We propose a novel method to embed a functional magnetic resonance imaging (fMRI) dataset in a low-dimensional space. The embedding optimally preserves the local functional coupling between fMRI time series and provides a low-dimensional coordinate system for detecting activated voxels. To compute the embedding, we build a graph of functionally connected voxels. We use the commute time, instead of the geodesic distance, to measure functional distances on the graph. Because the commute time can be computed directly from the eigenvectors of (a symmetric version) the graph probability transition matrix, we use these eigenvectors to embed the dataset in low dimensions. After clustering the datasets in low dimensions, coherent structures emerge that can be easily interpreted. We performed an extensive evaluation of our method comparing it to linear and nonlinear techniques using synthetic datasets and in vivo datasets. We analyzed datasets from the EBC competition obtained with subjects interacting in an urban virtual reality environment. Our exploratory approach is able to detect independently visual areas (V1/V2, V5/MT), auditory areas, and language areas. Our method can be used to analyze fMRI collected during ``natural stimuli''.
Yale University（耶鲁大学）；Yale School of Medicine（耶鲁医学院）
Recurrent neural networks (RNNs) were designed for dealing with time-series data and have recently been used for creating predictive models from functional magnetic resonance imaging (fMRI) data. However, gathering large fMRI datasets for learning is a difficult task. Furthermore, network interpretability is unclear. To address these issues, we utilize multitask learning and design a novel RNN-based model that learns to discriminate between classes while simultaneously learning to generate the fMRI time-series data. Employing the long short-term memory (LSTM) structure, we develop a discrimina…
Northeastern University（东北大学）；University of Oregon（俄勒冈大学）
Neuroimaging studies produce gigabytes of spatio-temporal data for a small number of participants and stimuli. Rarely do researchers attempt to model and examine how individual participants vary from each other -- a question that should be addressable even in small samples given the right statistical tools. We propose Neural Topographic Factor Analysis (NTFA), a probabilistic factor analysis model that infers embeddings for participants and stimuli. These embeddings allow us to reason about differences between participants and stimuli as signal rather than noise. We evaluate NTFA on data from …
Nanjing University of Aeronautics and Astronautics（南京航空航天大学）；University of Alberta（阿尔伯塔大学）；Purdue University Fort Wayne（普渡大学韦恩堡分校）；Manchester Metropolitan University（曼彻斯特城市大学）
Hyperalignment has been widely employed in Multivariate Pattern (MVP) analysis to discover the cognitive states in the human brains based on multi-subject functional Magnetic Resonance Imaging (fMRI) datasets. Most of the existing HA methods utilized unsupervised approaches, where they only maximized the correlation between the voxels with the same position in the time series. However, these unsupervised solutions may not be optimum for handling the functional alignment in the supervised MVP problems. This paper proposes a Supervised Hyperalignment (SHA) method to ensure better functional alig…
BrainCast: A Spatio-Temporal Forecasting Model for Whole-Brain fMRI Time Series Prediction
Institute of Advanced Technology, University of Science and Technology of China（科学技术大学先进技术研究院）；MoE Key Laboratory of Brain-Inspired Intelligence Perception and Cognition, University of Science and Technology of China（科学技术大学脑启发智能感知与认知教育部重点实验室）；School of Mathematics and Computer Sciences, Nanchang University（南昌大学数学与计算机科学学院）；School of Data Science, University of Virginia（弗吉尼亚大学数据科学学院）；Department of Biomedical Engineering, Tulane University（路易斯安那大学医学工程系）
We present a comparison between various algorithms of inference of covariance and precision matrices in small datasets of real vectors, of the typical length and dimension of human brain activity time series retrieved by functional Magnetic Resonance Imaging (fMRI). Assuming a Gaussian model underlying the neural activity, the problem consists in denoising the empirically observed matrices in order to obtain a better estimator of the true precision and covariance matrices. We consider several standard noise-cleaning algorithms and compare them on two types of datasets. The first type are time …
Advances on signal, image and video generation underly major breakthroughs on generative medical imaging tasks, including Brain Image Synthesis. Still, the extent to which functional Magnetic Ressonance Imaging (fMRI) can be mapped from the brain electrophysiology remains largely unexplored. This work provides the first comprehensive view on how to use state-of-the-art principles from Neural Processing to synthesize fMRI data from electroencephalographic (EEG) data. Given the distinct spatiotemporal nature of haemodynamic and electrophysiological signals, this problem is formulated as the task…
