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The emergence of foundation models in neuroimaging is driven by the increasing availability of large-scale and heterogeneous brain imaging datasets. Recent advances in self-supervised learning, particularly reconstruction-based objectives,…

Machine Learning · Computer Science 2025-11-04 Ruthwik Reddy Doodipala , Pankaj Pandey , Carolina Torres Rojas , Manob Jyoti Saikia , Ranganatha Sitaram

Large Language Models have achieved remarkable success in language understanding and reasoning, and their multimodal extensions enable comprehension of images, video, and audio. Inspired by this, foundation models for brain functional…

Artificial Intelligence · Computer Science 2026-03-03 Xingcan Hu , Wei Wang , Li Xiao

Brain foundation models (BFMs) have emerged as a transformative paradigm in computational neuroscience, offering a revolutionary framework for processing diverse neural signals across different brain-related tasks. These models leverage…

Machine Learning · Computer Science 2025-07-22 Xinliang Zhou , Chenyu Liu , Zhisheng Chen , Kun Wang , Yi Ding , Ziyu Jia , Qingsong Wen

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where…

Computer Vision and Pattern Recognition · Computer Science 2024-03-12 Peirong Liu , Oula Puonti , Xiaoling Hu , Daniel C. Alexander , Juan E. Iglesias

Brain connectivity analysis is crucial for understanding brain structure and neurological function, shedding light on the mechanisms of mental illness. To study the association between individual brain connectivity networks and the clinical…

Foundation models in artificial intelligence (AI) are transforming medical imaging by enabling general-purpose feature learning from large-scale, unlabeled datasets. In this work, we introduce BrainFound, a self-supervised foundation model…

Computer Vision and Pattern Recognition · Computer Science 2026-01-01 Moona Mazher , Geoff J. M. Parker , Daniel C. Alexander

Foundation models (FMs), powered by self-supervised learning (SSL), have redefined the capabilities of artificial intelligence, demonstrating exceptional performance in domains like natural language processing and computer vision. These…

Machine Learning · Computer Science 2025-06-23 Hamdi Altaheri , Fakhri Karray , Md. Milon Islam , S M Taslim Uddin Raju , Amir-Hossein Karimi

Recent neuroimaging studies that focus on predicting brain disorders via modern machine learning approaches commonly include a single modality and rely on supervised over-parameterized models.However, a single modality provides only a…

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

We propose the Neural Functional Alignment Space (NFAS), a brain-referenced representational framework for characterizing artificial neural networks on equal functional grounds. NFAS departs from conventional alignment approaches that rely…

Computer Vision and Pattern Recognition · Computer Science 2026-03-03 Ruiyu Yan , Hanqi Jiang , Yi Pan , Xiaobo Li , Tianming Liu , Xi Jiang , Lin Zhao

Neuroscience research has made immense progress over the last decade, but our understanding of the brain remains fragmented and piecemeal: the dream of probing an arbitrary brain region and automatically reading out the information encoded…

Brain network analysis based on functional Magnetic Resonance Imaging (fMRI) is pivotal for diagnosing brain disorders. Existing approaches typically rely on predefined functional sub-networks to construct sub-network associations. However,…

Machine Learning · Computer Science 2026-03-11 Jingfeng Tang , Peng Cao , Guangqi Wen , Jinzhu Yang , Xiaoli Liu , Osmar R. Zaiane

Interpretable deep learning models have received widespread attention in the field of image recognition. Due to the unique multi-instance learning of medical images and the difficulty in identifying decision-making regions, many…

Computer Vision and Pattern Recognition · Computer Science 2023-12-05 Yitao Peng , Lianghua He , Die Hu , Yihang Liu , Longzhen Yang , Shaohua Shang

The use of supervised deep learning techniques to detect pathologies in brain MRI scans can be challenging due to the diversity of brain anatomy and the need for annotated data sets. An alternative approach is to use unsupervised anomaly…

Image and Video Processing · Electrical Eng. & Systems 2023-03-08 Finn Behrendt , Debayan Bhattacharya , Julia Krüger , Roland Opfer , Alexander Schlaefer

With the growing interest in foundation models for brain signals, graph-based pretraining has emerged as a promising paradigm for learning transferable representations from connectome data. However, existing contrastive and masked…

Machine Learning · Computer Science 2026-03-10 Xinxu Wei , Rong Zhou , Lifang He , Yu Zhang

Brain functional network has become an increasingly used approach in understanding brain functions and diseases. Many network construction methods have been developed, whereas the majority of the studies still used static pairwise Pearson's…

Neurons and Cognition · Quantitative Biology 2020-03-13 Zhen Zhou , Xiaobo Chen , Yu Zhang , Lishan Qiao , Renping Yu , Gang Pan , Han Zhang , Dinggang Shen

3D structural Magnetic Resonance Imaging (MRI) brain scans are commonly acquired in clinical settings to monitor a wide range of neurological conditions, including neurodegenerative disorders and stroke. While deep learning models have…

Computer Vision and Pattern Recognition · Computer Science 2025-09-16 Emily Kaczmarek , Justin Szeto , Brennan Nichyporuk , Tal Arbel

This paper presents a comprehensive and quality collection of functional human brain network data for potential research in the intersection of neuroscience, machine learning, and graph analytics. Anatomical and functional MRI images have…

The burgeoning field of brain health research increasingly leverages artificial intelligence (AI) to interpret and analyze neurological data. This study introduces a novel approach towards the creation of medical foundation models by…

Image and Video Processing · Electrical Eng. & Systems 2024-11-08 Joseph Cox , Peng Liu , Skylar E. Stolte , Yunchao Yang , Kang Liu , Kyle B. See , Huiwen Ju , Ruogu Fang

Estimating a representative and discriminative brain network atlas (BNA) is a nascent research field in mapping a population of brain networks in health and disease. Although limited, existing BNA estimation methods have several…

Machine Learning · Computer Science 2020-09-24 Islem Mhiri , Mohamed Ali Mahjoub , Islem Rekik