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The problem of accelerating drug discovery relies heavily on automatic tools to optimize precursor molecules to afford them with better biochemical properties. Our work in this paper substantially extends prior state-of-the-art on…

Chemical Physics · Physics 2019-10-22 Wengong Jin , Regina Barzilay , Tommi Jaakkola

Hyperbolic geometry has emerged as an effective latent space for representing complex networks, owing to its ability to capture hierarchical organization and heterogeneous connectivity patterns using low-dimensional embeddings. As a result,…

Machine Learning · Computer Science 2026-05-01 Sofía Pérez Casulo , Marcelo Fiori , Bernardo Marenco , Federico Larroca

Recent studies on knowledge graph embedding focus on mapping entities and relations into low-dimensional vector spaces. While most existing models primarily exploit structural information, knowledge graphs also contain rich contextual and…

Computation and Language · Computer Science 2025-09-03 Qisong Li , Ji Lin , Sijia Wei , Neng Liu

Graph Transformers (GTs) have demonstrated a strong capability in modeling graph structures by addressing the intrinsic limitations of graph neural networks (GNNs), such as over-smoothing and over-squashing. Recent studies have proposed…

Machine Learning · Computer Science 2025-02-28 Chaohao Yuan , Kangfei Zhao , Ercan Engin Kuruoglu , Liang Wang , Tingyang Xu , Wenbing Huang , Deli Zhao , Hong Cheng , Yu Rong

Knowledge graphs can be used in many areas related to data semantics such as question-answering systems, knowledge based systems. However, the currently constructed knowledge graphs need to be complemented for better knowledge in terms of…

Artificial Intelligence · Computer Science 2023-07-25 Chun-Hee Lee , Dong-oh Kang , Hwa Jeon Song

Deep learning currently dominates the benchmarks for various NLP tasks and, at the basis of such systems, words are frequently represented as embeddings --vectors in a low dimensional space-- learned from large text corpora and various…

Computation and Language · Computer Science 2019-09-25 Ronald Denaux , Jose Manuel Gomez-Perez

Representation Learning of words and Knowledge Graphs (KG) into low dimensional vector spaces along with its applications to many real-world scenarios have recently gained momentum. In order to make use of multiple KG embeddings for…

Computation and Language · Computer Science 2020-04-16 Russa Biswas , Mehwish Alam , Harald Sack

Network embedding assigns nodes in a network to low-dimensional representations and effectively preserves the network structure. Recently, a significant amount of progresses have been made toward this emerging network analysis paradigm. In…

Social and Information Networks · Computer Science 2017-11-27 Peng Cui , Xiao Wang , Jian Pei , Wenwu Zhu

Knowledge graph embedding is an important task and it will benefit lots of downstream applications. Currently, deep neural networks based methods achieve state-of-the-art performance. However, most of these existing methods are very complex…

Artificial Intelligence · Computer Science 2020-11-02 Feiliang Ren , Juchen Li , Huihui Zhang , Shilei Liu , Bochao Li , Ruicheng Ming , Yujia Bai

Determining the number of embeddings of Laman graph frameworks is an open problem which corresponds to understanding the solutions of the resulting systems of equations. In this paper we investigate the bounds which can be obtained from the…

Combinatorics · Mathematics 2009-03-13 Reinhard Steffens , Thorsten Theobald

Graph embedding aims at learning a vector-based representation of vertices that incorporates the structure of the graph. This representation then enables inference of graph properties. Existing graph embedding techniques, however, do not…

Knowledge Graph Completion has been increasingly adopted as a useful method for helping address several tasks in biomedical research, such as drug repurposing or drug-target identification. To that end, a variety of datasets and Knowledge…

Machine Learning · Computer Science 2025-11-07 Alberto Cattaneo , Stephen Bonner , Thomas Martynec , Edward Morrissey , Carlo Luschi , Ian P Barrett , Daniel Justus

The persistence diagram (PD) is an increasingly popular topological descriptor. By encoding the size and prominence of topological features at varying scales, the PD provides important geometric and topological information about a space.…

Representation learning on graphs has been gaining attention due to its wide applicability in predicting missing links, and classifying and recommending nodes. Most embedding methods aim to preserve certain properties of the original graph…

Social and Information Networks · Computer Science 2019-09-13 Palash Goyal , Di Huang , Sujit Rokka Chhetri , Arquimedes Canedo , Jaya Shree , Evan Patterson

The objective of knowledge graph embedding is to encode both entities and relations of knowledge graphs into continuous low-dimensional vector spaces. Previously, most works focused on symbolic representation of knowledge graph with…

Computation and Language · Computer Science 2016-12-14 Jiacheng Xu , Kan Chen , Xipeng Qiu , Xuanjing Huang

Graph drawing research traditionally focuses on producing geometric embeddings of graphs satisfying various aesthetic constraints. After the geometric embedding is specified, there is an additional step that is often overlooked or ignored:…

Computational Geometry · Computer Science 2007-05-23 Michael B. Dillencourt , David Eppstein , Michael T. Goodrich

In this paper, we propose a new geometric approach for knowledge graph completion via low rank tensor approximation. We augment a pretrained and well-established Euclidean model based on a Tucker tensor decomposition with a novel hyperbolic…

Machine Learning · Computer Science 2025-04-04 Viacheslav Yusupov , Maxim Rakhuba , Evgeny Frolov

Following the success of Word2Vec embeddings, graph embeddings (GEs) have gained substantial traction. GEs are commonly generated and evaluated extrinsically on downstream applications, but intrinsic evaluations of the original graph…

Machine Learning · Computer Science 2023-09-06 Hong Yung Yip , Chidaksh Ravuru , Neelabha Banerjee , Shashwat Jha , Amit Sheth , Aman Chadha , Amitava Das

Knowledge graphs (KGs) are powerful tools that codify relational behaviour between entities in knowledge bases. KGs can simultaneously model many different types of subject-predicate-object and higher-order relations. As such, they offer a…

Social and Information Networks · Computer Science 2020-10-27 Charilaos I. Kanatsoulis , Nicholas D. Sidiropoulos

Graphs face challenges when dealing with massive datasets. They are essential tools for modeling interconnected data and often become computationally expensive. Graph embedding techniques, on the other hand, provide an efficient approach.…

Databases · Computer Science 2024-12-16 Plácido A Souza Neto