2,383 research outputs found
Structure controllability of complex network based on preferential matching
Minimum driver node sets (MDSs) play an important role in studying the
structural controllability of complex networks. Recent research has shown that
MDSs tend to avoid high-degree nodes. However, this observation is based on the
analysis of a small number of MDSs, because enumerating all of the MDSs of a
network is a #P problem. Therefore, past research has not been sufficient to
arrive at a convincing conclusion. In this paper, first, we propose a
preferential matching algorithm to find MDSs that have a specific degree
property. Then, we show that the MDSs obtained by preferential matching can be
composed of high- and medium-degree nodes. Moreover, the experimental results
also show that the average degree of the MDSs of some networks tends to be
greater than that of the overall network, even when the MDSs are obtained using
previous research method. Further analysis shows that whether the driver nodes
tend to be high-degree nodes or not is closely related to the edge direction of
the network
An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner.
Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological networks holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology-the "structure" of the network-is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment-which is an essentially solved problem-network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used.Here we introduce SANA, the Simulated Annealing Network Aligner. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between two or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks
On Submodularity and Controllability in Complex Dynamical Networks
Controllability and observability have long been recognized as fundamental
structural properties of dynamical systems, but have recently seen renewed
interest in the context of large, complex networks of dynamical systems. A
basic problem is sensor and actuator placement: choose a subset from a finite
set of possible placements to optimize some real-valued controllability and
observability metrics of the network. Surprisingly little is known about the
structure of such combinatorial optimization problems. In this paper, we show
that several important classes of metrics based on the controllability and
observability Gramians have a strong structural property that allows for either
efficient global optimization or an approximation guarantee by using a simple
greedy heuristic for their maximization. In particular, the mapping from
possible placements to several scalar functions of the associated Gramian is
either a modular or submodular set function. The results are illustrated on
randomly generated systems and on a problem of power electronic actuator
placement in a model of the European power grid.Comment: Original arXiv version of IEEE Transactions on Control of Network
Systems paper (Volume 3, Issue 1), with a addendum (located in the ancillary
documents) that explains an error in a proof of the original paper and
provides a counterexample to the corresponding resul
An efficient algorithm for finding all possible input nodes for controlling complex networks
Understanding structural controllability of a complex network requires to
identify a Minimum Input nodes Set (MIS) of the network. It has been suggested
that finding an MIS is equivalent to computing a maximum matching of the
network, where the unmatched nodes constitute an MIS. However, maximum matching
of a network is often not unique, and finding all MISs may provide deep
insights to the controllability of the network. Finding all possible input
nodes, which form the union of all MISs, is computationally challenging for
large networks. Here we present an efficient enumerative algorithm for the
problem. The main idea is to modify a maximum matching algorithm to make it
efficient for finding all possible input nodes by computing only one MIS. We
rigorously proved the correctness of the new algorithm and evaluated its
performance on synthetic and large real networks. The experimental results
showed that the new algorithm ran several orders of magnitude faster than the
existing method on large real networks
Significant Subgraph Mining with Multiple Testing Correction
The problem of finding itemsets that are statistically significantly enriched
in a class of transactions is complicated by the need to correct for multiple
hypothesis testing. Pruning untestable hypotheses was recently proposed as a
strategy for this task of significant itemset mining. It was shown to lead to
greater statistical power, the discovery of more truly significant itemsets,
than the standard Bonferroni correction on real-world datasets. An open
question, however, is whether this strategy of excluding untestable hypotheses
also leads to greater statistical power in subgraph mining, in which the number
of hypotheses is much larger than in itemset mining. Here we answer this
question by an empirical investigation on eight popular graph benchmark
datasets. We propose a new efficient search strategy, which always returns the
same solution as the state-of-the-art approach and is approximately two orders
of magnitude faster. Moreover, we exploit the dependence between subgraphs by
considering the effective number of tests and thereby further increase the
statistical power.Comment: 18 pages, 5 figure, accepted to the 2015 SIAM International
Conference on Data Mining (SDM15
Systems approaches and algorithms for discovery of combinatorial therapies
Effective therapy of complex diseases requires control of highly non-linear
complex networks that remain incompletely characterized. In particular, drug
intervention can be seen as control of signaling in cellular networks.
Identification of control parameters presents an extreme challenge due to the
combinatorial explosion of control possibilities in combination therapy and to
the incomplete knowledge of the systems biology of cells. In this review paper
we describe the main current and proposed approaches to the design of
combinatorial therapies, including the empirical methods used now by clinicians
and alternative approaches suggested recently by several authors. New
approaches for designing combinations arising from systems biology are
described. We discuss in special detail the design of algorithms that identify
optimal control parameters in cellular networks based on a quantitative
characterization of control landscapes, maximizing utilization of incomplete
knowledge of the state and structure of intracellular networks. The use of new
technology for high-throughput measurements is key to these new approaches to
combination therapy and essential for the characterization of control
landscapes and implementation of the algorithms. Combinatorial optimization in
medical therapy is also compared with the combinatorial optimization of
engineering and materials science and similarities and differences are
delineated.Comment: 25 page
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