653 research outputs found
Local-Aggregate Modeling for Big-Data via Distributed Optimization: Applications to Neuroimaging
Technological advances have led to a proliferation of structured big data
that have matrix-valued covariates. We are specifically motivated to build
predictive models for multi-subject neuroimaging data based on each subject's
brain imaging scans. This is an ultra-high-dimensional problem that consists of
a matrix of covariates (brain locations by time points) for each subject; few
methods currently exist to fit supervised models directly to this tensor data.
We propose a novel modeling and algorithmic strategy to apply generalized
linear models (GLMs) to this massive tensor data in which one set of variables
is associated with locations. Our method begins by fitting GLMs to each
location separately, and then builds an ensemble by blending information across
locations through regularization with what we term an aggregating penalty. Our
so called, Local-Aggregate Model, can be fit in a completely distributed manner
over the locations using an Alternating Direction Method of Multipliers (ADMM)
strategy, and thus greatly reduces the computational burden. Furthermore, we
propose to select the appropriate model through a novel sequence of faster
algorithmic solutions that is similar to regularization paths. We will
demonstrate both the computational and predictive modeling advantages of our
methods via simulations and an EEG classification problem.Comment: 41 pages, 5 figures and 3 table
Calibrated Multivariate Regression with Application to Neural Semantic Basis Discovery
We propose a calibrated multivariate regression method named CMR for fitting
high dimensional multivariate regression models. Compared with existing
methods, CMR calibrates regularization for each regression task with respect to
its noise level so that it simultaneously attains improved finite-sample
performance and tuning insensitiveness. Theoretically, we provide sufficient
conditions under which CMR achieves the optimal rate of convergence in
parameter estimation. Computationally, we propose an efficient smoothed
proximal gradient algorithm with a worst-case numerical rate of convergence
\cO(1/\epsilon), where is a pre-specified accuracy of the
objective function value. We conduct thorough numerical simulations to
illustrate that CMR consistently outperforms other high dimensional
multivariate regression methods. We also apply CMR to solve a brain activity
prediction problem and find that it is as competitive as a handcrafted model
created by human experts. The R package \texttt{camel} implementing the
proposed method is available on the Comprehensive R Archive Network
\url{http://cran.r-project.org/web/packages/camel/}.Comment: Journal of Machine Learning Research, 201
Multi-scale Mining of fMRI data with Hierarchical Structured Sparsity
International audienceInverse inference, or "brain reading", is a recent paradigm for analyzing functional magnetic resonance imaging (fMRI) data, based on pattern recognition and statistical learning. By predicting some cognitive variables related to brain activation maps, this approach aims at decoding brain activity. Inverse inference takes into account the multivariate information between voxels and is currently the only way to assess how precisely some cognitive information is encoded by the activity of neural populations within the whole brain. However, it relies on a prediction function that is plagued by the curse of dimensionality, since there are far more features than samples, i.e., more voxels than fMRI volumes. To address this problem, different methods have been proposed, such as, among others, univariate feature selection, feature agglomeration and regularization techniques. In this paper, we consider a sparse hierarchical structured regularization. Specifically, the penalization we use is constructed from a tree that is obtained by spatially-constrained agglomerative clustering. This approach encodes the spatial structure of the data at different scales into the regularization, which makes the overall prediction procedure more robust to inter-subject variability. The regularization used induces the selection of spatially coherent predictive brain regions simultaneously at different scales. We test our algorithm on real data acquired to study the mental representation of objects, and we show that the proposed algorithm not only delineates meaningful brain regions but yields as well better prediction accuracy than reference methods
LOCUS: A Novel Decomposition Method for Brain Network Connectivity Matrices using Low-rank Structure with Uniform Sparsity
Network-oriented research has been increasingly popular in many scientific
areas. In neuroscience research, imaging-based network connectivity measures
have become the key for understanding brain organizations, potentially serving
as individual neural fingerprints. There are major challenges in analyzing
connectivity matrices including the high dimensionality of brain networks,
