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We introduce copresheaf topological neural networks (CTNNs), a powerful unifying framework that encapsulates a wide spectrum of deep learning architectures, designed to operate on structured data, including images, point clouds, graphs,…

Graph neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on molecular graphs, GNNs offer an intuitive and expressive…

Biomolecules · Quantitative Biology 2025-06-10 Odin Zhang , Haitao Lin , Xujun Zhang , Xiaorui Wang , Zhenxing Wu , Qing Ye , Weibo Zhao , Jike Wang , Kejun Ying , Yu Kang , Chang-yu Hsieh , Tingjun Hou

Message-passing neural networks (MPNN) have shown extremely high efficiency and accuracy in predicting the physical properties of molecules and crystals, and are expected to become the next-generation material simulation tool after the…

Materials Science · Physics 2022-01-19 Yang Zhong , Hongyu Yu , Xingao Gong , Hongjun Xiang

Graph neural networks (GNNs) have demonstrated success in modeling relational data, especially for data that exhibits homophily: when a connection between nodes tends to imply that they belong to the same class. However, while this…

Machine Learning · Computer Science 2023-06-23 Andreea Deac , Jian Tang

Various classes of Graph Neural Networks (GNN) have been proposed and shown to be successful in a wide range of applications with graph structured data. In this paper, we propose a theoretical framework able to compare the expressive power…

Machine Learning · Computer Science 2021-06-08 Waïss Azizian , Marc Lelarge

Euclidean deep learning is often inadequate for addressing real-world signals where the representation space is irregular and curved with complex topologies. Interpreting the geometric properties of such feature spaces has become paramount…

Computer Vision and Pattern Recognition · Computer Science 2024-09-12 Ramzan Basheer , Deepak Mishra

Graph Neural Networks (GNNs) have significant advantages in handling non-Euclidean data and have been widely applied across various areas, thus receiving increasing attention in recent years. The framework of GNN models mainly includes the…

Machine Learning · Computer Science 2025-02-05 Shengda Zhuo , Jiwang Fang , Hongguang Lin , Yin Tang , Min Chen , Changdong Wang , Shuqiang Huang

Graph neural networks (GNNs) are commonly described as being permutation equivariant with respect to node relabeling in the graph. This symmetry of GNNs is often compared to the translation equivariance of Euclidean convolution neural…

Machine Learning · Statistics 2023-11-20 Ningyuan Huang , Ron Levie , Soledad Villar

Computer networks are the foundation of modern digital infrastructure, facilitating global communication and data exchange. As demand for reliable high-bandwidth connectivity grows, advanced network modeling techniques become increasingly…

Jet tagging techniques that make use of deep learning show great potential for improving physics analyses at colliders. One such method is the Energy Flow Network (EFN) - a recently introduced neural network architecture that represents…

High Energy Physics - Phenomenology · Physics 2021-04-29 Matthew J. Dolan , Ayodele Ore

Graph neural networks (GNNs) have been widely used in deep learning on graphs. They can learn effective node representations that achieve superior performances in graph analysis tasks such as node classification and node clustering.…

Machine Learning · Computer Science 2021-04-19 Jianxin Li , Hao Peng , Yuwei Cao , Yingtong Dou , Hekai Zhang , Philip S. Yu , Lifang He

The expressive power of Graph Neural Networks (GNNs) has been studied extensively through the Weisfeiler-Leman (WL) graph isomorphism test. However, standard GNNs and the WL framework are inapplicable for geometric graphs embedded in…

Machine Learning · Computer Science 2024-03-05 Chaitanya K. Joshi , Cristian Bodnar , Simon V. Mathis , Taco Cohen , Pietro Liò

We present a PDE-based framework that generalizes Group equivariant Convolutional Neural Networks (G-CNNs). In this framework, a network layer is seen as a set of PDE-solvers where geometrically meaningful PDE-coefficients become the…

Machine Learning · Computer Science 2022-08-24 Bart Smets , Jim Portegies , Erik Bekkers , Remco Duits

Representing and learning from graphs is essential for developing effective machine learning models tailored to non-Euclidean data. While Graph Neural Networks (GNNs) strive to address the challenges posed by complex, high-dimensional graph…

Quantum Physics · Physics 2025-01-15 Wenxuan Wang

Equivariant machine learning is an approach for designing deep learning models that respect the symmetries of the problem, with the aim of reducing model complexity and improving generalization. In this paper, we focus on an extension of…

Machine Learning · Computer Science 2024-12-10 Ya-Wei Eileen Lin , Ronen Talmon , Ron Levie

Convolutional Neural Networks (CNN) have been successful in processing data signals that are uniformly sampled in the spatial domain (e.g., images). However, most data signals do not natively exist on a grid, and in the process of being…

Computer Vision and Pattern Recognition · Computer Science 2019-01-09 Chiyu "Max" Jiang , Dequan Wang , Jingwei Huang , Philip Marcus , Matthias Nießner

Deep Neural Networks (DNNs) are widely used for their ability to effectively approximate large classes of functions. This flexibility, however, makes the strict enforcement of constraints on DNNs an open problem. Here we present a framework…

Machine Learning · Computer Science 2023-02-10 Eric Marcus , Ray Sheombarsing , Jan-Jakob Sonke , Jonas Teuwen

The accurate prediction of changes in protein stability under multiple amino acid substitutions is essential for realising true in-silico protein re-design. To this purpose, we propose improvements to state-of-the-art Deep learning (DL)…

Biomolecules · Quantitative Biology 2023-06-01 Sebastien Boyer , Sam Money-Kyrle , Oliver Bent

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

Effectively predicting molecular interactions has the potential to accelerate molecular dynamics by multiple orders of magnitude and thus revolutionize chemical simulations. Graph neural networks (GNNs) have recently shown great successes…

Computational Physics · Physics 2024-06-25 Johannes Gasteiger , Florian Becker , Stephan Günnemann
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