Decoding the Encoding of Functional Brain Networks: an fMRI Classification Comparison of Non-negative Matrix Factorization (NMF), Independent Component Analysis (ICA), and Sparse Coding Algorithms
University of California, Los Angeles（加州大学洛杉矶分校）
Jianwen Xie, Pamela K. Douglas, Ying Nian Wu, Arthur L. Brody, Ariana E. Anderson
Brain networks in fMRI are typically identified using spatial independent component analysis (ICA), yet mathematical constraints such as sparse coding and positivity both provide alternate biologically-plausible frameworks for generating brain networks. Non-negative Matrix Factorization (NMF) would suppress negative BOLD signal by enforcing positivity. Spatial sparse coding algorithms ($L1$ Regularized Learning and K-SVD) would impose local specialization and a discouragement of multitasking, where the total observed activity in a single voxel originates from a restricted number of possible brain networks.
The assumptions of independence, positivity, and sparsity to encode task-related brain networks are compared; the resulting brain networks for different constraints are used as basis functions to encode the observed functional activity at a given time point. These encodings are decoded using machine learning to compare both the algorithms and their assumptions, using the time series weights to predict whether a subject is viewing a video, listening to an audio cue, or at rest, in 304 fMRI scans from 51 subjects.
For classifying cognitive activity, the sparse coding algorithm of $L1$ Regularized Learning consistently outperformed 4 variations of ICA across different numbers of networks and noise levels (p$<$0.001). The NMF algorithms, which suppressed negative BOLD signal, had the poorest accuracy. Within each algorithm, encodings using sparser spatial networks (containing more zero-valued voxels) had higher classification accuracy (p$<$0.001). The success of sparse coding algorithms may suggest that algorithms which enforce sparse coding, discourage multitasking, and promote local specialization may capture better the underlying source processes than those which allow inexhaustible local processes such as ICA.
KU Leuven（鲁汶大学）；University of Piraeus（比雷埃夫斯大学）；KU Leuven Kulak（鲁汶大学科特赖克校区）；Chinese University of Hong Kong, Shenzhen（香港中文大学（深圳））
Data fusion refers to the joint analysis of multiple datasets which provide complementary views of the same task. In this preprint, the problem of jointly analyzing electroencephalography (EEG) and functional Magnetic Resonance Imaging (fMRI) data is considered. Jointly analyzing EEG and fMRI measurements is highly beneficial for studying brain function because these modalities have complementary spatiotemporal resolution: EEG offers good temporal resolution while fMRI is better in its spatial resolution. The fusion methods reported so far ignore the underlying multi-way nature of the data in …
Future University Hakodate（公立函馆未来大学）；RIKEN AIP（理化学研究所先进智能项目中心）；University College London（伦敦大学学院）；Université Paris-Saclay（巴黎-萨克雷大学）；Inria（法国国家信息与自动化研究所）；CEA（法国原子能和替代能源委员会）；Helsinki Institute for Information Technology HIIT（赫尔辛基信息技术研究所 HIIT）；University of Helsinki（赫尔辛基大学）
Nonlinear independent component analysis (ICA) is a general framework for unsupervised representation learning, and aimed at recovering the latent variables in data. Recent practical methods perform nonlinear ICA by solving a series of classification problems based on logistic regression. However, it is well-known that logistic regression is vulnerable to outliers, and thus the performance can be strongly weakened by outliers. In this paper, we first theoretically analyze nonlinear ICA models in the presence of outliers. Our analysis implies that estimation in nonlinear ICA can be seriously ha…
University of Regensburg（雷根斯堡大学）；Universidade de Aveiro（阿威罗大学）
Independent component analysis (ICA), as a data driven method, has shown to be a powerful tool for functional magnetic resonance imaging (fMRI) data analysis. One drawback of this multivariate approach is, that it is not compatible to the analysis of group data in general. Therefore various techniques have been proposed in order to overcome this limitation of ICA. In this paper a novel ICA-based work-flow for extracting resting state networks from fMRI group studies is proposed. An empirical mode decomposition (EMD) is used to generate reference signals in a data driven manner, which can be in…
