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Related papers: Batch Effects In Brain Foundation Model Embeddings

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Foundation models, pre-trained on large image datasets and capable of capturing rich feature representations, have recently shown potential for zero-shot image registration. However, their performance has mostly been tested in the context…

Image and Video Processing · Electrical Eng. & Systems 2025-08-12 Hanxue Gu , Yaqian Chen , Nicholas Konz , Qihang Li , Maciej A. Mazurowski

Foundation models refer to artificial intelligence (AI) models that are trained on massive amounts of data and demonstrate broad generalizability across various tasks with high accuracy. These models offer versatile, one-for-many or…

Image and Video Processing · Electrical Eng. & Systems 2024-11-06 Rina Bao , Erfan Darzi , Sheng He , Chuan-Heng Hsiao , Mohammad Arafat Hussain , Jingpeng Li , Atle Bjornerud , Ellen Grant , Yangming Ou

In the rapidly evolving landscape of artificial intelligence, generative models such as Generative Adversarial Networks (GANs) and Diffusion Models have become cornerstone technologies, driving innovation in diverse fields from art creation…

Machine Learning · Computer Science 2024-08-01 Jack He , Jianxing Zhao , Andrew Bai , Cho-Jui Hsieh

Neural Language Models (NLMs) have made tremendous advances during the last years, achieving impressive performance on various linguistic tasks. Capitalizing on this, studies in neuroscience have started to use NLMs to study neural activity…

Artificial Intelligence · Computer Science 2022-07-08 Alexandre Pasquiou , Yair Lakretz , John Hale , Bertrand Thirion , Christophe Pallier

Foundation Models (FMs) are models trained on large corpora of data that, at very large scale, can generalize to new tasks without any task-specific finetuning. As these models continue to grow in size, innovations continue to push the…

Machine Learning · Computer Science 2022-12-27 Avanika Narayan , Ines Chami , Laurel Orr , Simran Arora , Christopher Ré

Representation learning is a fundamental building block for analyzing entities in a database. While the existing embedding learning methods are effective in various data mining problems, their applicability is often limited because these…

Machine Learning · Computer Science 2020-09-24 Chin-Chia Michael Yeh , Dhruv Gelda , Zhongfang Zhuang , Yan Zheng , Liang Gou , Wei Zhang

Foundation models (FMs) are driving a prominent shift in biomedical imaging from task-specific models to unified backbone models for diverse tasks. This opens an avenue to integrate imaging, pathology, clinical records, and genomics data…

Quantitative Methods · Quantitative Biology 2026-04-23 Amgad Muneer , Kai Zhang , Ibraheem Hamdi , Rizwan Qureshi , Muhammad Waqas , Shereen Fouad , Hazrat Ali , Syed Muhammad Anwar , Jia Wu

While brain-inspired artificial intelligence(AI) has demonstrated promising results, current understanding of the parallels between artificial neural networks (ANNs) and human brain processing remains limited: (1) unimodal ANN studies fail…

Computer Vision and Pattern Recognition · Computer Science 2025-10-21 Yudan Ren , Xinlong Wang , Kexin Wang , Tian Xia , Zihan Ma , Zhaowei Li , Xiangrong Bi , Xiao Li , Xiaowei He

Recent work has found that neural networks with stronger generalization tend to exhibit higher representational alignment with one another across architectures and training paradigms. In this work, we show that models with stronger…

Machine Learning · Computer Science 2026-02-02 Junjie Yu , Wenxiao Ma , Chen Wei , Jianyu Zhang , Haotian Deng , Zihan Deng , Quanying Liu

Functional magnetic resonance imaging (fMRI) is a powerful tool for investigating human brain function. However, the high cost of data acquisition and the inherent subjectivity of psychiatric rating scales often lead to datasets with small…

Machine Learning · Computer Science 2026-05-29 Jiyao Wang , Peiyu Duan , Nicha C. Dvornek , Lawrence H. Staib , Denis Sukhodolsky , Pamela Ventola , James S. Duncan

Despite the significant potential of Foundation Models (FMs) in medical imaging, their application to prognosis prediction remains challenging due to data scarcity, class imbalance, and task complexity, which limit their clinical adoption.…

Computer Vision and Pattern Recognition · Computer Science 2026-01-16 Filippo Ruffini , Elena Mulero Ayllon , Linlin Shen , Paolo Soda , Valerio Guarrasi

Neurophysiological time series recordings like the electroencephalogram (EEG) or local field potentials are obtained from multiple sensors. They can be decoded by machine learning models in order to estimate the ongoing brain state of a…

Signal Processing · Electrical Eng. & Systems 2023-04-14 Pierre Guetschel , Théodore Papadopoulo , Michael Tangermann

Large Language Models (LLMs) have been shown to be effective models of the human language system, with some models predicting most explainable variance of brain activity in current datasets. Even in untrained models, the representations…

Computation and Language · Computer Science 2024-06-24 Badr AlKhamissi , Greta Tuckute , Antoine Bosselut , Martin Schrimpf

Recent advances in artificial intelligence (AI), in particular self-supervised learning of foundation models (FMs), are revolutionizing medical imaging and computational pathology (CPath). A constant challenge in the analysis of digital…

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

The successful adaptation of foundation models to multi-modal medical imaging is a critical yet unresolved challenge. Existing models often struggle to effectively fuse information from multiple sources and adapt to the heterogeneous nature…

Computer Vision and Pattern Recognition · Computer Science 2026-01-23 Shadi Alijani , Fereshteh Aghaee Meibodi , Homayoun Najjaran

What role does phenotypic complexity play in the systems-level function of an embodied agent? The organismal phenotype is a topologically complex structure that interacts with a genotype, developmental physics, and an informational…

Neurons and Cognition · Quantitative Biology 2022-08-15 Bradly Alicea , Jesse Parent

Speech contains both acoustic and linguistic patterns that reflect cognitive decline, and therefore models describing only one domain cannot fully capture such complexity. This study investigates how early fusion (EF) of speech and its…

Audio and Speech Processing · Electrical Eng. & Systems 2026-02-02 Krystof Novotny , Laureano Moro-Velázquez , Jiri Mekyska

Concept Bottleneck Models (CBMs) tackle the opacity of neural architectures by constructing and explaining their predictions using a set of high-level concepts. A special property of these models is that they permit concept interventions,…

Graphs are a natural abstraction for many problems where nodes represent entities and edges represent a relationship across entities. An important area of research that has emerged over the last decade is the use of graphs as a vehicle for…