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Article
Open AccessePyDGGA: automatic configuration for fitting epidemic curves
Many epidemiological models and algorithms are used to fit the parameters of a given epidemic curve. On many occasions, fitting algorithms are interleaved with the actual epidemic models, which yields combinat...
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Article
Open AccessRNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory
RNA inverse folding is the problem of finding one or more sequences that fold into a user-specified target structure s 0, i.e. whose minimum free energy secondary structure is identical...
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Article
Open AccessDesigning synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements
The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor c...
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Article
RNA folding pathways and kinetics using 2D energy landscapes
RNA folding pathways play an important role in various biological processes, such as (i) the hok/sok (host-killing/suppression of killing) system in E. coli to check for sufficient plasmid copy number, (ii) the c...
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Chapter and Conference Paper
Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches
We describe the broad outline of a new thermodynamics-based algorithm, FFTbor, that uses the fast Fourier transform to perform polynomial interpolation to compute the Boltzmann probability that secondary structur...
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Article
On the page number of RNA secondary structures with pseudoknots
Let \({\mathcal {S}}\) denote the set of (possibly noncanonical) base pairs {i, j} of an RNA tertiary structure; i.e....
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Article
Boosting video tracking performance by means of Tabu Search in intelligent visual surveillance systems
In this paper, we present a fast and efficient technique for the data association problem applied to visual tracking systems. Visual tracking process is formulated as a combinatorial hypotheses search with a h...
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Chapter and Conference Paper
Real-Time Tabu Search for Video Tracking Association
Intelligent Visual Surveillance (IVS) systems are becoming a ubiquitous security component as they aim at monitoring, in real time, persistent and transcient activities in specific environments. This paper con...
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Chapter and Conference Paper
Protein Structure Prediction with Large Neighborhood Constraint Programming Search
Protein structure predictions is regarded as a highly challenging problem both for the biology and for the computational communities. Many approaches have been developed in the recent years, moving to increasi...
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Article
Local Search-based Hybrid Algorithms for Finding Golomb Rulers
The Golomb ruler problem is a very hard combinatorial optimization problem that has been tackled with many different approaches, such as constraint programming (CP), local search (LS), and evolutionary algorit...
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Chapter and Conference Paper
Scheduling Social Golfers with Memetic Evolutionary Programming
The social golfer problem (SGP) has attracted significant attention in recent years because of its highly symmetrical, constrained, and combinatorial nature. Nowadays, it constitutes one of the standard benchm...
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Chapter and Conference Paper
A Memetic Approach to Golomb Rulers
Finding Golomb rulers is an extremely challenging optimization problem with many practical applications. This problem has been approached by a variety of search methods in recent years. We consider in this wor...
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Chapter and Conference Paper
A Note on Low Autocorrelation Binary Sequences
The Low Autocorrelation Binary Sequences problem (LABS) is problem 005 in the CSPLIB library, where it is stated that “these problems pose a significant challenge to local search methods”. This paper presents ...
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Chapter and Conference Paper
Scheduling Social Tournaments
Tournament scheduling problems arise in many practical applications and their highly symmetric and combinatorial nature makes them particularly challenging for search algorithms. This research generalizes the ...
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Chapter and Conference Paper
Scheduling Social Golfers Locally
The scheduling of social golfers has attracted significant attention in recent years because of its highly symmetrical and combinatorial nature. In particular, it has become one of the standard benchmarks for ...
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Chapter and Conference Paper
Redundant Modeling for the QuasiGroup Completion Problem
The Quasigroup Completion Problem (QCP) is a very challenging benchmark among combinatorial problems, and the focus of much recent interest in the area of constraint programming. [5] reports that QCPs of order...
