18,727 research outputs found
Using temporal correlation in factor analysis for reconstructing transcription factor activities
Two-level gene regulatory networks consist of the transcription factors (TFs) in the top level and their regulated genes in the second level. The expression profiles of the regulated genes are the observed high-throughput data given by experiments such as microarrays. The activity profiles of the TFs are treated as hidden variables as well as the connectivity matrix that indicates the regulatory relationships of TFs with their regulated genes. Factor analysis (FA) as well as other methods, such as the network component algorithm, has been suggested for reconstructing gene regulatory networks and also for predicting TF activities. They have been applied to E. coli and yeast data with the assumption that these datasets consist of identical and independently distributed samples. Thus, the main drawback of these algorithms is that they ignore any time correlation existing within the TF profiles. In this paper, we extend previously studied FA algorithms to include time correlation within the transcription factors. At the same time, we consider connectivity matrices that are sparse in order to capture the existing sparsity present in gene regulatory networks. The TFs activity profiles obtained by this approach are significantly smoother than profiles from previous FA algorithms. The periodicities in profiles from yeast expression data become prominent in our reconstruction. Moreover, the strength of the correlation between time points is estimated and can be used to assess the suitability of the experimental time interval
Boolean Dynamics with Random Couplings
This paper reviews a class of generic dissipative dynamical systems called
N-K models. In these models, the dynamics of N elements, defined as Boolean
variables, develop step by step, clocked by a discrete time variable. Each of
the N Boolean elements at a given time is given a value which depends upon K
elements in the previous time step.
We review the work of many authors on the behavior of the models, looking
particularly at the structure and lengths of their cycles, the sizes of their
basins of attraction, and the flow of information through the systems. In the
limit of infinite N, there is a phase transition between a chaotic and an
ordered phase, with a critical phase in between.
We argue that the behavior of this system depends significantly on the
topology of the network connections. If the elements are placed upon a lattice
with dimension d, the system shows correlations related to the standard
percolation or directed percolation phase transition on such a lattice. On the
other hand, a very different behavior is seen in the Kauffman net in which all
spins are equally likely to be coupled to a given spin. In this situation,
coupling loops are mostly suppressed, and the behavior of the system is much
more like that of a mean field theory.
We also describe possible applications of the models to, for example, genetic
networks, cell differentiation, evolution, democracy in social systems and
neural networks.Comment: 69 pages, 16 figures, Submitted to Springer Applied Mathematical
Sciences Serie
Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming
A fundamental question in systems biology is the construction and training to
data of mathematical models. Logic formalisms have become very popular to model
signaling networks because their simplicity allows us to model large systems
encompassing hundreds of proteins. An approach to train (Boolean) logic models
to high-throughput phospho-proteomics data was recently introduced and solved
using optimization heuristics based on stochastic methods. Here we demonstrate
how this problem can be solved using Answer Set Programming (ASP), a
declarative problem solving paradigm, in which a problem is encoded as a
logical program such that its answer sets represent solutions to the problem.
ASP has significant improvements over heuristic methods in terms of efficiency
and scalability, it guarantees global optimality of solutions as well as
provides a complete set of solutions. We illustrate the application of ASP with
in silico cases based on realistic networks and data
Predicting protein functions with message passing algorithms
Motivation: In the last few years a growing interest in biology has been
shifting towards the problem of optimal information extraction from the huge
amount of data generated via large scale and high-throughput techniques. One of
the most relevant issues has recently become that of correctly and reliably
predicting the functions of observed but still functionally undetermined
proteins starting from information coming from the network of co-observed
proteins of known functions.
Method: The method proposed in this article is based on a message passing
algorithm known as Belief Propagation, which takes as input the network of
proteins physical interactions and a catalog of known proteins functions, and
returns the probabilities for each unclassified protein of having one chosen
function. The implementation of the algorithm allows for fast on-line analysis,
and can be easily generalized to more complex graph topologies taking into
account hyper-graphs, {\em i.e.} complexes of more than two interacting
proteins.Comment: 12 pages, 9 eps figures, 1 additional html tabl
Hearing the clusters in a graph: A distributed algorithm
We propose a novel distributed algorithm to cluster graphs. The algorithm
recovers the solution obtained from spectral clustering without the need for
expensive eigenvalue/vector computations. We prove that, by propagating waves
through the graph, a local fast Fourier transform yields the local component of
every eigenvector of the Laplacian matrix, thus providing clustering
information. For large graphs, the proposed algorithm is orders of magnitude
faster than random walk based approaches. We prove the equivalence of the
proposed algorithm to spectral clustering and derive convergence rates. We
demonstrate the benefit of using this decentralized clustering algorithm for
community detection in social graphs, accelerating distributed estimation in
sensor networks and efficient computation of distributed multi-agent search
strategies
A path following algorithm for the graph matching problem
We propose a convex-concave programming approach for the labeled weighted
graph matching problem. The convex-concave programming formulation is obtained
by rewriting the weighted graph matching problem as a least-square problem on
the set of permutation matrices and relaxing it to two different optimization
problems: a quadratic convex and a quadratic concave optimization problem on
the set of doubly stochastic matrices. The concave relaxation has the same
global minimum as the initial graph matching problem, but the search for its
global minimum is also a hard combinatorial problem. We therefore construct an
approximation of the concave problem solution by following a solution path of a
convex-concave problem obtained by linear interpolation of the convex and
concave formulations, starting from the convex relaxation. This method allows
to easily integrate the information on graph label similarities into the
optimization problem, and therefore to perform labeled weighted graph matching.
The algorithm is compared with some of the best performing graph matching
methods on four datasets: simulated graphs, QAPLib, retina vessel images and
handwritten chinese characters. In all cases, the results are competitive with
the state-of-the-art.Comment: 23 pages, 13 figures,typo correction, new results in sections 4,5,
Community detection in networks via nonlinear modularity eigenvectors
Revealing a community structure in a network or dataset is a central problem
arising in many scientific areas. The modularity function is an established
measure quantifying the quality of a community, being identified as a set of
nodes having high modularity. In our terminology, a set of nodes with positive
modularity is called a \textit{module} and a set that maximizes is thus
called \textit{leading module}. Finding a leading module in a network is an
important task, however the dimension of real-world problems makes the
maximization of unfeasible. This poses the need of approximation techniques
which are typically based on a linear relaxation of , induced by the
spectrum of the modularity matrix . In this work we propose a nonlinear
relaxation which is instead based on the spectrum of a nonlinear modularity
operator . We show that extremal eigenvalues of
provide an exact relaxation of the modularity measure , however at the price
of being more challenging to be computed than those of . Thus we extend the
work made on nonlinear Laplacians, by proposing a computational scheme, named
\textit{generalized RatioDCA}, to address such extremal eigenvalues. We show
monotonic ascent and convergence of the method. We finally apply the new method
to several synthetic and real-world data sets, showing both effectiveness of
the model and performance of the method
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