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Multimodal neuroimaging modeling has becomes a widely used approach but confronts considerable challenges due to heterogeneity, which encompasses variability in data types, scales, and formats across modalities. This variability…

Neurons and Cognition · Quantitative Biology 2025-04-15 Gang Qu , Ziyu Zhou , Vince D. Calhoun , Aiying Zhang , Yu-Ping Wang

Electroencephalography (EEG) foundation models hold significant promise for universal Brain-Computer Interfaces (BCIs). However, existing approaches often rely on end-to-end fine-tuning and exhibit limited efficacy under frozen-probing…

Machine Learning · Computer Science 2026-03-20 Jiquan Wang , Sha Zhao , Yangxuan Zhou , Yiming Kang , Shijian Li , Gang Pan

Multimodal learning, especially large-scale multimodal pre-training, has developed rapidly over the past few years and led to the greatest advances in artificial intelligence (AI). Despite its effectiveness, understanding the underlying…

Neural and Evolutionary Computing · Computer Science 2022-08-18 Haoyu Lu , Qiongyi Zhou , Nanyi Fei , Zhiwu Lu , Mingyu Ding , Jingyuan Wen , Changde Du , Xin Zhao , Hao Sun , Huiguang He , Ji-Rong Wen

Functional connectivity (FC) derived from resting-state fMRI plays a critical role in personalized predictions such as age and cognitive performance. However, applying foundation models(FM) to fMRI data remains challenging due to its high…

Neurons and Cognition · Quantitative Biology 2025-08-26 Yanwen Wang , Xinglin Zhao , Yijin Song , Xiaobo Liu , Yanrong Hao , Rui Cao , Xin Wen

A reliable foundation model of functional neuroimages is critical to promote clinical applications where the performance of current AI models is significantly impeded by a limited sample size. To that end, tremendous efforts have been made…

Machine Learning · Computer Science 2025-10-23 Ziquan Wei , Tingting Dan , Guorong Wu

In neuroimaging analysis, fMRI can well assess the function changes for brain diseases with no obvious structural lesions. To date, most deep-learning-based fMRI studies have employed functional connectivity (FC) as the basic feature for…

Image and Video Processing · Electrical Eng. & Systems 2023-03-03 Wei Dai , Ziyao Zhang , Lixia Tian , Shengyuan Yu , Shuhui Wang , Zhao Dong , Hairong Zheng

Functional magnetic resonance imaging (fMRI) is widely used for studying and diagnosing brain disorders, with functional connectivity (FC) matrices providing powerful representations of large-scale neural interactions. However, existing…

Tissues and Organs · Quantitative Biology 2026-04-17 Qianyu Chen , Shujian Yu

Foundation models (FMs), large neural networks pretrained on extensive and diverse datasets, have revolutionized artificial intelligence and shown significant promise in medical imaging by enabling robust performance with limited labeled…

Image and Video Processing · Electrical Eng. & Systems 2025-06-17 Salah Ghamizi , Georgia Kanli , Yu Deng , Magali Perquin , Olivier Keunen

Accurate fMRI analysis requires sensitivity to temporal structure across multiple scales, as BOLD signals encode cognitive processes that emerge from fast transient dynamics to slower, large-scale fluctuations. Existing deep learning (DL)…

Signal Processing · Electrical Eng. & Systems 2026-01-06 Furkan Genç , Boran İsmet Macun , Sait Sarper Özaslan , Emine U. Saritas , Tolga Çukur

Aggregating multi-subject functional magnetic resonance imaging (fMRI) data is indispensable for generating valid and general inferences from patterns distributed across human brains. The disparities in anatomical structures and functional…

Machine Learning · Computer Science 2019-11-20 Weida Li , Mingxia Liu , Fang Chen , Daoqiang Zhang

Human brains exhibit highly organized multiscale neurophysiological dynamics. Understanding those dynamic changes and the neuronal networks involved is critical for understanding how the brain functions in health and disease. Functional…

Neurons and Cognition · Quantitative Biology 2024-09-09 Manuel Morante , Kristian Frølich , Naveed ur Rehman

As large language models (LLMs) continue to revolutionize AI research, there is a growing interest in building large-scale brain foundation models to advance neuroscience. While most existing brain foundation models are pre-trained on…

Neurons and Cognition · Quantitative Biology 2026-02-11 Xinxu Wei , Kanhao Zhao , Yong Jiao , Lifang He , Yu Zhang

Understanding how the brain represents visual information is a fundamental challenge in neuroscience and artificial intelligence. While AI-driven decoding of neural data has provided insights into the human visual system, integrating…

Neural and Evolutionary Computing · Computer Science 2025-10-07 Dongyang Li , Haoyang Qin , Mingyang Wu , Chen Wei , Quanying Liu

Functional magnetic resonance imaging (fMRI) is a powerful tool for probing brain function, yet reliable clinical diagnosis is hampered by low signal-to-noise ratios, inter-subject variability, and the limited frequency awareness of…

Computer Vision and Pattern Recognition · Computer Science 2026-03-03 Junhao Jia , Yifei Sun , Yunyou Liu , Cheng Yang , Changmiao Wang , Feiwei Qin , Yong Peng , Wenwen Min

Brain diseases, such as Alzheimer's disease and brain tumors, present profound challenges due to their complexity and societal impact. Recent advancements in brain foundation models have shown significant promise in addressing a range of…

Computer Vision and Pattern Recognition · Computer Science 2025-05-02 Zhongying Deng , Haoyu Wang , Ziyan Huang , Lipei Zhang , Angelica I. Aviles-Rivero , Chaoyu Liu , Junjun He , Zoe Kourtzi , Carola-Bibiane Schönlieb

We present a foundation model for brain MRI that can work with different combinations of imaging sequences. The model uses one encoder with learnable modality embeddings, conditional layer normalization, and a masked autoencoding objective…

Computer Vision and Pattern Recognition · Computer Science 2025-11-06 Minh Sao Khue Luu , Bair N. Tuchinov

Neural electrical activity is fundamental to brain function, underlying a range of cognitive and behavioral processes, including movement, perception, decision-making, and consciousness. Abnormal patterns of neural signaling often indicate…

Neurons and Cognition · Quantitative Biology 2025-09-03 Zhizhang Yuan , Fanqi Shen , Meng Li , Yuguo Yu , Chenhao Tan , Yang Yang

Multimodal MRI offers complementary multi-scale information to characterize the brain structure. However, it remains challenging to effectively integrate multimodal MRI while achieving neuroscience interpretability. Here we propose to use…

Neurons and Cognition · Quantitative Biology 2025-12-15 Chengzhi Xia , Jianwei Chen , Yixuan Jiang , Qi Yan , Chao Li

Contemporary computational neuroscience features two prominent modeling traditions. Bottom-up whole-brain modeling (WBM) builds biophysically detailed simulations of brain structure and dynamics, whereas top-down neuroconnectionism…

Neurons and Cognition · Quantitative Biology 2026-05-19 Mario Senden , Leonardo Dalla Porta , Jan Fousek , Jorge F. Mejias , Gorka Zamora-López

Scientific foundation models are expected to reuse representations under changes in dataset, acquisition protocol, and deployment domain, yet many sequence backbones treat scientific temporal structure as an unconstrained pattern to be…

Machine Learning · Computer Science 2026-05-19 Sangyoon Bae , Shinjae Yoo , Jiook Cha