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Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…

Biomolecules · Quantitative Biology 2021-01-26 Stephan Eismann , Raphael J. L. Townshend , Nathaniel Thomas , Milind Jagota , Bowen Jing , Ron O. Dror

Simplicial complexes describe collaboration networks, protein interaction networks and brain networks and in general network structures in which the interactions can include more than two nodes. In real applications, often simplicial…

Physics and Society · Physics 2017-06-21 Owen T. Courtney , Ginestra Bianconi

Equivariant neural networks are neural networks with symmetry. Motivated by the theory of group representations, we decompose the layers of an equivariant neural network into simple representations. The nonlinear activation functions lead…

Machine Learning · Computer Science 2026-03-30 Joel Gibson , Daniel Tubbenhauer , Geordie Williamson

Graphs are ubiquitous to model the irregular (non-Euclidean) structure of complex data, but they are limited to pairwise relationships and fail to model the complexities of the datasets exhibiting higher-order interactions. In that context,…

Signal Processing · Electrical Eng. & Systems 2025-02-28 A. Buciulea , E. Isufi , G. Leus , A. G. Marques

The evolution of convolutional neural networks (CNNs) can be largely attributed to the design of its architecture, i.e., the network wiring pattern. Neural architecture search (NAS) advances this by automating the search for the optimal…

Neural and Evolutionary Computing · Computer Science 2023-04-21 Lin Zhao , Haixing Dai , Zihao Wu , Dajiang Zhu , Tianming Liu

The past two decades have seen significant successes in our understanding of complex networked systems, from the mapping of real-world social, biological and technological networks to the establishment of generative models recovering their…

Simplicial complexes provide a powerful framework for modeling higher-order interactions in structured data, making them particularly suitable for applications such as trajectory prediction and mesh processing. However, existing simplicial…

Machine Learning · Computer Science 2025-10-27 Aref Einizade , Dorina Thanou , Fragkiskos D. Malliaros , Jhony H. Giraldo

Reconstructing the states of the nodes of a dynamical network is a problem of fundamental importance in the study of neuronal and genetic networks. An underlying related problem is that of observability, i.e., identifying the conditions…

Pattern Formation and Solitons · Physics 2017-03-31 Afroza Shirin , Dionicio F. Rios , Francesco Sorrentino

Neural architectures tend to fit their data with relatively simple functions. This "simplicity bias" is widely regarded as key to their success. This paper explores the limits of this principle. Building on recent findings that the…

Machine Learning · Computer Science 2025-03-14 Damien Teney , Liangze Jiang , Florin Gogianu , Ehsan Abbasnejad

Neural networks trained with gradient descent often learn solutions of increasing complexity over time, a phenomenon known as simplicity bias. Despite being widely observed across architectures, existing theoretical treatments lack a…

Machine Learning · Computer Science 2026-03-12 Yedi Zhang , Andrew Saxe , Peter E. Latham

Equivariance of linear neural network layers is well studied. In this work, we relax the equivariance condition to only be true in a projective sense. We propose a way to construct a projectively equivariant neural network through building…

Computer Vision and Pattern Recognition · Computer Science 2023-12-21 Georg Bökman , Axel Flinth , Fredrik Kahl

The language of graph theory, or network science, has proven to be an exceptional tool for addressing myriad problems in neuroscience. Yet, the use of networks is predicated on a critical simplifying assumption: that the quintessential unit…

Neurons and Cognition · Quantitative Biology 2016-01-14 Chad Giusti , Robert Ghrist , Danielle S. Bassett

Higher-order structures, consisting of more than two individuals, provide a new perspective to reveal the missed non-trivial characteristics under pairwise networks. Prior works have researched various higher-order networks, but research…

Physics and Society · Physics 2023-09-07 Rongmei Yang , Fang Zhou , Bo Liu , Linyuan Lü

Neural networks based on metric recognition methods have a strictly determined architecture. Number of neurons, connections, as well as weights and thresholds values are calculated analytically, based on the initial conditions of tasks:…

Neural and Evolutionary Computing · Computer Science 2025-06-10 Polad Geidarov

In recent years, there has been a growing recognition that higher-order structures are important features in real-world networks. A particular class of structures that has gained prominence is known as a simplicial complex. Despite their…

Social and Information Networks · Computer Science 2022-04-12 Mayank Kejriwal , Ke Shen

By extending the extreme learning machine by additional control inputs, we achieved almost complete reproduction of bifurcation structures of dynamical systems. The learning ability of the proposed neural network system is striking in that…

Chaotic Dynamics · Physics 2024-10-21 Satoru Tadokoro , Akihiro Yamaguchi , Takao Namiki , Ichiro Tsuda

Simplicial complexes constitute the underlying topology of interacting complex systems including among the others brain and social interaction networks. They are generalized network structures that allow to go beyond the framework of…

Disordered Systems and Neural Networks · Physics 2020-06-02 Joaquín J. Torres , Ginestra Bianconi

Complex networks can be used to represent complex systems which originate in the real world. Here we study a transformation of these complex networks into simplicial complexes, where cliques represent the simplices of the complex. We extend…

Social and Information Networks · Computer Science 2017-09-04 Ernesto Estrada , Grant Ross

The results of training a neural network are heavily dependent on the architecture chosen; and even a modification of only its size, however small, typically involves restarting the training process. In contrast to this, we begin training…

Machine Learning · Computer Science 2024-02-12 Rupert Mitchell , Robin Menzenbach , Kristian Kersting , Martin Mundt

In recent years, the use of machine learning has become increasingly popular in the context of lattice field theories. An essential element of such theories is represented by symmetries, whose inclusion in the neural network properties can…

High Energy Physics - Lattice · Physics 2021-12-24 Srinath Bulusu , Matteo Favoni , Andreas Ipp , David I. Müller , Daniel Schuh