557 research outputs found
Learning Discriminative Bayesian Networks from High-dimensional Continuous Neuroimaging Data
Due to its causal semantics, Bayesian networks (BN) have been widely employed
to discover the underlying data relationship in exploratory studies, such as
brain research. Despite its success in modeling the probability distribution of
variables, BN is naturally a generative model, which is not necessarily
discriminative. This may cause the ignorance of subtle but critical network
changes that are of investigation values across populations. In this paper, we
propose to improve the discriminative power of BN models for continuous
variables from two different perspectives. This brings two general
discriminative learning frameworks for Gaussian Bayesian networks (GBN). In the
first framework, we employ Fisher kernel to bridge the generative models of GBN
and the discriminative classifiers of SVMs, and convert the GBN parameter
learning to Fisher kernel learning via minimizing a generalization error bound
of SVMs. In the second framework, we employ the max-margin criterion and build
it directly upon GBN models to explicitly optimize the classification
performance of the GBNs. The advantages and disadvantages of the two frameworks
are discussed and experimentally compared. Both of them demonstrate strong
power in learning discriminative parameters of GBNs for neuroimaging based
brain network analysis, as well as maintaining reasonable representation
capacity. The contributions of this paper also include a new Directed Acyclic
Graph (DAG) constraint with theoretical guarantee to ensure the graph validity
of GBN.Comment: 16 pages and 5 figures for the article (excluding appendix
Visual and Contextual Modeling for the Detection of Repeated Mild Traumatic Brain Injury.
Currently, there is a lack of computational methods for the evaluation of mild traumatic brain injury (mTBI) from magnetic resonance imaging (MRI). Further, the development of automated analyses has been hindered by the subtle nature of mTBI abnormalities, which appear as low contrast MR regions. This paper proposes an approach that is able to detect mTBI lesions by combining both the high-level context and low-level visual information. The contextual model estimates the progression of the disease using subject information, such as the time since injury and the knowledge about the location of mTBI. The visual model utilizes texture features in MRI along with a probabilistic support vector machine to maximize the discrimination in unimodal MR images. These two models are fused to obtain a final estimate of the locations of the mTBI lesion. The models are tested using a novel rodent model of repeated mTBI dataset. The experimental results demonstrate that the fusion of both contextual and visual textural features outperforms other state-of-the-art approaches. Clinically, our approach has the potential to benefit both clinicians by speeding diagnosis and patients by improving clinical care
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
Pattern recognition and machine learning for magnetic resonance images with kernel methods
The aim of this thesis is to apply a particular category of machine learning and
pattern recognition algorithms, namely the kernel methods, to both functional and
anatomical magnetic resonance images (MRI). This work specifically focused on
supervised learning methods. Both methodological and practical aspects are described
in this thesis.
Kernel methods have the computational advantage for high dimensional data,
therefore they are idea for imaging data. The procedures can be broadly divided into
two components: the construction of the kernels and the actual kernel algorithms
themselves. Pre-processed functional or anatomical images can be computed into a
linear kernel or a non-linear kernel. We introduce both kernel regression and kernel
classification algorithms in two main categories: probabilistic methods and
non-probabilistic methods. For practical applications, kernel classification methods
were applied to decode the cognitive or sensory states of the subject from the fMRI
signal and were also applied to discriminate patients with neurological diseases from
normal people using anatomical MRI. Kernel regression methods were used to predict
the regressors in the design of fMRI experiments, and clinical ratings from the
anatomical scans
Dimensional Neuroimaging Endophenotypes: Neurobiological Representations of Disease Heterogeneity Through Machine Learning
Machine learning has been increasingly used to obtain individualized
neuroimaging signatures for disease diagnosis, prognosis, and response to
treatment in neuropsychiatric and neurodegenerative disorders. Therefore, it
has contributed to a better understanding of disease heterogeneity by
identifying disease subtypes that present significant differences in various
brain phenotypic measures. In this review, we first present a systematic
literature overview of studies using machine learning and multimodal MRI to
unravel disease heterogeneity in various neuropsychiatric and neurodegenerative
disorders, including Alzheimer disease, schizophrenia, major depressive
disorder, autism spectrum disorder, multiple sclerosis, as well as their
potential in transdiagnostic settings. Subsequently, we summarize relevant
machine learning methodologies and discuss an emerging paradigm which we call
dimensional neuroimaging endophenotype (DNE). DNE dissects the neurobiological
heterogeneity of neuropsychiatric and neurodegenerative disorders into a low
dimensional yet informative, quantitative brain phenotypic representation,
serving as a robust intermediate phenotype (i.e., endophenotype) largely
reflecting underlying genetics and etiology. Finally, we discuss the potential
clinical implications of the current findings and envision future research
avenues
Scalable Machine Learning Methods for Massive Biomedical Data Analysis.
Modern data acquisition techniques have enabled biomedical researchers to collect and analyze datasets of substantial size and complexity. The massive size of these datasets allows us to comprehensively study the biological system of interest at an unprecedented level of detail, which may lead to the discovery of clinically relevant biomarkers. Nonetheless, the dimensionality of these datasets presents critical computational and statistical challenges, as traditional statistical methods break down when the number of predictors dominates the number of observations, a setting frequently encountered in biomedical data analysis. This difficulty is compounded by the fact that biological data tend to be noisy and often possess complex correlation patterns among the predictors. The central goal of this dissertation is to develop a computationally tractable machine learning framework that allows us to extract scientifically meaningful information from these massive and highly complex biomedical datasets. We motivate the scope of our study by considering two important problems with clinical relevance: (1) uncertainty analysis for biomedical image registration, and (2) psychiatric disease prediction based on functional connectomes, which are high dimensional correlation maps generated from resting state functional MRI.PhDElectrical Engineering: SystemsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/111354/1/takanori_1.pd
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