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We propose a novel matrix autoencoder to map functional connectomes from resting state fMRI (rs-fMRI) to structural connectomes from Diffusion Tensor Imaging (DTI), as guided by subject-level phenotypic measures. Our specialized autoencoder…

Modeling the behavior of coupled networks is challenging due to their intricate dynamics. For example in neuroscience, it is of critical importance to understand the relationship between the functional neural processes and anatomical…

Machine Learning · Computer Science 2021-04-20 Hongyuan You , Sikun Lin , Ambuj K. Singh

We propose a novel optimization framework to predict clinical severity from resting state fMRI (rs-fMRI) data. Our model consists of two coupled terms. The first term decomposes the correlation matrices into a sparse set of representative…

Neurons and Cognition · Quantitative Biology 2024-11-25 Niharika Shimona D'Souza , Mary Beth Nebel , Nicholas Wymbs , Stewart H. Mostofsky , Archana Venkataraman

Mental and cognitive representations are believed to reside on low-dimensional, non-linear manifolds embedded within high-dimensional brain activity. Uncovering these manifolds is key to understanding individual differences in brain…

Machine Learning · Computer Science 2025-05-02 Eloy Geenjaar , Vince Calhoun

We propose a unified optimization framework that combines neural networks with dictionary learning to model complex interactions between resting state functional MRI and behavioral data. The dictionary learning objective decomposes patient…

Machine Learning · Computer Science 2024-11-21 Niharika Shimona D'Souza , Mary Beth Nebel , Nicholas Wymbs , Stewart Mostofsky , Archana Venkataraman

The problem of jointly analysing functional connectomics and behavioral data is extremely challenging owing to the complex interactions between the two domains. In addition, clinical rs-fMRI studies often have to contend with limited…

Machine Learning · Computer Science 2023-01-18 Niharika Shimona D'Souza

Fusion and inference from multiple and massive disparate data sources - the requirement for our most challenging data analysis problems and the goal of our most ambitious statistical pattern recognition methodologies - -has many and varied…

Methodology · Statistics 2011-12-26 Carey E. Priebe , David J. Marchette , Zhiliang Ma , Sancar Adali

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by atypical functional brain connectivity and subtle structural alterations. rs-fMRI has been widely used to identify disruptions in large-scale brain…

Computer Vision and Pattern Recognition · Computer Science 2026-03-17 Ansar Rahman , Hassan Shojaee-Mend , Sepideh Hatamikia

To explain individual differences in development, behavior, and cognition, most previous studies focused on projecting resting-state functional MRI (fMRI) based functional connectivity (FC) data into a low-dimensional space via linear…

Neurons and Cognition · Quantitative Biology 2018-11-01 Li Xiao , Julia M. Stephen , Tony W. Wilson , Vince D. Calhoun , Yu-Ping Wang

We establish a broad methodological foundation for mixed-integer optimization with learned constraints. We propose an end-to-end pipeline for data-driven decision making in which constraints and objectives are directly learned from data…

Optimization and Control · Mathematics 2023-10-30 Donato Maragno , Holly Wiberg , Dimitris Bertsimas , S. Ilker Birbil , Dick den Hertog , Adejuyigbe Fajemisin

We introduce a manifold-based framework for addressing optimization problems with equality and inequality constraints found in robotics. Our approach transforms the original problem into an unconstrained optimization problem directly on the…

Robotics · Computer Science 2026-05-21 Yetong Zhang , Frank Dellaert

In recent years, manifold methods have moved into focus as tools for dimension reduction. Assuming that the high-dimensional data actually lie on or close to a low-dimensional nonlinear manifold, these methods have shown convincing results…

Machine Learning · Statistics 2020-12-23 Moritz Herrmann , Fabian Scheipl

This article introduces a new data-driven approach that leverages a manifold embedding generated by the invertible neural network to improve the robustness, efficiency, and accuracy of the constitutive-law-free simulations with limited…

Machine Learning · Computer Science 2022-05-19 Bahador Bahmani , WaiChing Sun

The correlation matrix is a central representation of functional brain networks in neuroimaging. Traditional analyses often treat pairwise interactions independently in a Euclidean setting, overlooking the intrinsic geometry of correlation…

Machine Learning · Statistics 2025-04-10 Kisung You , Yelim Lee , Hae-Jeong Park

Multi-modal brain functional connectivity (FC) data have shown great potential for providing insights into individual variations in behavioral and cognitive traits. The joint learning of multi-modal imaging data can utilize the intrinsic…

Quantitative Methods · Quantitative Biology 2019-01-18 Li Xiao , Julia M. Stephen , Tony W. Wilson , Vince D. Calhoun , Yu-Ping Wang

Many machine learning tasks, such as principal component analysis and low-rank matrix completion, give rise to manifold optimization problems. Although there is a large body of work studying the design and analysis of algorithms for…

Machine Learning · Computer Science 2024-06-13 Jiaojiao Zhang , Jiang Hu , Anthony Man-Cho So , Mikael Johansson

Computer-aided diagnosis (CAD) systems play a crucial role in analyzing neuroimaging data for neurological and psychiatric disorders. However, small-sample studies suffer from low reproducibility, while large-scale datasets introduce…

Machine Learning · Computer Science 2025-08-12 Xinglin Zhao , Yanwen Wang , Xiaobo Liu , Yanrong Hao , Rui Cao , Xin 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

We consider the problem of reconstructing missing data on a smooth manifold from incomplete and nonuniform samples. While classical methods for manifold approximation typically assume quasi-uniform data, their performance deteriorates…

Numerical Analysis · Mathematics 2026-04-15 David Levin

In neuroscience, functional brain connectivity describes the connectivity between brain regions that share functional properties. Neuroscientists often characterize it by a time series of covariance matrices between functional measurements…

Methodology · Statistics 2019-07-09 Zhenhua Lin , Dehan Kong , Qiang Sun
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