Words similar to optimization
Example sentences for: optimization
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Subsequently, codon usage in a few species has been extensively characterized, and linked causally to a wide variety of both adaptive and nonadaptive factors including tRNA abundance [ 8, 9, 10, 11, 12, 13, 14], gene expression level [ 15, 16, 17, 18, 19, 20, 21, 22, 23], local compositional biases [ 24, 25, 26, 27, 28], rates and patterns of mutation [ 29, 30, 31, 32], protein composition [ 33, 34, 35, 36], protein structure [ 37, 38, 39], translation optimization [ 40, 41, 42] (but see [ 43]), gene length [ 44, 45, 46, 47], and mRNA secondary structure [ 48, 49, 50, 51, 52].
Table 1shows the resultsfrom the traditional BPNN architecture optimization technique onone data set from each epistasis model generated with the two functionalSNPs only.
Because bootstrap analysis using ML is not computationally feasible for large data sets [ 85 ] , we conducted a Bayesian analysis as an alternative employing optimization parameters similar to the nucleotide substitution model that we used for ML [ 86 87 ] . The distinction between ML and Bayesian inference is that Bayesian provides probabilities for hypotheses, not probabilities of data given a hypothesis [ 85 87 88 ] . Bayesian analysis uses Markov Chain Monte Carlo (MCMC) methods to approximate posterior probability distributions that are a direct estimation of branch support because they are the true probabilities of the resulting clades under the assumed models, unlike bootstrap values [ 87 88 ] . Additionally, bootstrap values and posterior probabilities derived from Bayesian analyses for multiple data sets appear to be correlated [ 88 ] . The Bayesian analysis was conducted with the software MrBayes 2.0 [ 89 ] . A GTR substitution model with 6 rate frequencies was selected as the most similar model to the Trn+G substitution model (the latter model is not available in MrBayes).
Further work should incorporate more complicated sequence models, as well as optimization methods that restrict the search space of sequence combinations.
Inherently, the functional resolution in the ET method relies on an optimization based on ET results from multiple partitions, each corresponding to unique definitions of subclade invariance.
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