Independent component analysis (ICA) is an unsupervised learning method popular in functional magnetic resonance imaging (fMRI). Group ICA has been used to search for biomarkers in neurological disorders including autism spectrum disorder and dementia. However, current methods use a principal component analysis (PCA) step that may remove low-variance features. Linear non-Gaussian component analysis (LNGCA) enables simultaneous dimension reduction and feature estimation including low-variance features in single-subject fMRI. We present a group LNGCA model to extract group components shared by m…
Princeton University（普林斯顿大学）；Johns Hopkins University（约翰斯·霍普金斯大学）；University of Toronto（多伦多大学）
Several research groups have shown how to correlate fMRI responses to the meanings of presented stimuli. This paper presents new methods for doing so when only a natural language annotation is available as the description of the stimulus. We study fMRI data gathered from subjects watching an episode of BBCs Sherlock [1], and learn bidirectional mappings between fMRI responses and natural language representations. We show how to leverage data from multiple subjects watching the same movie to improve the accuracy of the mappings, allowing us to succeed at a scene classification task with 72% acc…
Middle Tennessee State University（中田纳西州立大学）；St. Ambrose University（圣安布罗斯大学）
The objective of this study is to derive functional networks for the autism spectrum disorder (ASD) population using the group ICA and dictionary learning model together and to classify ASD and typically developing (TD) participants using the functional connectivity calculated from the derived functional networks. In our experiments, the ASD functional networks were derived from resting-state functional magnetic resonance imaging (rs-fMRI) data. We downloaded a total of 120 training samples, including 58 ASD and 62 TD participants, which were obtained from the public repository: Autism Brain I…
Independent component analysis (ICA) is a powerful computational tool for separating independent source signals from their linear mixtures. ICA has been widely applied in neuroimaging studies to identify and characterize underlying brain functional networks. An important goal in such studies is to assess the effects of subjects' clinical and demographic covariates on the spatial distributions of the functional networks. Currently, covariate effects are not incorporated in existing group ICA decomposition methods. Hence, they can only be evaluated through ad-hoc approaches which may not be accu…
Independent component analysis (ICA) is popular in many applications, including cognitive neuroscience and signal processing. Due to computational constraints, principal component analysis is used for dimension reduction prior to ICA (PCA+ICA), which could remove important information. The problem is that interesting independent components (ICs) could be mixed in several principal components that are discarded and then these ICs cannot be recovered. We formulate a linear non-Gaussian component model with Gaussian noise components. To estimate this model, we propose likelihood component analysi…
Graph Signal Processing (GSP) is a promising framework to analyze multi-dimensional neuroimaging datasets, while taking into account both the spatial and functional dependencies between brain signals. In the present work, we apply dimensionality reduction techniques based on graph representations of the brain to decode brain activity from real and simulated fMRI datasets. We introduce seven graphs obtained from a) geometric structure and/or b) functional connectivity between brain areas at rest, and compare them when performing dimension reduction for classification. We show that mixed graphs …
Analysis of data from functional magnetic resonance imaging (fMRI) results in constructing functional brain networks. Principal component analysis (PCA) and independent component analysis (ICA) are widely used to generate functional brain networks. Moreover, dictionary learning and sparse representation provide some latent patterns that rules brain activities and they can be interpreted as brain networks. However, these methods lack modeling dependencies of the discovered networks. In this study an alternative to these conventional methods is presented in which dependencies of the networks are…
Werner Reichardt Center for Integrative Neuroscience（维尔纳·赖希哈特综合神经科学中心）；Eberhard Karls Universität Tübingen（图宾根大学）；Bernstein Center for Computational Neuroscience（伯恩斯坦计算神经科学中心）；Institute for Theoretical Physics（理论物理研究所）；Department of Neurophysiology（神经生理学系）；Donders Institute for Brain, Cognition and Behaviour（东德斯脑认知与行为研究所）；Radboud University（拉德堡德大学）；Max Planck Institute for Biological Cybernetics（马克斯·普朗克生物控制论研究所）