Background: Functional magnetic resonance imaging (fMRI) provides non-invasive measures of neuronal activity using an endogenous Blood Oxygenation-Level Dependent (BOLD) contrast. This article introduces a nonlinear dimensionality reduction (Locally Linear Embedding) to extract informative measures of the underlying neuronal activity from BOLD time-series. The method is validated using the Leave-One-Out-Cross-Validation (LOOCV) accuracy of classifying psychiatric diagnoses using resting-state and task-related fMRI. Methods: Locally Linear Embedding of BOLD time-series (into each voxel's respec…
Significant progress has been made using fMRI to characterize the brain changes that occur in ASD, a complex neuro-developmental disorder. However, due to the high dimensionality and low signal-to-noise ratio of fMRI, embedding informative and robust brain regional fMRI representations for both graph-level classification and region-level functional difference detection tasks between ASD and healthy control (HC) groups is difficult. Here, we model the whole brain fMRI as a graph, which preserves geometrical and temporal information and use a Graph Neural Network (GNN) to learn from the graph-st…
National Kapodistrian Univ. of Athens (NKUA/UoA)（雅典国家卡波季斯特里安大学）
Functional Magnetic Resonance Imaging (fMRI) is a powerful non-invasive tool for localizing and analyzing brain activity. This study focuses on one very important aspect of the functional properties of human brain, specifically the estimation of the level of parallelism when performing complex cognitive tasks. Using fMRI as the main modality, the human brain activity is investigated through a purely data-driven signal processing and dimensionality analysis approach. Specifically, the fMRI signal is treated as a multi-dimensional data space and its intrinsic `complexity' is studied via dataset …
University of Toronto（多伦多大学）；Centre for Addiction and Mental Health（成瘾与心理健康中心）
Multi-subject fMRI studies are challenging due to the high variability of both brain anatomy and functional brain topographies across participants. An effective way of aggregating multi-subject fMRI data is to extract a shared representation that filters out unwanted variability among subjects. Some recent work has implemented probabilistic models to extract a shared representation in task fMRI. In the present work, we improve upon these models by incorporating temporal information in the common latent structures. We introduce a new model, Shared Gaussian Process Factor Analysis (S-GPFA), that…
Columbia University（哥伦比亚大学）；Stanford University（斯坦福大学）
We propose a hierarchical Bayesian recurrent state space model for modeling switching network connectivity in resting state fMRI data. Our model allows us to uncover shared network patterns across disease conditions. We evaluate our method on the ADNI2 dataset by inferring latent state patterns corresponding to altered neural circuits in individuals with Mild Cognitive Impairment (MCI). In addition to states shared across healthy and individuals with MCI, we discover latent states that are predominantly observed in individuals with MCI. Our model outperforms current state of the art deep learn…
Technische Universität Berlin（柏林工业大学）；Max Planck School of Cognition（马克斯·普朗克认知学院）；Korea University（高丽大学）；Max Planck Institute for Informatics（马克斯·普朗克信息学研究所）；Fraunhofer Heinrich Hertz Institute（弗劳恩霍夫海因里希·赫兹研究所）
The application of deep learning (DL) models to the decoding of cognitive states from whole-brain functional Magnetic Resonance Imaging (fMRI) data is often hindered by the small sample size and high dimensionality of these datasets. Especially, in clinical settings, where patient data are scarce. In this work, we demonstrate that transfer learning represents a solution to this problem. Particularly, we show that a DL model, which has been previously trained on a large openly available fMRI dataset of the Human Connectome Project, outperforms a model variant with the same architecture, but whi…
Nanjing University of Aeronautics and Astronautics（南京航空航天大学）；Taishan University（泰山学院）
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 topographies of human brains warrant aligning fMRI data across subjects. However, the existing functional alignment methods cannot handle well various kinds of fMRI datasets today, especially when they are not temporally-aligned, i.e., some of the subjects probably lack the responses to some stimuli, or different subjects might follow different sequences of …
Nanjing University of Aeronautics and Astronautics（南京航空航天大学）
In order to decode the human brain, Multivariate Pattern (MVP) classification generates cognitive models by using functional Magnetic Resonance Imaging (fMRI) datasets. As a standard pipeline in the MVP analysis, brain patterns in multi-subject fMRI dataset must be mapped to a shared space and then a classification model is generated by employing the mapped patterns. However, the MVP models may not provide stable performance on a new fMRI dataset because the standard pipeline uses disjoint steps for generating these models. Indeed, each step in the pipeline includes an objective function with …
