5,235 research outputs found
Casting Polymer Nets to Optimize Noisy Molecular Codes
Life relies on the efficient performance of molecular codes, which relate
symbols and meanings via error-prone molecular recognition. We describe how
optimizing a code to withstand the impact of molecular recognition noise may be
approximated by the statistics of a two-dimensional network made of polymers.
The noisy code is defined by partitioning the space of symbols into regions
according to their meanings. The "polymers" are the boundaries between these
regions and their statistics defines the cost and the quality of the noisy
code. When the parameters that control the cost-quality balance are varied, the
polymer network undergoes a first-order transition, where the number of encoded
meanings rises discontinuously. Effects of population dynamics on the evolution
of molecular codes are discussed.Comment: PNAS 200
Partitioning networks into cliques: a randomized heuristic approach
In the context of community detection in social networks, the term community can be grounded in the strict way that simply everybody should know each other within the community. We consider the corresponding community detection problem. We search for a partitioning of a network into the minimum number of non-overlapping cliques, such that the cliques cover all vertices. This problem is called the clique covering problem (CCP) and is one of the classical NP-hard problems. For CCP, we propose a randomized heuristic approach. To construct a high quality solution to CCP, we present an iterated greedy (IG) algorithm. IG can also be combined with a heuristic used to determine how far the algorithm is from the optimum in the worst case. Randomized local search (RLS) for maximum independent set was proposed to find such a bound. The experimental results of IG and the bounds obtained by RLS indicate that IG is a very suitable technique for solving CCP in real-world graphs. In addition, we summarize our basic rigorous results, which were developed for analysis of IG and understanding of its behavior on several relevant graph classes
Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape.
Vaccination has essentially eradicated poliovirus. Yet, its mutation rate is higher than that of viruses like HIV, for which no effective vaccine exists. To investigate this, we infer a fitness model for the poliovirus viral protein 1 (vp1), which successfully predicts in vitro fitness measurements. This is achieved by first developing a probabilistic model for the prevalence of vp1 sequences that enables us to isolate and remove data that are subject to strong vaccine-derived biases. The intrinsic fitness constraints derived for vp1, a capsid protein subject to antibody responses, are compared with those of analogous HIV proteins. We find that vp1 evolution is subject to tighter constraints, limiting its ability to evade vaccine-induced immune responses. Our analysis also indicates that circulating poliovirus strains in unimmunized populations serve as a reservoir that can seed outbreaks in spatio-temporally localized sub-optimally immunized populations
Extremal optimization for sensor report pre-processing
We describe the recently introduced extremal optimization algorithm and apply
it to target detection and association problems arising in pre-processing for
multi-target tracking.
Here we consider the problem of pre-processing for multiple target tracking
when the number of sensor reports received is very large and arrives in large
bursts. In this case, it is sometimes necessary to pre-process reports before
sending them to tracking modules in the fusion system. The pre-processing step
associates reports to known tracks (or initializes new tracks for reports on
objects that have not been seen before). It could also be used as a pre-process
step before clustering, e.g., in order to test how many clusters to use.
The pre-processing is done by solving an approximate version of the original
problem. In this approximation, not all pair-wise conflicts are calculated. The
approximation relies on knowing how many such pair-wise conflicts that are
necessary to compute. To determine this, results on phase-transitions occurring
when coloring (or clustering) large random instances of a particular graph
ensemble are used.Comment: 10 page
Two novel evolutionary formulations of the graph coloring problem
We introduce two novel evolutionary formulations of the problem of coloring
the nodes of a graph. The first formulation is based on the relationship that
exists between a graph's chromatic number and its acyclic orientations. It
views such orientations as individuals and evolves them with the aid of
evolutionary operators that are very heavily based on the structure of the
graph and its acyclic orientations. The second formulation, unlike the first
one, does not tackle one graph at a time, but rather aims at evolving a
`program' to color all graphs belonging to a class whose members all have the
same number of nodes and other common attributes. The heuristics that result
from these formulations have been tested on some of the Second DIMACS
Implementation Challenge benchmark graphs, and have been found to be
competitive when compared to the several other heuristics that have also been
tested on those graphs.Comment: To appear in Journal of Combinatorial Optimizatio
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