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Protein-ligand binding prediction is central to virtual screening and affinity ranking, two fundamental tasks in drug discovery. While recent retrieval-based methods embed ligands and protein pockets into Euclidean space for…

Machine Learning · Computer Science 2025-11-25 Jianhui Wang , Wenyu Zhu , Bowen Gao , Xin Hong , Ya-Qin Zhang , Wei-Ying Ma , Yanyan Lan

Recently, link prediction algorithms based on neural embeddings have gained tremendous popularity in the Semantic Web community, and are extensively used for knowledge graph completion. While algorithmic advances have strongly focused on…

Artificial Intelligence · Computer Science 2020-08-31 Asan Agibetov , Matthias Samwald

Graph embeddings have emerged as a powerful tool for representing complex network structures in a low-dimensional space, enabling the use of efficient methods that employ the metric structure in the embedding space as a proxy for the…

Social and Information Networks · Computer Science 2024-04-18 Radosław Nowak , Adam Małkowski , Daniel Cieślak , Piotr Sokół , Paweł Wawrzyński

Knowledge Graph Embedding (KGE) methods have gained enormous attention from a wide range of AI communities including Natural Language Processing (NLP) for text generation, classification and context induction. Embedding a huge number of…

Artificial Intelligence · Computer Science 2022-09-19 Mojtaba Moattari , Sahar Vahdati , Farhana Zulkernine

Benefiting from the effectiveness of graph neural networks (GNNs) and contrastive learning, GNN-based contrastive learning has become mainstream for knowledge-aware recommendation. However, most existing contrastive learning-based methods…

Information Retrieval · Computer Science 2025-05-14 Shengyin Sun , Chen Ma

In this paper, we introduce an embedding model, named CapsE, exploring a capsule network to model relationship triples (subject, relation, object). Our CapsE represents each triple as a 3-column matrix where each column vector represents…

Computation and Language · Computer Science 2019-03-07 Dai Quoc Nguyen , Thanh Vu , Tu Dinh Nguyen , Dat Quoc Nguyen , Dinh Phung

Knowledge graph embedding, which projects symbolic entities and relations into continuous vector spaces, is gaining increasing attention. Previous methods allow a single static embedding for each entity or relation, ignoring their intrinsic…

Artificial Intelligence · Computer Science 2020-04-07 Quan Wang , Pingping Huang , Haifeng Wang , Songtai Dai , Wenbin Jiang , Jing Liu , Yajuan Lyu , Yong Zhu , Hua Wu

Knowledge graph embedding refers to projecting entities and relations in knowledge graph into continuous vector spaces. State-of-the-art methods, such as TransE, TransH, and TransR build embeddings by treating relation as translation from…

Computation and Language · Computer Science 2015-09-11 Jun Feng , Mantong Zhou , Yu Hao , Minlie Huang , Xiaoyan Zhu

Knowledge graphs contain rich relational structures of the world, and thus complement data-driven machine learning in heterogeneous data. One of the most effective methods in representing knowledge graphs is to embed symbolic relations and…

Artificial Intelligence · Computer Science 2018-01-29 Kien Do , Truyen Tran , Svetha Venkatesh

Joint representation learning of text and knowledge within a unified semantic space enables us to perform knowledge graph completion more accurately. In this work, we propose a novel framework to embed words, entities and relations into the…

Computation and Language · Computer Science 2016-11-15 Xu Han , Zhiyuan Liu , Maosong Sun

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In…

Computation and Language · Computer Science 2021-04-02 Shaoxiong Ji , Shirui Pan , Erik Cambria , Pekka Marttinen , Philip S. Yu

Graph convolutional neural networks (GCNs) embed nodes in a graph into Euclidean space, which has been shown to incur a large distortion when embedding real-world graphs with scale-free or hierarchical structure. Hyperbolic geometry offers…

Machine Learning · Computer Science 2019-10-30 Ines Chami , Rex Ying , Christopher Ré , Jure Leskovec

Knowledge bases often consist of facts which are harvested from a variety of sources, many of which are noisy and some of which conflict, resulting in a level of uncertainty for each triple. Knowledge bases are also often incomplete,…

Artificial Intelligence · Computer Science 2021-04-13 Xuelu Chen , Michael Boratko , Muhao Chen , Shib Sankar Dasgupta , Xiang Lorraine Li , Andrew McCallum

The cascade of 2D geometric transformations were exploited to model relations between entities in a knowledge graph (KG), leading to an effective KG embedding (KGE) model, CompoundE. Furthermore, the rotation in the 3D space was proposed as…

Artificial Intelligence · Computer Science 2023-04-04 Xiou Ge , Yun-Cheng Wang , Bin Wang , C. -C. Jay Kuo

Many knowledge graph embedding methods operate on triples and are therefore implicitly limited by a very local view of the entire knowledge graph. We present a new framework MOHONE to effectively model higher order network effects in…

Computation and Language · Computer Science 2018-11-02 Hao Yu , Vivek Kulkarni , William Wang

Aiming to alleviate data sparsity and cold-start problems of traditional recommender systems, incorporating knowledge graphs (KGs) to supplement auxiliary information has recently gained considerable attention. Via unifying the KG with…

Information Retrieval · Computer Science 2022-01-04 Yankai Chen , Menglin Yang , Yingxue Zhang , Mengchen Zhao , Ziqiao Meng , Jianye Hao , Irwin King

Label inventories for fine-grained entity typing have grown in size and complexity. Nonetheless, they exhibit a hierarchical structure. Hyperbolic spaces offer a mathematically appealing approach for learning hierarchical representations of…

Computation and Language · Computer Science 2020-10-06 Federico López , Michael Strube

Quaternion contains one real part and three imaginary parts, which provided a more expressive hypercomplex space for learning knowledge graph. Existing quaternion embedding models measure the plausibility of a triplet either through…

Machine Learning · Computer Science 2024-12-13 Weihua Wang , Qiuyu Liang , Feilong Bao , Guanglai Gao

Learning knowledge graph (KG) embeddings has received increasing attention in recent years. Most embedding models in literature interpret relations as linear or bilinear mapping functions to operate on entity embeddings. However, we find…

Artificial Intelligence · Computer Science 2020-04-29 Zequn Sun , Jiacheng Huang , Wei Hu , Muchao Chen , Lingbing Guo , Yuzhong Qu

Due to their flexibility to represent almost any kind of relational data, graph-based models have enjoyed a tremendous success over the past decades. While graphs are inherently only combinatorial objects, however, many prominent analysis…

Social and Information Networks · Computer Science 2024-03-27 Michaël Fanuel , Antoine Aspeel , Michael T. Schaub , Jean-Charles Delvenne
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