Georgia State University（佐治亚州立大学）；Georgia Institute of Technology（佐治亚理工学院）；TReNDS Center（TReNDS中心）
As a mental disorder progresses, it may affect brain structure, but brain function expressed in brain dynamics is affected much earlier. Capturing the moment when brain dynamics express the disorder is crucial for early diagnosis. The traditional approach to this problem via training classifiers either proceeds from handcrafted features or requires large datasets to combat the $m>>n$ problem when a high dimensional fMRI volume only has a single label that carries learning signal. Large datasets may not be available for a study of each disorder, or rare disorder types or sub-populations may not…
University of Cambridge（剑桥大学）；University of Granada（格拉纳达大学）
Deep learning models for MRI classification face two recurring problems: they are typically limited by low sample size, and are abstracted by their own complexity (the "black box problem"). In this paper, we train a convolutional neural network (CNN) with the largest multi-source, functional MRI (fMRI) connectomic dataset ever compiled, consisting of 43,858 datapoints. We apply this model to a cross-sectional comparison of autism (ASD) vs typically developing (TD) controls that has proved difficult to characterise with inferential statistics. To contextualise these findings, we additionally pe…
Cognitive neuroscience is enjoying rapid increase in extensive public brain-imaging datasets. It opens the door to large-scale statistical models. Finding a unified perspective for all available data calls for scalable and automated solutions to an old challenge: how to aggregate heterogeneous information on brain function into a universal cognitive system that relates mental operations/cognitive processes/psychological tasks to brain networks? We cast this challenge in a machine-learning approach to predict conditions from statistical brain maps across different studies. For this, we leverage…
Nanjing University of Aeronautics and Astronautics（南京航空航天大学）
Multi-subject fMRI data analysis is an interesting and challenging problem in human brain decoding studies. The inherent anatomical and functional variability across subjects make it necessary to do both anatomical and functional alignment before classification analysis. Besides, when it comes to big data, time complexity becomes a problem that cannot be ignored. This paper proposes Gradient Hyperalignment (Gradient-HA) as a gradient-based functional alignment method that is suitable for multi-subject fMRI datasets with large amounts of samples and voxels. The advantage of Gradient-HA is that …
DynDepNet: Learning Time-Varying Dependency Structures from fMRI Data via Dynamic Graph Structure Learning
University of Cambridge（剑桥大学）；The Alan Turing Institute（阿兰·图灵研究所）；University of Milano-Bicocca（米兰比可卡大学）；University of Rome Tor Vergata（罗马第二大学）；Harvard Medical School（哈佛医学院）
Objective: Joint analysis of multi-subject brain imaging datasets has wide applications in biomedical engineering. In these datasets, some sources belong to all subjects (joint), a subset of subjects (partially-joint), or a single subject (individual). In this paper, this source model is referred to as joint/partially-joint/individual multiple datasets multidimensional (JpJI-MDM), and accordingly, a source extraction method is developed. Method: We present a deflation-based algorithm utilizing higher order cumulants to analyze the JpJI-MDM source model. The algorithm maximizes a cost function …
Over the last twenty five years, advances in the collection and analysis of fMRI data have enabled new insights into the brain basis of human health and disease. Individual behavioral variation can now be visualized at a neural level as patterns of connectivity among brain regions. Functional brain imaging is enhancing our understanding of clinical psychiatric disorders by revealing ties between regional and network abnormalities and psychiatric symptoms. Initial success in this arena has recently motivated collection of larger datasets which are needed to leverage fMRI to generate brain-based…
Budapest University of Technology and Economics（布达佩斯技术与经济大学）；Research Centre for Natural Sciences, Hungarian Academy of Sciences（匈牙利科学院自然科学研究中心）
Machine learning techniques have become increasingly popular in the field of resting state fMRI (functional magnetic resonance imaging) network based classification. However, the application of convolutional networks has been proposed only very recently and has remained largely unexplored. In this paper we describe a convolutional neural network architecture for functional connectome classification called connectome-convolutional neural network (CCNN). Our results on simulated datasets and a publicly available dataset for amnestic mild cognitive impairment classification demonstrate that our C…
