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We introduce a novel recurrent neural network (RNN) approach to account for temporal dynamics and dependencies in brain networks observed via functional magnetic resonance imaging (fMRI). Our approach directly parameterizes temporal…

Neural and Evolutionary Computing · Computer Science 2018-08-28 R Devon Hjelm , Eswar Damaraju , Kyunghyun Cho , Helmut Laufs , Sergey M. Plis , Vince Calhoun

Independent component analysis is commonly applied to functional magnetic resonance imaging (fMRI) data to extract independent components (ICs) representing functional brain networks. While ICA produces reliable group-level estimates,…

Methodology · Statistics 2020-06-05 Amanda F. Mejia , David Bolin , Yu Ryan Yue , Jiongran Wang , Brian S. Caffo , Mary Beth Nebel

Using functional magnetic resonance imaging (fMRI) and deep learning to explore functional brain networks (FBNs) has attracted many researchers. However, most of these studies are still based on the temporal correlation between the sources…

Neurons and Cognition · Quantitative Biology 2022-11-07 Yiheng Liu , Enjie Ge , Ning Qiang , Tianming Liu , Bao Ge

Recently, the potential of dynamic brain networks as a neuroimaging biomarkers for mental illnesses is being increasingly recognized. However, there are several unmet challenges in developing such biomarkers, including the need for methods…

Neurons and Cognition · Quantitative Biology 2019-10-10 Suprateek Kundu , Jin Ming , Jennifer Stevens

Simultaneous modeling of the spatio-temporal variation patterns of brain functional network from 4D fMRI data has been an important yet challenging problem for the field of cognitive neuroscience and medical image analysis. Inspired by the…

Computer Vision and Pattern Recognition · Computer Science 2021-03-24 Yu Zhao , Xiang Li , Wei Zhang , Shijie Zhao , Milad Makkie , Mo Zhang , Quanzheng Li , Tianming Liu

Recent advances in deep learning structured state space models, especially the Mamba architecture, have demonstrated remarkable performance improvements while maintaining linear complexity. In this study, we introduce functional…

Machine Learning · Computer Science 2025-03-24 Yuxiang Wei , Anees Abrol , Vince Calhoun

How to identify and characterize functional brain networks (BN) is fundamental to gain system-level insights into the mechanisms of brain organizational architecture. Current functional magnetic resonance (fMRI) analysis highly relies on…

Neurons and Cognition · Quantitative Biology 2022-06-28 Xiaowei Yu , Lu Zhang , Lin Zhao , Yanjun Lyu , Tianming Liu , Dajiang Zhu

Dynamic functional connectivity analysis provides valuable information for understanding brain functional activity underlying different cognitive processes. Besides sliding window based approaches, a variety of methods have been developed…

Computer Vision and Pattern Recognition · Computer Science 2018-09-18 Hongming Li , Yong Fan

Dynamic functional connectivity (dFC) using resting-state functional magnetic resonance imaging (rs-fMRI) is an advanced technique for capturing the dynamic changes of neural activities, and can be very useful in the studies of brain…

Image and Video Processing · Electrical Eng. & Systems 2025-01-29 Jing Zhang , Yanjun Lyu , Xiaowei Yu , Lu Zhang , Chao Cao , Tong Chen , Minheng Chen , Yan Zhuang , Tianming Liu , Dajiang Zhu

Activity in the human brain moves between diverse functional states to meet the demands of our dynamic environment, but fundamental principles guiding these transitions remain poorly understood. Here, we capitalize on recent advances in…

Spatial Independent Component Analysis (ICA) is an increasingly used data-driven method to analyze functional Magnetic Resonance Imaging (fMRI) data. To date, it has been used to extract sets of mutually correlated brain regions without…

Applications · Statistics 2011-02-08 G. Varoquaux , S. Sadaghiani , P. Pinel , A. Kleinschmidt , J. B. Poline , B. Thirion

Characterizing time-evolving networks is a challenging task, but it is crucial for understanding the dynamic behavior of complex systems such as the brain. For instance, how spatial networks of functional connectivity in the brain evolve…

Applications · Statistics 2021-01-27 Marie Roald , Suchita Bhinge , Chunying Jia , Vince Calhoun , Tülay Adalı , Evrim Acar

This paper studies the link between resting-state functional connectivity (FC), measured by the correlations of the fMRI BOLD time courses, and structural connectivity (SC), estimated through fiber tractography. Instead of a static analysis…

Examining task-free functional connectivity (FC) in the human brain offers insights on how spontaneous integration and segregation of information relate to human cognition, and how this organization may be altered in different conditions,…

Neural computation is associated with the emergence, reconfiguration and dissolution of cell assemblies in the context of varying oscillatory states. Here, we describe the complex spatio-temporal dynamics of cell assemblies through temporal…

Neurons and Cognition · Quantitative Biology 2020-01-20 Nicola Pedreschi , Christophe Bernard , Wesley Clawson , Pascale Quilichini , Alain Barrat , Demian Battaglia

Understanding the complex neural activity dynamics is crucial for the development of the field of neuroscience. Although current functional MRI classification approaches tend to be based on static functional connectivity or cannot capture…

Machine Learning · Computer Science 2025-08-20 Amirali Arbab , Zeinab Davarani , Mehran Safayani

Time Varying Functional Connectivity (TVFC) investigates how the interactions among brain regions vary over the course of an fMRI experiment. The transitions between different individual connectivity states can be modulated by changes in…

Independent Component Analysis (ICA) is a computational technique for revealing latent factors that underlie sets of measurements or signals. It has become a standard technique in functional neuroimaging. In functional neuroimaging, so…

Finding an appropriate representation of dynamic activities in the brain is crucial for many downstream applications. Due to its highly dynamic nature, temporally averaged fMRI (functional magnetic resonance imaging) can only provide a…

Machine Learning · Computer Science 2022-08-18 Sikun Lin , Shuyun Tang , Scott Grafton , Ambuj Singh

Functional Magnetic Resonance Imaging (fMRI) is an imaging technique widely used to study human brain activity. fMRI signals in areas across the brain transiently synchronise and desynchronise their activity in a highly structured manner,…

Machine Learning · Computer Science 2025-08-12 Yiran Huang , Amirhossein Nouranizadeh , Christine Ahrends , Mengjia Xu
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