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Biomolecular networks have to perform their functions robustly. A robust function may have preferences in the topological structures of the underlying network. We carried out an exhaustive computational analysis on network topologies in…

Molecular Networks · Quantitative Biology 2007-05-23 Wenzhe Ma , Luhua Lai , Qi Ouyang , Chao Tang

Correlations in sensory neural networks have both extrinsic and intrinsic origins. Extrinsic or stimulus correlations arise from shared inputs to the network, and thus depend strongly on the stimulus ensemble. Intrinsic or noise…

Neurons and Cognition · Quantitative Biology 2018-11-05 Ulisse Ferrari , Stephane Deny , Matthew Chalk , Gasper Tkacik , Olivier Marre , Thierry Mora

The activity of ensembles of simultaneously recorded neurons can be represented as a set of points in the space of firing rates. Even though the dimension of this space is equal to the ensemble size, neural activity can be effectively…

Neurons and Cognition · Quantitative Biology 2016-03-17 Luca Mazzucato , Alfredo Fontanini , Giancarlo La Camera

The collective behaviour of neural networks depends on the cellular and synaptic properties of the neurons. The phase-response curve (PRC) is an experimentally obtainable measure of cellular properties that quantifies the shift in the next…

Adaptation and Self-Organizing Systems · Physics 2019-12-24 Abolfazl Ziaeemehr , Mina Zarei , Aida Sheshbolouki

Identifying stimulus-driven neural activity patterns is critical for studying the neural basis of cognition. This can be particularly challenging in intracranial datasets, where electrode locations typically vary across patients. This…

Neurons and Cognition · Quantitative Biology 2022-02-07 Jeremy R. Manning

Correlations between intrinsic dynamics and local topology have become a new trend in the study of synchronization in complex networks. In this paper, we investigate in this paradigm the influence of topology on dynamics of networks made up…

Chaotic Dynamics · Physics 2015-06-18 Peng Ji , Thomas K. DM. Peron , Francisco A. Rodrigues , Jürgen Kurths

Caenorhabditis elegans (C. elegans) illustrated remarkable behavioral plasticities including complex non-associative and associative learning representations. Understanding the principles of such mechanisms presumably leads to constructive…

Neurons and Cognition · Quantitative Biology 2017-03-28 Ramin M. Hasani , Magdalena Fuchs , Victoria Beneder , Radu Grosu

Generalized linear models are one of the most efficient paradigms for predicting the correlated stochastic activity of neuronal networks in response to external stimuli, with applications in many brain areas. However, when dealing with…

Disordered Systems and Neural Networks · Physics 2020-11-17 Gabriel Mahuas , Giulio Isacchini , Olivier Marre , Ulisse Ferrari , Thierry Mora

We study a novel architecture and training procedure for locomotion tasks. A high-frequency, low-level "spinal" network with access to proprioceptive sensors learns sensorimotor primitives by training on simple tasks. This pre-trained…

Robotics · Computer Science 2016-10-18 Nicolas Heess , Greg Wayne , Yuval Tassa , Timothy Lillicrap , Martin Riedmiller , David Silver

Modularity is an important topological attribute for functional brain networks. Recent studies have reported that modularity of functional networks varies not only across individuals being related to demographics and cognitive performance,…

Neurons and Cognition · Quantitative Biology 2018-10-05 Makoto Fukushima , Richard F. Betzel , Ye He , Marcel A. de Reus , Martijn P. van den Heuvel , Xi-Nian Zuo , Olaf Sporns

In signal processing, exploring complex systems through network representations has become an area of growing interest. This study introduces the modularity graph, a new graph-based feature, to highlight the relationship across the graph…

Neurons and Cognition · Quantitative Biology 2024-10-23 Tiziana Cattai , Camilla Caporali , Marie-Constance Corsi , Stefania Colonnese

We propose a method that allows for a rigorous statistical analysis of neural responses to natural stimuli which are non-Gaussian and exhibit strong correlations. We have in mind a model in which neurons are selective for a small number of…

Biological Physics · Physics 2007-05-23 Tatyana Sharpee , Nicole C. Rust , William Bialek

The neural dynamics of the nematode C. elegans are experimentally low-dimensional and correspond to discrete behavioral states, where previous modeling work has found neural proxies for some of these states. Experimental results further…

Neurons and Cognition · Quantitative Biology 2015-09-04 James Kunert , Eli Shlizerman , Andrew Walker , J. Nathan Kutz

Foundation models have shown remarkable success in fitting biological visual systems; however, their black-box nature inherently limits their utility for understanding brain function. Here, we peek inside a SOTA foundation model of neural…

Neurons and Cognition · Quantitative Biology 2025-12-10 Johannes Bertram , Luciano Dyballa , T. Anderson Keller , Savik Kinger , Steven W. Zucker

We use topological data analysis to study neural population activity in the Sensorium 2023 dataset, which records responses from thousands of mouse visual cortex neurons to diverse video stimuli. For each video, we build frame-by-frame…

Algebraic Topology · Mathematics 2026-03-04 Yuri Gardinazzi , Alessio Ansuini , Eugenio Piasini , Fabio Anselmi , Matteo Biagetti

Small-World Networks (SWNs) represent a fundamental model for the comprehension of many complex man-made and biological networks. In the central nervous system, SWN models have been shown to fit well both anatomical and functional maps at…

Most humans have the good fortune to live their lives embedded in richly structured social groups. Yet, it remains unclear how humans acquire knowledge about these social structures to successfully navigate social relationships. Here we…

Neurons and Cognition · Quantitative Biology 2019-04-23 Steven H. Tompson , Ari E. Kahn , Emily B. Falk , Jean M. Vettel , Danielle S. Bassett

Neural synchronization is central to cognition However, incomplete synchronization often produces chimera states where coherent and incoherent dynamics coexist. While previous studies have explored such patterns using networks of coupled…

Neurons and Cognition · Quantitative Biology 2026-05-15 Thomas Zdyrski , Scott Pauls , Feng Fu

We advance our approach of analyzing the dynamics of interacting complex systems with the nonlinear dynamics of interacting nonlinear elements. We replace the widely used lattice-like connection topology of cellular neural networks (CNN) by…

Neurons and Cognition · Quantitative Biology 2016-10-10 Henning Dickten , Christian E. Elger , Klaus Lehnertz

Human learning is a complex phenomenon requiring flexibility to adapt existing brain function and precision in selecting new neurophysiological activities to drive desired behavior. These two attributes -- flexibility and selection -- must…

Neurons and Cognition · Quantitative Biology 2013-06-28 Danielle S. Bassett , Nicholas F. Wymbs , Mason A. Porter , Peter J. Mucha , Jean M. Carlson , Scott T. Grafton
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