25,786 research outputs found
Automatic Segmentation of Fluorescence Lifetime Microscopy Images of Cells Using Multi-Resolution Community Detection
We have developed an automatic method for segmenting fluorescence lifetime
(FLT) imaging microscopy (FLIM) images of cells inspired by a multi-resolution
community detection (MCD) based network segmentation method. The image
processing problem is framed as identifying segments with respective average
FLTs against a background in FLIM images. The proposed method segments a FLIM
image for a given resolution of the network composed using image pixels as the
nodes and similarity between the pixels as the edges. In the resulting
segmentation, low network resolution leads to larger segments and high network
resolution leads to smaller segments. Further, the mean-square error (MSE) in
estimating the FLT segments in a FLIM image using the proposed method was found
to be consistently decreasing with increasing resolution of the corresponding
network. The proposed MCD method outperformed a popular spectral clustering
based method in performing FLIM image segmentation. The spectral segmentation
method introduced noisy segments in its output at high resolution. It was
unable to offer a consistent decrease in MSE with increasing resolution.Comment: 21 pages, 6 figure
One-class classifiers based on entropic spanning graphs
One-class classifiers offer valuable tools to assess the presence of outliers
in data. In this paper, we propose a design methodology for one-class
classifiers based on entropic spanning graphs. Our approach takes into account
the possibility to process also non-numeric data by means of an embedding
procedure. The spanning graph is learned on the embedded input data and the
outcoming partition of vertices defines the classifier. The final partition is
derived by exploiting a criterion based on mutual information minimization.
Here, we compute the mutual information by using a convenient formulation
provided in terms of the -Jensen difference. Once training is
completed, in order to associate a confidence level with the classifier
decision, a graph-based fuzzy model is constructed. The fuzzification process
is based only on topological information of the vertices of the entropic
spanning graph. As such, the proposed one-class classifier is suitable also for
data characterized by complex geometric structures. We provide experiments on
well-known benchmarks containing both feature vectors and labeled graphs. In
addition, we apply the method to the protein solubility recognition problem by
considering several representations for the input samples. Experimental results
demonstrate the effectiveness and versatility of the proposed method with
respect to other state-of-the-art approaches.Comment: Extended and revised version of the paper "One-Class Classification
Through Mutual Information Minimization" presented at the 2016 IEEE IJCNN,
Vancouver, Canad
Emergence of social networks via direct and indirect reciprocity
Many models of social network formation implicitly assume that network properties are static in steady-state. In contrast, actual social networks are highly dynamic: allegiances and collaborations expire and may or may not be renewed at a later date. Moreover, empirical studies show that human social networks are dynamic at the individual level but static at the global level: individuals' degree rankings change considerably over time, whereas network-level metrics such as network diameter and clustering coefficient are relatively stable. There have been some attempts to explain these properties of empirical social networks using agent-based models in which agents play social dilemma games with their immediate neighbours, but can also manipulate their network connections to
strategic advantage. However, such models cannot straightforwardly account for reciprocal behaviour based on reputation scores ("indirect reciprocity"), which is known to play an important role in many economic interactions. In
order to account for indirect reciprocity, we model the network in a bottom-up fashion: the network emerges from the low-level interactions between agents. By so doing we are able to simultaneously account for the effect of both direct reciprocity (e.g. "tit-for-tat") as well as indirect
reciprocity (helping strangers in order to increase one's reputation). This leads to a strategic equilibrium in the frequencies with which strategies are adopted in the population as a whole, but intermittent cycling over different strategies at the level of individual agents, which in turn gives rise to social networks which
are dynamic at the individual level but stable at the network level
Deep unsupervised clustering with Gaussian mixture variational autoencoders