unknown latent sources underlying the observed connectivity, and the large
number of brain connections leading to spurious findings. In this paper, we
propose a novel blind source separation method with low-rank structure and
uniform sparsity (LOCUS) as a fully data-driven decomposition method for
network measures. Compared with the existing method that vectorizes
connectivity matrices ignoring brain network topology, LOCUS achieves more
efficient and accurate source separation for connectivity matrices using
low-rank structure. We propose a novel angle-based uniform sparsity
regularization that demonstrates better performance than the existing sparsity
controls for low-rank tensor methods. We propose a highly efficient iterative
Node-Rotation algorithm that exploits the block multi-convexity of the
objective function to solve the non-convex optimization problem for learning
LOCUS. We illustrate the advantage of LOCUS through extensive simulation
studies. Application of LOCUS to Philadelphia Neurodevelopmental Cohort
neuroimaging study reveals biologically insightful connectivity traits which
are not found using the existing method
Tensor Analysis and Fusion of Multimodal Brain Images
Current high-throughput data acquisition technologies probe dynamical systems
with different imaging modalities, generating massive data sets at different
spatial and temporal resolutions posing challenging problems in multimodal data
fusion. A case in point is the attempt to parse out the brain structures and
networks that underpin human cognitive processes by analysis of different
neuroimaging modalities (functional MRI, EEG, NIRS etc.). We emphasize that the
multimodal, multi-scale nature of neuroimaging data is well reflected by a
multi-way (tensor) structure where the underlying processes can be summarized
by a relatively small number of components or "atoms". We introduce
Markov-Penrose diagrams - an integration of Bayesian DAG and tensor network
notation in order to analyze these models. These diagrams not only clarify
matrix and tensor EEG and fMRI time/frequency analysis and inverse problems,
but also help understand multimodal fusion via Multiway Partial Least Squares
and Coupled Matrix-Tensor Factorization. We show here, for the first time, that
Granger causal analysis of brain networks is a tensor regression problem, thus
allowing the atomic decomposition of brain networks. Analysis of EEG and fMRI
recordings shows the potential of the methods and suggests their use in other
scientific domains.Comment: 23 pages, 15 figures, submitted to Proceedings of the IEE
Generative-Discriminative Low Rank Decomposition for Medical Imaging Applications
In this thesis, we propose a method that can be used to extract biomarkers from medical images toward early diagnosis of abnormalities. Surge of demand for biomarkers and availability of medical images in the recent years call for accurate, repeatable, and interpretable approaches for extracting meaningful imaging features. However, extracting such information from medical images is a challenging task because the number of pixels (voxels) in a typical image is in order of millions while even a large sample-size in medical image dataset does not usually exceed a few hundred. Nevertheless, depending on the nature of an abnormality, only a parsimonious subset of voxels is typically relevant to the disease; therefore various notions of sparsity are exploited in this thesis to improve the generalization performance of the prediction task.
We propose a novel discriminative dimensionality reduction method that yields good classification performance on various datasets without compromising the clinical interpretability of the results. This is achieved by combining the modelling strength of generative learning framework and the classification performance of discriminative learning paradigm. Clinical interpretability can be viewed as an additional measure of evaluation and is also helpful in designing methods that account for the clinical prior such as association of certain areas in a brain to a particular cognitive task or connectivity of some brain regions via neural fibres.
We formulate our method as a large-scale optimization problem to solve a constrained matrix factorization. Finding an optimal solution of the large-scale matrix factorization renders off-the-shelf solver computationally prohibitive; therefore, we designed an efficient algorithm based on the proximal method to address the computational bottle-neck of the optimization problem. Our formulation is readily extended for different scenarios such as cases where a large cohort of subjects has uncertain or no class labels (semi-supervised learning) or a case where each subject has a battery of imaging channels (multi-channel), \etc. We show that by using various notions of sparsity as feasible sets of the optimization problem, we can encode different forms of prior knowledge ranging from brain parcellation to brain connectivity
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