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CFinder is one of the most popular clique-based methods, which searches adjacent cliques in the network [ 8, 10, 11].
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Therefore, it has the ability to avoid being trapped in a local optimal solution like traditional methods, which search from a single point.
A traditional way to estimate such ranges is to use enclosing surface methods, which search for convex enclosures like balls or prisms, of the entire history path in stress or strain diagrams.
Our focus for the benchmark is methods which search for TFBS using known models of binding sites, not ab initio TFBS discovery.
The focus here is on three dimensional (3D) template methods, which search for local structural similarity of key functional residues in separate proteins [45] using methods such as geometric hashing [46] [48].
A correlation study was performed using an R script (see Methods) which searched for a link between the presence/absence of a cluster of orthologous proteins in the genome of a strain able/unable to degrade a specific sugar.
Multivariable filter methods include mRMR [ 9], correlation-based feature selection [ 10], and Markov blanket filter [ 11]; (ii) wrapper methods, which search for an optimal feature set that maximizes the classification performance, defined in terms of an evaluation function (such as cross-validation accuracy).
Contrary to previous methods which search for synteny blocks and simply return what remains in the genome as BPRs, the framework of C ASSIS consists in building synteny blocks from orthologous markers and in further investigating the BPRs themselves in order to refine their coordinates.
The method which searches for these local minimum and maximums in the projection vector is as follows.
We stress-test CTP with a quantitative testing method which searches for topologies using evolutionary algorithms combined with protocol simulation.
The independent component analysis (ICA) represents a main BSS method which searches for stochastically independent signals from the multivariate observations.
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