14 research outputs found
Guided Graph Spectral Embedding: Application to the C. elegans Connectome
Graph spectral analysis can yield meaningful embeddings of graphs by
providing insight into distributed features not directly accessible in nodal
domain. Recent efforts in graph signal processing have proposed new
decompositions-e.g., based on wavelets and Slepians-that can be applied to
filter signals defined on the graph. In this work, we take inspiration from
these constructions to define a new guided spectral embedding that combines
maximizing energy concentration with minimizing modified embedded distance for
a given importance weighting of the nodes. We show these optimization goals are
intrinsically opposite, leading to a well-defined and stable spectral
decomposition. The importance weighting allows to put the focus on particular
nodes and tune the trade-off between global and local effects. Following the
derivation of our new optimization criterion and its linear approximation, we
exemplify the methodology on the C. elegans structural connectome. The results
of our analyses confirm known observations on the nematode's neural network in
terms of functionality and importance of cells. Compared to Laplacian
embedding, the guided approach, focused on a certain class of cells (sensory,
inter- and motoneurons), provides more biological insights, such as the
distinction between somatic positions of cells, and their involvement in low or
high order processing functions.Comment: 43 pages, 7 figures, submitted to Network Neuroscienc
Finding Structure with Randomness: Probabilistic Algorithms for Constructing Approximate Matrix Decompositions
Low-rank matrix approximations, such as the truncated singular value decomposition and the rank-revealing QR decomposition, play a central role in data analysis and scientific computing. This work surveys and extends recent research which demonstrates that randomization offers a powerful tool for performing low-rank matrix approximation. These techniques exploit modern computational architectures more fully than classical methods and open the possibility of dealing with truly massive data sets. This paper presents a modular framework for constructing randomized algorithms that compute partial matrix decompositions. These methods use random sampling to identify a subspace that captures most of the action of a matrix. The input matrix is then compressed—either explicitly or
implicitly—to this subspace, and the reduced matrix is manipulated deterministically to obtain the desired low-rank factorization. In many cases, this approach beats its classical competitors in terms of accuracy, robustness, and/or speed. These claims are supported by extensive numerical experiments and a detailed error analysis. The specific benefits of randomized techniques depend on the computational environment. Consider the model problem of finding the k dominant components of the singular value decomposition of an m × n matrix. (i) For a dense input matrix, randomized algorithms require O(mn log(k))
floating-point operations (flops) in contrast to O(mnk) for classical algorithms. (ii) For a sparse input matrix, the flop count matches classical Krylov subspace methods, but the randomized approach is more robust and can easily be reorganized to exploit multiprocessor architectures. (iii) For a matrix that is too large to fit in fast memory, the randomized techniques require only a constant number of passes over the data, as opposed to O(k) passes for classical algorithms. In fact, it is sometimes possible to perform matrix approximation with a single pass over the data
Finding structure with randomness: Probabilistic algorithms for constructing approximate matrix decompositions
Low-rank matrix approximations, such as the truncated singular value
decomposition and the rank-revealing QR decomposition, play a central role in
data analysis and scientific computing. This work surveys and extends recent
research which demonstrates that randomization offers a powerful tool for
performing low-rank matrix approximation. These techniques exploit modern
computational architectures more fully than classical methods and open the
possibility of dealing with truly massive data sets.
This paper presents a modular framework for constructing randomized
algorithms that compute partial matrix decompositions. These methods use random
sampling to identify a subspace that captures most of the action of a matrix.
The input matrix is then compressed---either explicitly or implicitly---to this
subspace, and the reduced matrix is manipulated deterministically to obtain the
desired low-rank factorization. In many cases, this approach beats its
classical competitors in terms of accuracy, speed, and robustness. These claims
are supported by extensive numerical experiments and a detailed error analysis
Identifying Brain Network Topology Changes in Task Processes and Psychiatric Disorders
Hervorming Sociale Regelgevin
Nonlinear Dimensionality Reduction Methods in Climate Data Analysis
Linear dimensionality reduction techniques, notably principal component
analysis, are widely used in climate data analysis as a means to aid in the
interpretation of datasets of high dimensionality. These linear methods may not
be appropriate for the analysis of data arising from nonlinear processes
occurring in the climate system. Numerous techniques for nonlinear
dimensionality reduction have been developed recently that may provide a
potentially useful tool for the identification of low-dimensional manifolds in
climate data sets arising from nonlinear dynamics. In this thesis I apply three
such techniques to the study of El Nino/Southern Oscillation variability in
tropical Pacific sea surface temperatures and thermocline depth, comparing
observational data with simulations from coupled atmosphere-ocean general
circulation models from the CMIP3 multi-model ensemble.
The three methods used here are a nonlinear principal component analysis
(NLPCA) approach based on neural networks, the Isomap isometric mapping
algorithm, and Hessian locally linear embedding. I use these three methods to
examine El Nino variability in the different data sets and assess the
suitability of these nonlinear dimensionality reduction approaches for climate
data analysis.
I conclude that although, for the application presented here, analysis using
NLPCA, Isomap and Hessian locally linear embedding does not provide additional
information beyond that already provided by principal component analysis, these
methods are effective tools for exploratory data analysis.Comment: 273 pages, 76 figures; University of Bristol Ph.D. thesis; version
with high-resolution figures available from
http://www.skybluetrades.net/thesis/ian-ross-thesis.pdf (52Mb download