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Recent advances in molecular representation learning have produced highly effective encodings of molecules for numerous cheminformatics and bioinformatics tasks. However, extracting general chemical insight while balancing predictive…

Machine Learning · Computer Science 2025-09-26 Rahul Khorana

Hypergraphs, with their capacity to depict high-order relationships, have emerged as a significant extension of traditional graphs. Although Graph Neural Networks (GNNs) have remarkable performance in graph representation learning, their…

Machine Learning · Computer Science 2024-11-07 Khaled Mohammed Saifuddin , Mehmet Emin Aktas , Esra Akbas

Data-driven graph learning models a network by determining the strength of connections between its nodes. The data refers to a graph signal which associates a value with each graph node. Existing graph learning methods either use simplified…

Machine Learning · Computer Science 2020-11-05 Nafiseh Ghoroghchian , David M. Groppe , Roman Genov , Taufik A. Valiante , Stark C. Draper

Graphs are a commonly used construct for representing relationships between elements in complex high dimensional datasets. Many real-world phenomenon are dynamic in nature, meaning that any graph used to represent them is inherently…

Social and Information Networks · Computer Science 2018-11-21 Stephen Bonner , John Brennan , Ibad Kureshi , Georgios Theodoropoulos , Andrew Stephen McGough , Boguslaw Obara

Graph foundation models represent a transformative paradigm for learning transferable representations across diverse graph domains. Recent methods leverage large language models to unify graph and text modalities into a shared…

Machine Learning · Computer Science 2025-12-23 Heng Zhang , Tianyi Zhang , Yuling Shi , Xiaodong Gu , Yaomin Shen , Haochen You , Zijian Zhang , Yilei Yuan , Jin Huang

Heterogeneous graphs generally refers to graphs with different types of nodes and edges. A common approach for extracting useful information from heterogeneous graphs is to use meta-graphs, which can be seen as a special kind of directed…

Machine Learning · Computer Science 2023-09-04 Hansi Yang , Peiyu Zhang , Quanming Yao

Grouping the nodes of a graph into clusters is a standard technique for studying networks. We study a problem where we are given a directed network and are asked to partition the graph into a sequence of coherent groups. We assume that…

Social and Information Networks · Computer Science 2025-12-08 Iiro Kumpulainen , Nikolaj Tatti

Temporal graph is an abstraction for modeling dynamic systems that consist of evolving interaction elements. In this paper, we aim to solve an important yet neglected problem -- how to learn information from high-order neighbors in temporal…

Machine Learning · Computer Science 2023-04-17 Zehong Wang , Qi Li , Donghua Yu

Current graph clustering methods emphasize individual node and edge con nections, while ignoring higher-order organization at the level of motif. Re cently, higher-order graph clustering approaches have been designed by motif based…

Machine Learning · Computer Science 2024-05-21 Ye Liu , Xuelei Lin , Yejia Chen , Reynold Cheng

Graph Transformers, leveraging the global attention to capture long-range dependencies in graph structures, have significantly advanced graph machine learning, but face prohibitive computational complexity. Tokenized Graph Learning Models…

Machine Learning · Computer Science 2025-05-23 Zhibiao Wang , Yunlong Zhou , Ziwei Zhang , Mengmei Zhang , Shirui Pan , Chunming Hu , Xiao Wang

Fredman proposed in 1976 the following algorithmic problem: Given are a ground set $X$, some partial order $P$ over $X$, and some comparison oracle $O_L$ that specifies a linear order $L$ over $X$ that extends $P$. A query to $O_L$ has as…

Data Structures and Algorithms · Computer Science 2026-02-10 Ivor van der Hoog , Eva Rotenberg , Daniel Rutschmann

Growing graphs describe a multitude of developing processes from maturing brains to expanding vocabularies to burgeoning public transit systems. Each of these growing processes likely adheres to proliferation rules that establish an…

Quantitative Methods · Quantitative Biology 2020-05-27 Ann Sizemore Blevins , Danielle S. Bassett

Prediction and discovery of new materials with desired properties are at the forefront of quantum science and technology research. A major bottleneck in this field is the computational resources and time complexity related to finding new…

Graph neural networks (GNNs) are a powerful architecture for tackling graph learning tasks, yet have been shown to be oblivious to eminent substructures such as cycles. We present TOGL, a novel layer that incorporates global topological…

Machine Learning · Computer Science 2022-03-18 Max Horn , Edward De Brouwer , Michael Moor , Yves Moreau , Bastian Rieck , Karsten Borgwardt

Attributed graph clustering is challenging as it requires joint modelling of graph structures and node attributes. Recent progress on graph convolutional networks has proved that graph convolution is effective in combining structural and…

Machine Learning · Computer Science 2019-06-05 Xiaotong Zhang , Han Liu , Qimai Li , Xiao-Ming Wu

Many NLP applications can be framed as a graph-to-sequence learning problem. Previous work proposing neural architectures on this setting obtained promising results compared to grammar-based approaches but still rely on linearisation…

Computation and Language · Computer Science 2018-06-27 Daniel Beck , Gholamreza Haffari , Trevor Cohn

Decentralized learning has recently been attracting increasing attention for its applications in parallel computation and privacy preservation. Many recent studies stated that the underlying network topology with a faster consensus rate…

Machine Learning · Computer Science 2023-10-17 Yuki Takezawa , Ryoma Sato , Han Bao , Kenta Niwa , Makoto Yamada

Transformers, adapted from natural language processing, are emerging as a leading approach for graph representation learning. Contemporary graph transformers often treat nodes or edges as separate tokens. This approach leads to…

Machine Learning · Computer Science 2023-10-04 Zihan Pengmei , Zimu Li , Chih-chan Tien , Risi Kondor , Aaron R. Dinner

The graph identification problem consists of discovering the interactions among nodes in a network given their state/feature trajectories. This problem is challenging because the behavior of a node is coupled to all the other nodes by the…

Systems and Control · Electrical Eng. & Systems 2023-10-24 Eduardo Sebastian , Thai Duong , Nikolay Atanasov , Eduardo Montijano , Carlos Sagues

Graph Neural Networks (GNNs) have been highly successful for the node classification task. GNNs typically assume graphs are homophilic, i.e. neighboring nodes are likely to belong to the same class. However, a number of real-world graphs…

Machine Learning · Computer Science 2024-09-20 Yurui Lai , Taiyan Zhang , Rui Fan