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High-dimensional imaging of neural activity, such as widefield calcium and functional ultrasound imaging, provide a rich source of information for understanding the relationship between brain activity and behavior. Accurately modeling…

Neurons and Cognition · Quantitative Biology 2025-09-24 Mohammad Hosseini , Maryam M. Shanechi

The MRI-derived brain network serves as a pivotal instrument in elucidating both the structural and functional aspects of the brain, encompassing the ramifications of diseases and developmental processes. However, prevailing methodologies,…

Machine Learning · Computer Science 2024-05-24 Haoteng Tang , Guodong Liu , Siyuan Dai , Kai Ye , Kun Zhao , Wenlu Wang , Carl Yang , Lifang He , Alex Leow , Paul Thompson , Heng Huang , Liang Zhan

A central question in neuroscience is how self-organizing dynamic interactions in the brain emerge on their relatively static structural backbone. Due to the complexity of spatial and temporal dependencies between different brain areas,…

Neurons and Cognition · Quantitative Biology 2020-10-15 Simon Wein , Wilhelm Malloni , Ana Maria Tomé , Sebastian M. Frank , Gina-Isabelle Henze , Stefan Wüst , Mark W. Greenlee , Elmar W. Lang

Understanding how neuronal networks reorganize in response to external stimuli and give rise to behavior is a central challenge in neuroscience and artificial intelligence. However, existing methods often fail to capture the evolving…

Neurons and Cognition · Quantitative Biology 2025-06-02 Moein Khajehnejad , Forough Habibollahi , Ahmad Khajehnejad , Chris French , Brett J. Kagan , Adeel Razi

Accurate crowd simulation is crucial for public safety management, emergency evacuation planning, and intelligent transportation systems. However, existing methods, which typically model crowds as a collection of independent individual…

Machine Learning · Computer Science 2026-04-14 Zijin Liu , Xu Geng , Wenshuai Xu , Xiang Zhao , Yan Xia , You Song

Biological spiking neurons with intrinsic dynamics underlie the powerful representation and learning capabilities of the brain for processing multimodal information in complex environments. Despite recent tremendous progress in spiking…

Neural and Evolutionary Computing · Computer Science 2021-07-15 Mingkun Xu , Yujie Wu , Lei Deng , Faqiang Liu , Guoqi Li , Jing Pei

Neurons exhibit intricate geometries within their neurite networks, which play a crucial role in processes such as signaling and nutrient transport. Accurate simulation of material transport in the networks is essential for understanding…

Machine Learning · Computer Science 2025-07-16 Tsung Yeh Hsieh , Yongjie Jessica Zhang

The advent of large-scale neural recordings has enabled new methods to discover the computational mechanisms of neural circuits by understanding the rules that govern how their state evolves over time. While these \textit{neural dynamics}…

Neurons and Cognition · Quantitative Biology 2023-09-13 Christopher Versteeg , Andrew R. Sedler , Jonathan D. McCart , Chethan Pandarinath

Dynamic graphs (DGs), which capture time-evolving relationships between graph entities, have widespread real-world applications. To efficiently encode DGs for downstream tasks, most dynamic graph neural networks follow the traditional…

Machine Learning · Computer Science 2025-01-31 Xiang Wu , Xunkai Li , Rong-Hua Li , Kangfei Zhao , Guoren Wang

Resting-state functional magnetic resonance imaging (rsfMRI) is a powerful tool for investigating the relationship between brain function and cognitive processes as it allows for the functional organization of the brain to be captured…

Machine Learning · Computer Science 2025-02-25 Bishal Thapaliya , Esra Akbas , Jiayu Chen , Raam Sapkota , Bhaskar Ray , Pranav Suresh , Vince Calhoun , Jingyu Liu

The human brain can be considered as complex networks, composed of various regions that continuously exchange their information with each other, forming the brain network graph, from which nodes and edges are extracted using resting-state…

Machine Learning · Computer Science 2025-02-19 Parnian Jalali , Mehran Safayani

Encoding models are used for predicting brain activity in response to sensory stimuli with the objective of elucidating how sensory information is represented in the brain. Encoding models typically comprise a nonlinear transformation of…

Neurons and Cognition · Quantitative Biology 2017-03-13 Umut Güçlü , Marcel A. J. van Gerven

We present a multi-scale differentiable brain modeling workflow utilizing BrainPy, a unique differentiable brain simulator that combines accurate brain simulation with powerful gradient-based optimization. We leverage this capability of…

Neural and Evolutionary Computing · Computer Science 2024-09-26 Chaoming Wang , Muyang Lyu , Tianqiu Zhang , Sichao He , Si Wu

Deep Graph Neural Networks (GNNs) are essential for capturing complex dependencies in graph-structured data. However, scaling GNNs to depth remains challenging, as stacking layers leads to representation collapse and diminishing sensitivity…

Machine Learning · Computer Science 2026-05-26 Rémi Bourgerie , Šarūnas Girdzijauskas , Viktoria Fodor

Sheaf Neural Networks (SNNs) naturally extend Graph Neural Networks (GNNs) by endowing a cellular sheaf over the graph, equipping nodes and edges with vector spaces and defining linear mappings between them. While the attached geometric…

Machine Learning · Computer Science 2024-07-31 Ferran Hernandez Caralt , Guillermo Bernárdez Gil , Iulia Duta , Pietro Liò , Eduard Alarcón Cot

Sheaf Neural Networks (SNNs) represent a powerful generalization of Graph Neural Networks (GNNs) that significantly improve our ability to model complex relational data. While directionality has been shown to substantially boost performance…

Machine Learning · Computer Science 2025-06-04 Stefano Fiorini , Hakan Aktas , Iulia Duta , Stefano Coniglio , Pietro Morerio , Alessio Del Bue , Pietro Liò

Neural forecasting of spatiotemporal time series drives both research and industrial innovation in several relevant application domains. Graph neural networks (GNNs) are often the core component of the forecasting architecture. However, in…

Machine Learning · Computer Science 2023-02-21 Andrea Cini , Ivan Marisca , Filippo Maria Bianchi , Cesare Alippi

The purpose of this paper is to infer a global (collective) model of time-varying responses of a set of nodes as a dynamic graph, where the individual time series are respectively observed at each of the nodes. The motivation of this work…

Signal Processing · Electrical Eng. & Systems 2020-02-18 Bo Jiang , Ashkan Panahi , Hamid Krim , Yiyi Yu , Spencer L. Smith

Learning continuous-time dynamics on complex networks is crucial for understanding, predicting and controlling complex systems in science and engineering. However, this task is very challenging due to the combinatorial complexities in the…

Social and Information Networks · Computer Science 2020-06-19 Chengxi Zang , Fei Wang

Graphs are essential representations of many real-world data such as social networks. Recent years have witnessed the increasing efforts made to extend the neural network models to graph-structured data. These methods, which are usually…

Machine Learning · Computer Science 2018-11-07 Yao Ma , Ziyi Guo , Zhaochun Ren , Eric Zhao , Jiliang Tang , Dawei Yin