We study a variant of the variational autoencoder model with a Gaussian mixture as a prior distribution, with the goal of performing unsupervised clustering through deep generative models. We observe that the standard variational approach in these models is unsuited for unsupervised clustering, and mitigate this problem by leveraging a principled information-theoretic regularisation term known as consistency violation. Adding this term to the standard variational optimisation objective yields networks with both meaningful internal representations and well-defined clusters. We demonstrate the performance of this scheme on synthetic data, MNIST and SVHN, showing that the obtained clusters are distinct, interpretable and result in achieving higher performance on unsupervised clustering classification than previous approaches
Entropy-scaling search of massive biological data
Many datasets exhibit a well-defined structure that can be exploited to
design faster search tools, but it is not always clear when such acceleration
is possible. Here, we introduce a framework for similarity search based on
characterizing a dataset's entropy and fractal dimension. We prove that
searching scales in time with metric entropy (number of covering hyperspheres),
if the fractal dimension of the dataset is low, and scales in space with the
sum of metric entropy and information-theoretic entropy (randomness of the
data). Using these ideas, we present accelerated versions of standard tools,
with no loss in specificity and little loss in sensitivity, for use in three
domains---high-throughput drug screening (Ammolite, 150x speedup), metagenomics
(MICA, 3.5x speedup of DIAMOND [3,700x BLASTX]), and protein structure search
(esFragBag, 10x speedup of FragBag). Our framework can be used to achieve
"compressive omics," and the general theory can be readily applied to data
science problems outside of biology.Comment: Including supplement: 41 pages, 6 figures, 4 tables, 1 bo
Graph theoretic analysis of protein interaction networks of eukaryotes
Thanks to recent progress in high-throughput experimental techniques, the
datasets of large-scale protein interactions of prototypical multicellular
species, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila
melanogaster, have been assayed. The datasets are obtained mainly by using the
yeast hybrid method, which contains false-positive and false-negative
simultaneously. Accordingly, while it is desirable to test such datasets
through further wet experiments, here we invoke recent developed network theory
to test such high throughput datasets in a simple way. Based on the fact that
the key biological processes indispensable to maintaining life are universal
across eukaryotic species, and the comparison of structural properties of the
protein interaction networks (PINs) of the two species with those of the yeast
PIN, we find that while the worm and the yeast PIN datasets exhibit similar
structural properties, the current fly dataset, though most comprehensively
screened ever, does not reflect generic structural properties correctly as it
is. The modularity is suppressed and the connectivity correlation is lacking.
Addition of interlogs to the current fly dataset increases the modularity and
enhances the occurrence of triangular motifs as well. The connectivity
correlation function of the fly, however, remains distinct under such interlogs
addition, for which we present a possible scenario through an in silico
modeling.Comment: 7 pages, 6 figures, 2 table
Color naming reflects both perceptual structure and communicative need
Gibson et al. (2017) argued that color naming is shaped by patterns of
communicative need. In support of this claim, they showed that color naming
systems across languages support more precise communication about warm colors
than cool colors, and that the objects we talk about tend to be warm-colored
rather than cool-colored. Here, we present new analyses that alter this
picture. We show that greater communicative precision for warm than for cool
colors, and greater communicative need, may both be explained by perceptual
structure. However, using an information-theoretic analysis, we also show that
color naming across languages bears signs of communicative need beyond what
would be predicted by perceptual structure alone. We conclude that color naming
is shaped both by perceptual structure, as has traditionally been argued, and
by patterns of communicative need, as argued by Gibson et al. - although for
reasons other than those they advanced
Graph ambiguity
In this paper, we propose a rigorous way to define the concept of ambiguity in the domain of graphs. In past studies, the classical definition of ambiguity has been derived starting from fuzzy set and fuzzy information theories. Our aim is to show that also in the domain of the graphs it is possible to derive a formulation able to capture the same semantic and mathematical concept. To strengthen the theoretical results, we discuss the application of the graph ambiguity concept to the graph classification setting, conceiving a new kind of inexact graph matching procedure. The results prove that the graph ambiguity concept is a characterizing and discriminative property of graphs. (C) 2013 Elsevier B.V. All rights reserved
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