning (CL) performances as a rising approach to address the challenge of sparse and noisy recommendation data. Although having achieved promising results, most existing CL methods only perform either hand-crafted data or…

Information Retrieval · Computer Science 2023-11-22 Xiuyuan Qin , Huanhuan Yuan , Pengpeng Zhao , Junhua Fang , Fuzhen Zhuang , Guanfeng Liu , Victor Sheng

For graph self-supervised learning (GSSL), masked autoencoder (MAE) follows the generative paradigm and learns to reconstruct masked graph edges or node features. Contrastive Learning (CL) maximizes the similarity between augmented views of…

Machine Learning · Computer Science 2023-10-25 Yuxiang Wang , Xiao Yan , Chuang Hu , Fangcheng Fu , Wentao Zhang , Hao Wang , Shuo Shang , Jiawei Jiang

Multimodal representation learning is commonly built on a shared-private decomposition, treating latent information as either common to all modalities or specific to one. This binary view is often inadequate: many factors are shared by only…

Machine Learning · Statistics 2026-04-08 Huichao Li , Junhan Yu , Doudou Zhou