An important preprocessing step in most data analysis pipelines aims to extract a small set of sources that explain most of the data. Currently used algorithms for blind source separation (BSS), however, often fail to extract the desired sources and need extensive cross-validation. In contrast, their rarely used probabilistic counterparts can get away with little cross-validation and are more accurate and reliable but no simple and scalable implementations are available. Here we present a novel probabilistic BSS framework (DECOMPOSE) that can be flexibly adjusted to the data, is extensible and…
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 …
Structural and functional MRI studies of patients with post-stroke language deficits have contributed substantially to our understanding of how cognitive-behavioral impairments relate to the location of structural damage and to the activation of surviving brain regions during language processing, respectively. However, very little is known about how inter-patient variability in language task activation relates to variability in the structures affected by stroke. Here, we used parallel independent component analysis (pICA) to characterize links between patterns of structural damage and patterns…
Brain connectomics is a developing field in neurosciences which strives to understand cognitive processes and psychiatric diseases through the analysis of interactions between brain regions. However, in the high-dimensional, low-sample, and noisy regimes that typically characterize fMRI data, the recovery of such interactions remains an ongoing challenge: how can we discover patterns of co-activity between brain regions that could then be associated to cognitive processes or psychiatric disorders? In this paper, we investigate a constrained Bayesian ICA approach which, in comparison to current…
University of Toulouse（图卢兹大学）；IRIT/INP-ENSEEIHT（图卢兹信息研究所/图卢兹国立综合理工学院-国立高等电子技术、电子学、计算机、水力学与电信学院）；CNRS（法国国家科学研究中心）；UMRS Inserm U1023 IMIV-CEA SHFJ（法国国家健康与医学研究院 U1023 混合研究单位-生物医学成像实验室-法国原子能与替代能源委员会奥赛医院弗雷德里克·约里奥医院）；UMRS Inserm U930 - Université de Tours（法国国家健康与医学研究院 U930 混合研究单位-图尔大学）
To analyze dynamic positron emission tomography (PET) images, various generic multivariate data analysis techniques have been considered in the literature, such as principal component analysis (PCA), independent component analysis (ICA), factor analysis and nonnegative matrix factorization (NMF). Nevertheless, these conventional approaches neglect any possible nonlinear variations in the time activity curves describing the kinetic behavior of tissues with specific binding, which limits their ability to recover a reliable, understandable and interpretable description of the data. This paper pro…
TReND: Transformer derived features and Regularized NMF for neonatal functional network Delineation
University of Pennsylvania（宾夕法尼亚大学）；Children’s Hospital of Philadelphia（费城儿童医院）；Peking University（北京大学）；Beijing Children’s Hospital（北京儿童医院）；Beijing Normal University（北京师范大学）
University of Maryland Baltimore County（马里兰大学巴尔的摩县分校）；Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS)（三校神经影像与数据科学转化研究中心（TReNDS））；Georgia State University（佐治亚州立大学）；Georgia Institute of Technology（佐治亚理工学院）；Emory University（埃默里大学）
Independent component analysis (ICA) of multi-subject functional magnetic resonance imaging (fMRI) data has proven useful in providing a fully multivariate summary that can be used for multiple purposes. ICA can identify patterns that can discriminate between healthy controls (HC) and patients with various mental disorders such as schizophrenia (Sz). Temporal functional network connectivity (tFNC) obtained from ICA can effectively explain the interactions between brain networks. On the other hand, dictionary learning (DL) enables the discovery of hidden information in data using learnable basi…
Sorbonne Université（索邦大学）；INSERM（法国国家健康与医学研究院）；CNRS（法国国家科学研究中心）；Institut de la Vision（视觉研究所）；FIAS（法兰克福高等研究院）；Goethe-Universität Frankfurt am Main（法兰克福大学）；Zalando Research（Zalando研究院）；University of Sheffield（谢菲尔德大学）；d-fine GmbH（d-fine有限公司）；C. v. Ossietzky Universität Oldenburg（奥尔登堡大学）
ProSper is a python library containing probabilistic algorithms to learn dictionaries. Given a set of data points, the implemented algorithms seek to learn the elementary components that have generated the data. The library widens the scope of dictionary learning approaches beyond implementations of standard approaches such as ICA, NMF or standard L1 sparse coding. The implemented algorithms are especially well-suited in cases when data consist of components that combine non-linearly and/or for data requiring flexible prior distributions. Furthermore, the implemented algorithms go beyond stand…
