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Related papers: Batch Effects In Brain Foundation Model Embeddings

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Foundation models, first introduced in 2021, refer to large-scale pretrained models (e.g., large language models (LLMs) and vision-language models (VLMs)) that learn from extensive unlabeled datasets through unsupervised methods, enabling…

Foundation models (FMs) are large-scale deep learning models trained on massive datasets, often using self-supervised learning techniques. These models serve as a versatile base for a wide range of downstream tasks, including those in…

Machine Learning · Computer Science 2025-01-17 Wasif Khan , Seowung Leem , Kyle B. See , Joshua K. Wong , Shaoting Zhang , Ruogu Fang

Health foundation models (FMs) learn useful representations from wearable sensors, but interpreting what they encode and transferring that knowledge across modalities after training remains difficult. We present a post-training framework…

Machine Learning · Computer Science 2026-05-11 Gajendra Katuwal , Advait Koparkar , Salar Abbaspourazad , Anshuman Mishra , Sarvesh Kirthivasan

Electroencephalography foundation models (EEG-FMs) have advanced brain signal analysis, but the lack of standardized evaluation benchmarks impedes model comparison and scientific progress. Current evaluations rely on inconsistent protocols…

Signal Processing · Electrical Eng. & Systems 2026-02-16 Wei Xiong , Jiangtong Li , Jie Li , Kun Zhu , Changjun Jiang

Supervised fine-tuning (SFT) is a critical step in aligning large language models (LLMs) with human instructions and values, yet many aspects of SFT remain poorly understood. We trained a wide range of base models on a variety of datasets…

Computation and Language · Computer Science 2025-10-31 Yuto Harada , Yusuke Yamauchi , Yusuke Oda , Yohei Oseki , Yusuke Miyao , Yu Takagi

The field of computer vision is undergoing a paradigm shift toward large-scale foundation model pre-training via self-supervised learning (SSL). Leveraging large volumes of unlabeled brain MRI data, such models can learn anatomical priors…

Image and Video Processing · Electrical Eng. & Systems 2026-01-15 Petros Koutsouvelis , Matej Gazda , Leroy Volmer , Sina Amirrajab , Kamil Barbierik , Branislav Setlak , Jakub Gazda , Peter Drotar

Functional connections in the brain are frequently represented by weighted networks, with nodes representing locations in the brain, and edges representing the strength of connectivity between these locations. One challenge in analyzing…

Applications · Statistics 2022-09-28 Yura Kim , Daniel Kessler , Elizaveta Levina

Foundation models (FMs) are changing the way medical images are analyzed by learning from large collections of unlabeled data. Instead of relying on manually annotated examples, FMs are pre-trained to learn general-purpose visual features…

Brain development in the first few months of human life is a critical phase characterized by rapid structural growth and functional organization. Accurately predicting developmental outcomes during this time is crucial for identifying…

Neurons and Cognition · Quantitative Biology 2025-01-31 Patrick Styll , Dowon Kim , Jiook Cha

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that…

Foundation models hold promise for transforming AI in healthcare by providing modular components that are easily adaptable to downstream healthcare tasks, making AI development more scalable and cost-effective. Structured EHR foundation…

The strength of machine learning models stems from their ability to learn complex function approximations from data; however, this strength also makes training deep neural networks challenging. Notably, the complex models tend to memorize…

Computer Vision and Pattern Recognition · Computer Science 2023-04-17 Mofassir ul Islam Arif , Mohsan Jameel , Josif Grabocka , Lars Schmidt-Thieme

The extent to which different neural or artificial neural networks (models) rely on equivalent representations to support similar tasks remains a central question in neuroscience and machine learning. Prior work has typically compared…

Neurons and Cognition · Quantitative Biology 2026-04-06 Jialin Wu , Shreya Saha , Yiqing Bo , Meenakshi Khosla

Recent advancements in artificial intelligence (AI), particularly foundation models (FMs), have revolutionized medical image analysis, demonstrating strong zero- and few-shot performance across diverse medical imaging tasks, from…

Computer Vision and Pattern Recognition · Computer Science 2025-10-21 Praveenbalaji Rajendran , Mojtaba Safari , Wenfeng He , Mingzhe Hu , Shansong Wang , Jun Zhou , Xiaofeng Yang

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

Foundation models (FMs) have emerged as a transformative paradigm in medical image analysis, offering the potential to provide generalizable, task-agnostic solutions across a wide range of clinical tasks and imaging modalities. Their…

Computer Vision and Pattern Recognition · Computer Science 2025-11-04 Karma Phuntsho , Abdullah , Kyungmi Lee , Ickjai Lee , Euijoon Ahn

Knowledge sharing is crucial in healthcare, especially when leveraging data from multiple clinical sites to address data scarcity, reduce costs, and enable timely interventions. Transfer learning can facilitate cross-site knowledge…

Computation and Language · Computer Science 2024-09-24 Yuhe Gao , Runxue Bao , Yuelyu Ji , Yiming Sun , Chenxi Song , Jeffrey P. Ferraro , Ye Ye

Pathology foundation models (PFMs) have emerged as a core approach for learning transferable representations from whole slide images (WSIs), and they are typically benchmarked through downstream clinical endpoints. While such task level…

Computer Vision and Pattern Recognition · Computer Science 2026-05-26 Bokai Zhao , Yiyang Zhang , Yuanchi Zhu , Hanqing Chao , Long Bai , Tai Ma , Minfeng Xu , Ming Song , Tianzi Jiang

The biological behavior and treatment response of meningiomas depend on their grade, making an accurate diagnosis essential for treatment planning and prognosis assessment. We observed that the weighted fusion of spatial-frequency domain…

Computer Vision and Pattern Recognition · Computer Science 2026-02-17 Jiamiao Lu , Wei Wu , Ke Gao , Ping Mao , Weichuan Zhang , Tuo Wang , Lingkun Ma , Jiapan Guo , Zanyi Wu , Yuqing Hu , Changming Sun