67,454 research outputs found
Direct estimation of kinetic parametric images for dynamic PET.
Dynamic positron emission tomography (PET) can monitor spatiotemporal distribution of radiotracer in vivo. The spatiotemporal information can be used to estimate parametric images of radiotracer kinetics that are of physiological and biochemical interests. Direct estimation of parametric images from raw projection data allows accurate noise modeling and has been shown to offer better image quality than conventional indirect methods, which reconstruct a sequence of PET images first and then perform tracer kinetic modeling pixel-by-pixel. Direct reconstruction of parametric images has gained increasing interests with the advances in computing hardware. Many direct reconstruction algorithms have been developed for different kinetic models. In this paper we review the recent progress in the development of direct reconstruction algorithms for parametric image estimation. Algorithms for linear and nonlinear kinetic models are described and their properties are discussed
Robust and parallel scalable iterative solutions for large-scale finite cell analyses
The finite cell method is a highly flexible discretization technique for
numerical analysis on domains with complex geometries. By using a non-boundary
conforming computational domain that can be easily meshed, automatized
computations on a wide range of geometrical models can be performed.
Application of the finite cell method, and other immersed methods, to large
real-life and industrial problems is often limited due to the conditioning
problems associated with these methods. These conditioning problems have caused
researchers to resort to direct solution methods, which signifi- cantly limit
the maximum size of solvable systems. Iterative solvers are better suited for
large-scale computations than their direct counterparts due to their lower
memory requirements and suitability for parallel computing. These benefits can,
however, only be exploited when systems are properly conditioned. In this
contribution we present an Additive-Schwarz type preconditioner that enables
efficient and parallel scalable iterative solutions of large-scale multi-level
hp-refined finite cell analyses.Comment: 32 pages, 17 figure
Netter: re-ranking gene network inference predictions using structural network properties
Background: Many algorithms have been developed to infer the topology of gene regulatory networks from gene expression data. These methods typically produce a ranking of links between genes with associated confidence scores, after which a certain threshold is chosen to produce the inferred topology. However, the structural properties of the predicted network do not resemble those typical for a gene regulatory network, as most algorithms only take into account connections found in the data and do not include known graph properties in their inference process. This lowers the prediction accuracy of these methods, limiting their usability in practice.
Results: We propose a post-processing algorithm which is applicable to any confidence ranking of regulatory interactions obtained from a network inference method which can use, inter alia, graphlets and several graph-invariant properties to re-rank the links into a more accurate prediction. To demonstrate the potential of our approach, we re-rank predictions of six different state-of-the-art algorithms using three simple network properties as optimization criteria and show that Netter can improve the predictions made on both artificially generated data as well as the DREAM4 and DREAM5 benchmarks. Additionally, the DREAM5 E. coli. community prediction inferred from real expression data is further improved. Furthermore, Netter compares favorably to other post-processing algorithms and is not restricted to correlation-like predictions. Lastly, we demonstrate that the performance increase is robust for a wide range of parameter settings. Netter is available at http://bioinformatics. intec. ugent. be.
Conclusions: Network inference from high-throughput data is a long-standing challenge. In this work, we present Netter, which can further refine network predictions based on a set of user-defined graph properties. Netter is a flexible system which can be applied in unison with any method producing a ranking from omics data. It can be tailored to specific prior knowledge by expert users but can also be applied in general uses cases. Concluding, we believe that Netter is an interesting second step in the network inference process to further increase the quality of prediction
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
A two-way regularization method for MEG source reconstruction
The MEG inverse problem refers to the reconstruction of the neural activity
of the brain from magnetoencephalography (MEG) measurements. We propose a
two-way regularization (TWR) method to solve the MEG inverse problem under the
assumptions that only a small number of locations in space are responsible for
the measured signals (focality), and each source time course is smooth in time
(smoothness). The focality and smoothness of the reconstructed signals are
ensured respectively by imposing a sparsity-inducing penalty and a roughness
penalty in the data fitting criterion. A two-stage algorithm is developed for
fast computation, where a raw estimate of the source time course is obtained in
the first stage and then refined in the second stage by the two-way
regularization. The proposed method is shown to be effective on both synthetic
and real-world examples.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS531 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Outlier Detection Using Nonconvex Penalized Regression
This paper studies the outlier detection problem from the point of view of
penalized regressions. Our regression model adds one mean shift parameter for
each of the data points. We then apply a regularization favoring a sparse
vector of mean shift parameters. The usual penalty yields a convex
criterion, but we find that it fails to deliver a robust estimator. The
penalty corresponds to soft thresholding. We introduce a thresholding (denoted
by ) based iterative procedure for outlier detection (-IPOD). A
version based on hard thresholding correctly identifies outliers on some hard
test problems. We find that -IPOD is much faster than iteratively
reweighted least squares for large data because each iteration costs at most
(and sometimes much less) avoiding an least squares estimate.
We describe the connection between -IPOD and -estimators. Our
proposed method has one tuning parameter with which to both identify outliers
and estimate regression coefficients. A data-dependent choice can be made based
on BIC. The tuned -IPOD shows outstanding performance in identifying
outliers in various situations in comparison to other existing approaches. This
methodology extends to high-dimensional modeling with , if both the
coefficient vector and the outlier pattern are sparse
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