13,377 research outputs found
Local ciliate communities associated with aquatic macrophytes
This study, based within the catchment area of the River Frome, an important chalk stream in the south of England, compared ciliated protozoan communities associated with three species of aquatic macrophyte common to lotic habitats: Ranunculus penicillatus subsp. pseudofluitans, Nasturtium officinale and Sparganium emersum. A total of 77 ciliate species were counted. No species-specific ciliate assemblage was found to be typical of any one plant species. Ciliate abundance between plant species was determined to be significantly different. The ciliate communities from each plant species were unique in that the number of species increased with ciliate abundance. The community associated with R. penicillatus subsp. pseudofluitans showed the highest consistency and species richness whereas S. emersum ciliate communities were unstable. Most notably, N. officinale was associated with low ciliate abundances and an apparent reduction in biofilm formation, discussed herein in relation to the plantās production of the microbial toxin phenethyl isothiocyanate. We propose that the results reflect differences in the quantity and quality of biofilm present on the plants, which could be determined by the different plant morphologies, patterns of plant decay and herbivore defense systems, all of which suppress or promote the various conditions for biofilm growth
Next Generation Cluster Editing
This work aims at improving the quality of structural variant prediction from
the mapped reads of a sequenced genome. We suggest a new model based on cluster
editing in weighted graphs and introduce a new heuristic algorithm that allows
to solve this problem quickly and with a good approximation on the huge graphs
that arise from biological datasets
Laplacian Mixture Modeling for Network Analysis and Unsupervised Learning on Graphs
Laplacian mixture models identify overlapping regions of influence in
unlabeled graph and network data in a scalable and computationally efficient
way, yielding useful low-dimensional representations. By combining Laplacian
eigenspace and finite mixture modeling methods, they provide probabilistic or
fuzzy dimensionality reductions or domain decompositions for a variety of input
data types, including mixture distributions, feature vectors, and graphs or
networks. Provable optimal recovery using the algorithm is analytically shown
for a nontrivial class of cluster graphs. Heuristic approximations for scalable
high-performance implementations are described and empirically tested.
Connections to PageRank and community detection in network analysis demonstrate
the wide applicability of this approach. The origins of fuzzy spectral methods,
beginning with generalized heat or diffusion equations in physics, are reviewed
and summarized. Comparisons to other dimensionality reduction and clustering
methods for challenging unsupervised machine learning problems are also
discussed.Comment: 13 figures, 35 reference
Detection and localization of change points in temporal networks with the aid of stochastic block models
A framework based on generalized hierarchical random graphs (GHRGs) for the
detection of change points in the structure of temporal networks has recently
been developed by Peel and Clauset [1]. We build on this methodology and extend
it to also include the versatile stochastic block models (SBMs) as a parametric
family for reconstructing the empirical networks. We use five different
techniques for change point detection on prototypical temporal networks,
including empirical and synthetic ones. We find that none of the considered
methods can consistently outperform the others when it comes to detecting and
locating the expected change points in empirical temporal networks. With
respect to the precision and the recall of the results of the change points, we
find that the method based on a degree-corrected SBM has better recall
properties than other dedicated methods, especially for sparse networks and
smaller sliding time window widths.Comment: This is an author-created, un-copyedited version of an article
accepted for publication/published in Journal of Statistical Mechanics:
Theory and Experiment. IOP Publishing Ltd is not responsible for any errors
or omissions in this version of the manuscript or any version derived from
it. The Version of Record is available online at
http://dx.doi.org/10.1088/1742-5468/2016/11/11330
A survey of statistical network models
Networks are ubiquitous in science and have become a focal point for
discussion in everyday life. Formal statistical models for the analysis of
network data have emerged as a major topic of interest in diverse areas of
study, and most of these involve a form of graphical representation.
Probability models on graphs date back to 1959. Along with empirical studies in
social psychology and sociology from the 1960s, these early works generated an
active network community and a substantial literature in the 1970s. This effort
moved into the statistical literature in the late 1970s and 1980s, and the past
decade has seen a burgeoning network literature in statistical physics and
computer science. The growth of the World Wide Web and the emergence of online
networking communities such as Facebook, MySpace, and LinkedIn, and a host of
more specialized professional network communities has intensified interest in
the study of networks and network data. Our goal in this review is to provide
the reader with an entry point to this burgeoning literature. We begin with an
overview of the historical development of statistical network modeling and then
we introduce a number of examples that have been studied in the network
literature. Our subsequent discussion focuses on a number of prominent static
and dynamic network models and their interconnections. We emphasize formal
model descriptions, and pay special attention to the interpretation of
parameters and their estimation. We end with a description of some open
problems and challenges for machine learning and statistics.Comment: 96 pages, 14 figures, 333 reference
A Replica Inference Approach to Unsupervised Multi-Scale Image Segmentation
We apply a replica inference based Potts model method to unsupervised image
segmentation on multiple scales. This approach was inspired by the statistical
mechanics problem of "community detection" and its phase diagram. Specifically,
the problem is cast as identifying tightly bound clusters ("communities" or
"solutes") against a background or "solvent". Within our multiresolution
approach, we compute information theory based correlations among multiple
solutions ("replicas") of the same graph over a range of resolutions.
