28,185 research outputs found
Evaluating Graph Signal Processing for Neuroimaging Through Classification and Dimensionality Reduction
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
using both a) and b) offer the best performance. We also show that graph
sampling methods perform better than classical dimension reduction including
Principal Component Analysis (PCA) and Independent Component Analysis (ICA).Comment: 5 pages, GlobalSIP 201
Sampling and Reconstruction of Sparse Signals on Circulant Graphs - An Introduction to Graph-FRI
With the objective of employing graphs toward a more generalized theory of
signal processing, we present a novel sampling framework for (wavelet-)sparse
signals defined on circulant graphs which extends basic properties of Finite
Rate of Innovation (FRI) theory to the graph domain, and can be applied to
arbitrary graphs via suitable approximation schemes. At its core, the
introduced Graph-FRI-framework states that any K-sparse signal on the vertices
of a circulant graph can be perfectly reconstructed from its
dimensionality-reduced representation in the graph spectral domain, the Graph
Fourier Transform (GFT), of minimum size 2K. By leveraging the recently
developed theory of e-splines and e-spline wavelets on graphs, one can
decompose this graph spectral transformation into the multiresolution low-pass
filtering operation with a graph e-spline filter, and subsequent transformation
to the spectral graph domain; this allows to infer a distinct sampling pattern,
and, ultimately, the structure of an associated coarsened graph, which
preserves essential properties of the original, including circularity and,
where applicable, the graph generating set.Comment: To appear in Appl. Comput. Harmon. Anal. (2017
Out-of-sample generalizations for supervised manifold learning for classification
Supervised manifold learning methods for data classification map data samples
residing in a high-dimensional ambient space to a lower-dimensional domain in a
structure-preserving way, while enhancing the separation between different
classes in the learned embedding. Most nonlinear supervised manifold learning
methods compute the embedding of the manifolds only at the initially available
training points, while the generalization of the embedding to novel points,
known as the out-of-sample extension problem in manifold learning, becomes
especially important in classification applications. In this work, we propose a
semi-supervised method for building an interpolation function that provides an
out-of-sample extension for general supervised manifold learning algorithms
studied in the context of classification. The proposed algorithm computes a
radial basis function (RBF) interpolator that minimizes an objective function
consisting of the total embedding error of unlabeled test samples, defined as
their distance to the embeddings of the manifolds of their own class, as well
as a regularization term that controls the smoothness of the interpolation
function in a direction-dependent way. The class labels of test data and the
interpolation function parameters are estimated jointly with a progressive
procedure. Experimental results on face and object images demonstrate the
potential of the proposed out-of-sample extension algorithm for the
classification of manifold-modeled data sets
Visualizing dimensionality reduction of systems biology data
One of the challenges in analyzing high-dimensional expression data is the
detection of important biological signals. A common approach is to apply a
dimension reduction method, such as principal component analysis. Typically,
after application of such a method the data is projected and visualized in the
new coordinate system, using scatter plots or profile plots. These methods
provide good results if the data have certain properties which become visible
in the new coordinate system and which were hard to detect in the original
coordinate system. Often however, the application of only one method does not
suffice to capture all important signals. Therefore several methods addressing
different aspects of the data need to be applied. We have developed a framework
for linear and non-linear dimension reduction methods within our visual
analytics pipeline SpRay. This includes measures that assist the interpretation
of the factorization result. Different visualizations of these measures can be
combined with functional annotations that support the interpretation of the
results. We show an application to high-resolution time series microarray data
in the antibiotic-producing organism Streptomyces coelicolor as well as to
microarray data measuring expression of cells with normal karyotype and cells
with trisomies of human chromosomes 13 and 21
Nonlinear Supervised Dimensionality Reduction via Smooth Regular Embeddings
The recovery of the intrinsic geometric structures of data collections is an
important problem in data analysis. Supervised extensions of several manifold
learning approaches have been proposed in the recent years. Meanwhile, existing
methods primarily focus on the embedding of the training data, and the
generalization of the embedding to initially unseen test data is rather
ignored. In this work, we build on recent theoretical results on the
generalization performance of supervised manifold learning algorithms.
Motivated by these performance bounds, we propose a supervised manifold
learning method that computes a nonlinear embedding while constructing a smooth
and regular interpolation function that extends the embedding to the whole data
space in order to achieve satisfactory generalization. The embedding and the
interpolator are jointly learnt such that the Lipschitz regularity of the
interpolator is imposed while ensuring the separation between different
classes. Experimental results on several image data sets show that the proposed
method outperforms traditional classifiers and the supervised dimensionality
reduction algorithms in comparison in terms of classification accuracy in most
settings
A cDNA Microarray Gene Expression Data Classifier for Clinical Diagnostics Based on Graph Theory
Despite great advances in discovering cancer molecular profiles, the proper application of microarray technology to routine clinical diagnostics is still a challenge. Current practices in the classification of microarrays' data show two main limitations: the reliability of the training data sets used to build the classifiers, and the classifiers' performances, especially when the sample to be classified does not belong to any of the available classes. In this case, state-of-the-art algorithms usually produce a high rate of false positives that, in real diagnostic applications, are unacceptable. To address this problem, this paper presents a new cDNA microarray data classification algorithm based on graph theory and is able to overcome most of the limitations of known classification methodologies. The classifier works by analyzing gene expression data organized in an innovative data structure based on graphs, where vertices correspond to genes and edges to gene expression relationships. To demonstrate the novelty of the proposed approach, the authors present an experimental performance comparison between the proposed classifier and several state-of-the-art classification algorithm
- …