We introduce a novel recurrent neural network (RNN) approach to account for temporal dynamics and dependencies in brain networks observed via functional magnetic resonance imaging (fMRI). Our approach directly parameterizes temporal dynamics through recurrent connections, which can be used to formulate blind source separation with a conditional (rather than marginal) independence assumption, which we call RNN-ICA. This formulation enables us to visualize the temporal dynamics of both first order (activity) and second order (directed connectivity) information in brain networks that are widely s…
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 …
Johns Hopkins University（约翰斯·霍普金斯大学）；Microsoft（微软公司）；Johns Hopkins School of Medicine（约翰斯·霍普金斯医学院）；Malone Center for Engineering in Healthcare（马龙医疗保健工程中心）
The University of Georgia（佐治亚大学）；Innopolis University（因诺波利斯大学）
In recent years, analyzing task-based fMRI (tfMRI) data has become an essential tool for understanding brain function and networks. However, due to the sheer size of tfMRI data, its intrinsic complex structure, and lack of ground truth of underlying neural activities, modeling tfMRI data is hard and challenging. Previously proposed data-modeling methods including Independent Component Analysis (ICA) and Sparse Dictionary Learning only provided a weakly established model based on blind source separation under the strong assumption that original fMRI signals could be linearly decomposed into tim…
Resting state functional MRI (rs-fMRI) is a widespread and powerful tool for investigating functional connectivity and brain disorders. However, functional connectivity analysis can be seriously affected by random and structured noise from non-neural sources such as physiology. Thus, it is essential to first reduce thermal noise and then correctly identify and remove non-neural artefacts from rs-fMRI signals through optimized data processing methods. However, existing tools that correct for these effects have been developed for human brain and are not readily transposable to rat data. Therefor…
Scaling temporal dynamics in functional MRI (fMRI) signals have been evidenced for a decade as intrinsic characteristics of ongoing brain activity (Zarahn et al., 1997). Recently, scaling properties were shown to fluctuate across brain networks and to be modulated between rest and task (He, 2011): notably, Hurst exponent, quantifying long memory, decreases under task in activating and deactivating brain regions. In most cases, such results were obtained: First, from univariate (voxelwise or regionwise) analysis, hence focusing on specific cognitive systems such as Resting-State Networks (RSNs)…
A critical question for cognitive neuroscience regards how transitions between cognitive states emerge from the dynamic activity of functional brain networks. However, current methodologies cannot easily evaluate both the spatial and temporal changes in brain networks with cognitive state. Here we combine a simple data reorganization with spatial ICA, enabling a spatiotemporal ICA (stICA) which captures the consistent evolution of networks during onset and offset of a task. The technique was applied to FMRI datasets involving alternating between rest and task and to simple synthetic data. Star…
In recent years, there has been strong interest in neuroscience studies to investigate brain organization through networks of brain regions that demonstrate strong functional connectivity (FC). These networks are extracted from observed fMRI using data-driven analytic methods such as independent component analysis (ICA). A notable limitation of these FC methods is that they do not provide any information on the underlying structural connectivity (SC), which is believed to serve as the basis for interregional interactions in brain activity. We propose a new statistical measure of the strength o…
Independent-Component-Based Encoding Models of Brain Activity During Story Comprehension
School of Electrical and Computer Engineering, Georgia Institute of Technology（佐治亚理工学院电子与计算机工程学院）；School of Psychological and Brain Sciences, Georgia Institute of Technology（佐治亚理工学院心理学与脑科学学院）；Department of Linguistics, Stanford University（斯坦福大学语言学系）
Studies of functional MRI data are increasingly concerned with the estimation of differences in spatio-temporal networks across groups of subjects or experimental conditions. Unsupervised clustering and independent component analysis (ICA) have been used to identify such spatio-temporal networks. While these approaches have been useful for estimating these networks at the subject-level, comparisons over groups or experimental conditions require further methodological development. In this paper, we tackle this problem by showing how self-organizing maps (SOMs) can be compared within a Frechean …
