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There has been a lot of recent interest in mining patterns from graphs. Often, the exact structure of the patterns of interest is not known. This happens, for example, when molecular structures are mined to discover fragments useful as…

Data Structures and Algorithms · Computer Science 2007-05-23 Pavel Dmitriev , Carl Lagoze

Motivation: Molecular interaction networks summarize complex biological processes as graphs, whose structure is informative of biological function at multiple scales. Simultaneously, omics technologies measure the variation or activity of…

Quantitative Methods · Quantitative Biology 2020-12-24 Ramin Hasibi , Tom Michoel

Graph kernels are kernel methods measuring graph similarity and serve as a standard tool for graph classification. However, the use of kernel methods for node classification, which is a related problem to graph representation learning, is…

Machine Learning · Computer Science 2019-10-08 Yu Tian , Long Zhao , Xi Peng , Dimitris N. Metaxas

Modern data applications increasingly involve heterogeneous data managed in different models and stored across disparate database engines, often deployed as separate installs. Limited research has addressed cross-model query processing in…

Databases · Computer Science 2026-03-17 Xiuwen Zheng , Arun Kumar , Amarnath Gupta

The inherent connectivity and dependency of graph-structured data, combined with its unique topology-driven access patterns, pose fundamental challenges to conventional data replication and request routing strategies in geo-distributed…

Databases · Computer Science 2025-10-22 Feng Yao , Xiaokang Yang , Shufeng Gong , Song Yu , Yanfeng Zhang , Ge Yu

Graph similarity computation aims to predict a similarity score between one pair of graphs to facilitate downstream applications, such as finding the most similar chemical compounds similar to a query compound or Fewshot 3D Action…

Machine Learning · Computer Science 2021-01-06 Haoyan Xu , Ziheng Duan , Jie Feng , Runjian Chen , Qianru Zhang , Zhongbin Xu , Yueyang Wang

Graph reconstruction can efficiently detect the underlying topology of massive networks such as the Internet. Given a query oracle and a set of nodes, the goal is to obtain the edge set by performing as few queries as possible. An algorithm…

Data Structures and Algorithms · Computer Science 2024-07-29 Clara Stegehuis , Lotte Weedage

Graph retrieval based on subgraph isomorphism has several real-world applications such as scene graph retrieval, molecular fingerprint detection and circuit design. Roy et al. [35] proposed IsoNet, a late interaction model for subgraph…

Machine Learning · Computer Science 2025-10-28 Ashwin Ramachandran , Vaibhav Raj , Indrayumna Roy , Soumen Chakrabarti , Abir De

Column Generation (CG) is a popular method dedicated to enhancing computational efficiency in large scale Combinatorial Optimization (CO) problems. It reduces the number of decision variables in a problem by solving a pricing problem. For…

Machine Learning · Computer Science 2025-04-18 Abdo Abouelrous , Laurens Bliek , Adriana F. Gabor , Yaoxin Wu , Yingqian Zhang

As Generative Engines revolutionize information retrieval by synthesizing direct answers from retrieved sources, ensuring source visibility becomes a significant challenge. Improving it through targeted content revisions is a practical…

Information Retrieval · Computer Science 2026-01-21 Heyang Zhou , JiaJia Chen , Xiaolu Chen , Jie Bao , Zhen Chen , Yong Liao

Graph Neural Networks (GNNs) have demonstrated remarkable performance in a wide range of tasks, such as node classification, link prediction, and graph classification, by exploiting the structural information in graph-structured data.…

Machine Learning · Computer Science 2026-01-09 Oscar Llorente , Jaime Boal , Eugenio F. Sánchez-Úbeda , Antonio Diaz-Cano , Miguel Familiar

Graph data management (also called NoSQL) has revealed beneficial characteristics in terms of flexibility and scalability by differently balancing between query expressivity and schema flexibility. This peculiar advantage has resulted into…

Databases · Computer Science 2019-09-10 Harsh Thakkar , Dharmen Punjani , Soeren Auer , Maria-Esther Vidal

Subgraph matching is challenging as it necessitates time-consuming combinatorial searches. Recent Graph Neural Network (GNN)-based approaches address this issue by employing GNN encoders to extract graph information and hinge distance…

Machine Learning · Computer Science 2025-10-02 Zhouyang Liu , Ning Liu , Yixin Chen , Jiezhong He , Menghan Jia , Dongsheng Li

Graph Neural Networks (GNNs) excel at analyzing graph-structured data but struggle on heterophilic graphs, where connected nodes often belong to different classes. While this challenge is commonly addressed with specialized GNN…

Machine Learning · Computer Science 2025-05-20 Harel Mendelman , Haggai Maron , Ronen Talmon

Knowledge graph (KG) embedding methods which map entities and relations to unique embeddings in the KG have shown promising results on many reasoning tasks. However, the same embedding dimension for both dense entities and sparse entities…

Computation and Language · Computer Science 2022-05-06 Linlin Chao , Xiexiong Lin , Taifeng Wang , Wei Chu

Graph neural networks (GNNs) have emerged as a powerful approach for solving many network mining tasks. However, learning on large graphs remains a challenge - many recently proposed scalable GNN approaches rely on an expensive…

Graph-structured data is central to many scientific and industrial domains, where the goal is often to optimize objectives defined over graph structures. Given the combinatorial complexity of graph spaces, such optimization problems are…

Optimization and Control · Mathematics 2025-09-25 Shiqiang Zhang , Ruth Misener

Symmetry plays a major role in subgraph matching both in the description of the graphs in question and in how it confounds the search process. This work addresses how to quantify these effects and how to use symmetries to increase the…

Data Structures and Algorithms · Computer Science 2023-01-10 Dominic Yang , Yurun Ge , Thien Nguyen , Jacob Moorman , Denali Molitor , Andrea Bertozzi

The phenomenal growth of graph data from a wide variety of real-world applications has rendered graph querying to be a problem of paramount importance. Traditional techniques use structural as well as node similarities to find matches of a…

Databases · Computer Science 2021-05-14 Jithin Vachery , Akhil Arora , Sayan Ranu , Arnab Bhattacharya

We study the optimization of navigational graph queries, i.e., queries which combine recursive and pattern-matching fragments. Current approaches to their evaluation are not effective in practice. Towards addressing this, we present a…

Databases · Computer Science 2026-05-21 Thomas Mulder , George Fletcher , Nikolay Yakovets