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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

Molecular machine learning has gained popularity with the advancements of geometric deep learning. In parallel, retrieval-augmented generation has become a principled approach commonly used with language models. However, the optimal…

Machine Learning · Computer Science 2025-07-04 Runzhong Wang , Rui-Xi Wang , Mrunali Manjrekar , Connor W. Coley

The application of deep learning to symbolic domains remains an active research endeavour. Graph neural networks (GNN), consisting of trained neural modules which can be arranged in different topologies at run time, are sound alternatives…

Social and Information Networks · Computer Science 2019-12-02 Pedro H. C. Avelar , Henrique Lemos , Marcelo O. R. Prates , Luis Lamb

Recently, there have been some breakthroughs in graph analysis by applying the graph neural networks (GNNs) following a neighborhood aggregation scheme, which demonstrate outstanding performance in many tasks. However, we observe that the…

Machine Learning · Computer Science 2021-04-13 Hanchen Wang , Defu Lian , Ying Zhang , Lu Qin , Xiangjian He , Yiguang Lin , Xuemin Lin

Modeling the energy and forces of atomic systems is a fundamental problem in computational chemistry with the potential to help address many of the world's most pressing problems, including those related to energy scarcity and climate…

Graph algorithms are key tools in many fields of science and technology. Some of these algorithms depend on propagating information between distant nodes in a graph. Recently, there have been a number of deep learning architectures proposed…

Machine Learning · Computer Science 2018-10-30 Matthew K. Matlock , Arghya Datta , Na Le Dang , Kevin Jiang , S. Joshua Swamidass

Molecular representation learning has attracted much attention recently. A molecule can be viewed as a 2D graph with nodes/atoms connected by edges/bonds, and can also be represented by a 3D conformation with 3-dimensional coordinates of…

Machine Learning · Computer Science 2022-07-20 Jinhua Zhu , Yingce Xia , Lijun Wu , Shufang Xie , Tao Qin , Wengang Zhou , Houqiang Li , Tie-Yan Liu

Quantum theory has been remarkably successful in providing an understanding of physical systems at foundational scales. Solving the Schr\"odinger equation provides full knowledge of all dynamical quantities of the physical system. However…

Quantum Physics · Physics 2020-11-24 Cesar Lema , Anna Choromanska

Recently, graph neural networks (GNNs) have proved to be suitable in tasks on unstructured data. Particularly in tasks as community detection, node classification, and link prediction. However, most GNN models still operate with static…

Machine Learning · Computer Science 2019-06-07 Darwin Saire Pilco , Adín Ramírez Rivera

Symmetric functions, which take as input an unordered, fixed-size set, are known to be universally representable by neural networks that enforce permutation invariance. These architectures only give guarantees for fixed input sizes, yet in…

Machine Learning · Computer Science 2022-10-11 Aaron Zweig , Joan Bruna

The cornerstone of neural algorithmic reasoning is the ability to solve algorithmic tasks, especially in a way that generalises out of distribution. While recent years have seen a surge in methodological improvements in this area, they…

Neural networks, a central tool in machine learning, have demonstrated remarkable, high fidelity performance on image recognition and classification tasks. These successes evince an ability to accurately represent high dimensional…

Machine Learning · Statistics 2023-02-08 Grant M. Rotskoff , Eric Vanden-Eijnden

In the artificial neuron, I replace the dot product with the weighted Lehmer mean, which may emulate different cases of a generalized mean. The single neuron instance is replaced by a multiplet of neurons which have the same averaging…

Machine Learning · Computer Science 2020-06-03 Nathan E. Frick

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

Wavelets are closely related to the Schr\"odinger's wave functions and the interpretation of Born. Similarly to the appearance of atomic orbital, it is proposed to combine anti-symmetric wavelets into orbital wavelets. The proposed approach…

Signal Processing · Electrical Eng. & Systems 2020-10-02 H. M. de Oliveira , V. V. Vermehren , R. J. Cintra

Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

Biomolecules · Quantitative Biology 2023-10-10 Apakorn Kengkanna , Masahito Ohue

We present a graph bisection and partitioning algorithm based on graph neural networks. For each node in the graph, the network outputs probabilities for each of the partitions. The graph neural network consists of two modules: an embedding…

Machine Learning · Computer Science 2021-12-09 Alice Gatti , Zhixiong Hu , Tess Smidt , Esmond G. Ng , Pieter Ghysels

Ab initio quantum chemistry calculations for systems with large active spaces are notoriously difficult and cannot be successfully tackled by standard methods. In this letter, we generalize a Green's function QM/QM embedding method called…

Chemical Physics · Physics 2018-06-07 Tran Nguyen Lan , Dominika Zgid

Neural networks can be powerful function approximators, which are able to model high-dimensional feature distributions from a subset of examples drawn from the target distribution. Naturally, they perform well at generalizing within the…

Machine Learning · Computer Science 2021-08-06 Aaron Eisermann , Jae Hee Lee , Cornelius Weber , Stefan Wermter

Neural networks are a powerful class of nonlinear functions that can be trained end-to-end on various applications. While the over-parametrization nature in many neural networks renders the ability to fit complex functions and the strong…

Machine Learning · Computer Science 2020-07-23 Weiyang Liu , Rongmei Lin , Zhen Liu , Lixin Liu , Zhiding Yu , Bo Dai , Le Song