Significant multiresolution structures are identified by replica correlations
as manifest in information theory overlaps. With the aid of these correlations
as well as thermodynamic measures, the phase diagram of the corresponding Potts
model is analyzed both at zero and finite temperatures. Optimal parameters
corresponding to a sensible unsupervised segmentation correspond to the "easy
phase" of the Potts model. Our algorithm is fast and shown to be at least as
accurate as the best algorithms to date and to be especially suited to the
detection of camouflaged images.Comment: 26 pages, 22 figure
Properties of Healthcare Teaming Networks as a Function of Network Construction Algorithms
Network models of healthcare systems can be used to examine how providers
collaborate, communicate, refer patients to each other. Most healthcare service
network models have been constructed from patient claims data, using billing
claims to link patients with providers. The data sets can be quite large,
making standard methods for network construction computationally challenging
and thus requiring the use of alternate construction algorithms. While these
alternate methods have seen increasing use in generating healthcare networks,
there is little to no literature comparing the differences in the structural
properties of the generated networks. To address this issue, we compared the
properties of healthcare networks constructed using different algorithms and
the 2013 Medicare Part B outpatient claims data. Three different algorithms
were compared: binning, sliding frame, and trace-route. Unipartite networks
linking either providers or healthcare organizations by shared patients were
built using each method. We found that each algorithm produced networks with
substantially different topological properties. Provider networks adhered to a
power law, and organization networks to a power law with exponential cutoff.
Censoring networks to exclude edges with less than 11 shared patients, a common
de-identification practice for healthcare network data, markedly reduced edge
numbers and greatly altered measures of vertex prominence such as the
betweenness centrality. We identified patterns in the distance patients travel
between network providers, and most strikingly between providers in the
Northeast United States and Florida. We conclude that the choice of network
construction algorithm is critical for healthcare network analysis, and discuss
the implications for selecting the algorithm best suited to the type of
analysis to be performed.Comment: With links to comprehensive, high resolution figures and networks via
figshare.co
Local pre-processing for node classification in networks : application in protein-protein interaction
Network modelling provides an increasingly popular conceptualisation in a wide range of domains, including the analysis of protein structure. Typical approaches to analysis model parameter values at nodes within the network. The spherical locality around a node provides a microenvironment that can be used to characterise an area of a network rather than a particular point within it. Microenvironments that centre on the nodes in a protein chain can be used to quantify parameters that are related to protein functionality. They also permit particular patterns of such parameters in node-centred microenvironments to be used to locate sites of particular interest. This paper evaluates an approach to index generation that seeks to rapidly construct microenvironment data. The results show that index generation performs best when the radius of microenvironments matches the granularity of the index. Results are presented to show that such microenvironments improve the utility of protein chain parameters in classifying the structural characteristics of nodes using both support vector machines and neural networks
Overlapping modularity at the critical point of k-clique percolation
One of the most remarkable social phenomena is the formation of communities
in social networks corresponding to families, friendship circles, work teams,
etc. Since people usually belong to several different communities at the same
time, the induced overlaps result in an extremely complicated web of the
communities themselves. Thus, uncovering the intricate community structure of
social networks is a non-trivial task with great potential for practical
applications, gaining a notable interest in the recent years. The Clique
Percolation Method (CPM) is one of the earliest overlapping community finding
methods, which was already used in the analysis of several different social
networks. In this approach the communities correspond to k-clique percolation
clusters, and the general heuristic for setting the parameters of the method is
to tune the system just below the critical point of k-clique percolation.
However, this rule is based on simple physical principles and its validity was
never subject to quantitative analysis. Here we examine the quality of the
partitioning in the vicinity of the critical point using recently introduced
overlapping modularity measures. According to our results on real social- and
other networks, the overlapping modularities show a maximum close to the
critical point, justifying the original criteria for the optimal parameter
settings.Comment: 20 pages, 6 figure
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