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Advances in deep learning models have revolutionized the study of biomolecule systems and their mechanisms. Graph representation learning, in particular, is important for accurately capturing the geometric information of biomolecules at…

Quantitative Methods · Quantitative Biology 2023-04-07 Xinye Xiong , Bingxin Zhou , Yu Guang Wang

We propose Medial Atom Ray Fields (MARFs), a novel neural object representation that enables accurate differentiable surface rendering with a single network evaluation per camera ray. Existing neural ray fields struggle with multi-view…

Graphics · Computer Science 2023-07-04 Peder Bergebakken Sundt , Theoharis Theoharis

Lying at the interface between Network Science and Machine Learning, node embedding algorithms take a graph as input and encode its structure onto output vectors that represent nodes in an abstract geometric space, enabling various…

Physics and Society · Physics 2025-10-03 Riccardo Milocco , Fabian Jansen , Diego Garlaschelli

Representing a graph as a vector is a challenging task; ideally, the representation should be easily computable and conducive to efficient comparisons among graphs, tailored to the particular data and analytical task at hand. Unfortunately,…

Social and Information Networks · Computer Science 2018-11-16 Anton Tsitsulin , Davide Mottin , Panagiotis Karras , Alex Bronstein , Emmanuel Müller

We introduce the Hierarchical Unified Graph Representation (HUGR): a novel graph based intermediate representation for mixed quantum-classical programs. HUGR's design features high expressivity and extensibility to capture the capabilities…

A subgraph is constructed by using a subset of vertices and edges of a given graph. There exist many graph properties that are hereditary for subgraphs. Hence, researchers from different communities have paid a great deal of attention in…

Combinatorics · Mathematics 2023-06-06 Kai Siong Yow , Ningyi Liao , Siqiang Luo , Reynold Cheng , Chenhao Ma , Xiaolin Han

This work considers the distributed computation of the one-to-one vertex correspondences between two undirected and connected graphs, which is called \textit{graph matching}, over multi-agent networks. Given two \textit{isomorphic} and…

Optimization and Control · Mathematics 2020-02-21 Quoc Van Tran , Zhiyong Sun , Brian D. O. Anderson , Hyo-Sung Ahn

Graph matching is a challenging problem with very important applications in a wide range of fields, from image and video analysis to biological and biomedical problems. We propose a robust graph matching algorithm inspired in…

Optimization and Control · Mathematics 2013-11-26 Marcelo Fiori , Pablo Sprechmann , Joshua Vogelstein , Pablo Musé , Guillermo Sapiro

A path graph is the intersection graph of paths in a tree. A directed path graph is the intersection graph of paths in a directed tree. Even if path graphs and directed path graphs are characterized very similarly, their recognition…

Data Structures and Algorithms · Computer Science 2025-05-07 Lorenzo Balzotti

Graphs are a representation of structured data that captures the relationships between sets of objects. With the ubiquity of available network data, there is increasing industrial and academic need to quickly analyze graphs with billions of…

Machine Learning · Computer Science 2023-07-28 Brandon Mayer , Anton Tsitsulin , Hendrik Fichtenberger , Jonathan Halcrow , Bryan Perozzi

Graph-based methods have been proposed as a unified framework for discrete calculus of local and nonlocal image processing methods in the recent years. In order to translate variational models and partial differential equations to a graph,…

Numerical Analysis · Mathematics 2018-12-10 Ronny Bergmann , Daniel Tenbrinck

Bayesian networks are probabilistic graphical models widely employed to understand dependencies in high dimensional data, and even to facilitate causal discovery. Learning the underlying network structure, which is encoded as a directed…

Machine Learning · Statistics 2022-02-03 Jack Kuipers , Polina Suter , Giusi Moffa

Neural networks that process the parameters of other neural networks find applications in domains as diverse as classifying implicit neural representations, generating neural network weights, and predicting generalization errors. However,…

Unsupervised data representation and visualization using tools from topology is an active and growing field of Topological Data Analysis (TDA) and data science. Its most prominent line of work is based on the so-called Mapper graph, which…

Machine Learning · Computer Science 2025-06-04 Ziyad Oulhaj , Mathieu Carrière , Bertrand Michel

Machine learning on graph structured data has attracted much research interest due to its ubiquity in real world data. However, how to efficiently represent graph data in a general way is still an open problem. Traditional methods use…

Machine Learning · Computer Science 2019-11-14 Jiaqi Ma , Qiaozhu Mei

The graph partitioning problem is widely used and studied in many practical and theoretical applications. The multilevel strategies represent today one of the most effective and efficient generic frameworks for solving this problem on…

Data Structures and Algorithms · Computer Science 2012-04-04 Ilya Safro , Peter Sanders , Christian Schulz

Linear algebraic expressions are the essence of many computationally intensive problems, including scientific simulations and machine learning applications. However, translating high-level formulations of these expressions to efficient…

Distributed, Parallel, and Cluster Computing · Computer Science 2019-03-22 Dániel Berényi , András Leitereg , Gábor Lehel

In modern mathematics, graphs figure as one of the better-investigated class of mathematical objects. Various properties of graphs, as well as graph-processing algorithms, can be useful if graphs of a certain kind are used as denotations…

Logic in Computer Science · Computer Science 2007-05-23 Alex Shkotin

Multiresolution Matrix Factorization (MMF) is unusual amongst fast matrix factorization algorithms in that it does not make a low rank assumption. This makes MMF especially well suited to modeling certain types of graphs with complex…

Machine Learning · Computer Science 2021-11-04 Truong Son Hy , Risi Kondor

Stratified digraphs are popular models for feedforward neural networks. However, computation of their path homologies has been limited to low dimensions due to high computational complexity. A recursive algorithm is proposed to compute…

Computational Geometry · Computer Science 2024-12-12 Zhengtong Zhu , Zhiyi Chi