An adaptive orthogonal search algorithm for model subset selection and non-linear system identification

A new adaptive orthogonal search (AOS) algorithm is proposed for model subset selection and non-linear system identification. Model structure detection is a key step in any system identification problem. This consists of selecting significant model terms from a redundant dictionary of candidate model terms, and determining the model complexity (model length or model size). The final objective is to produce a parsimonious model that can well capture the inherent dynamics of the underlying system. In the new AOS algorithm, a modified generalized cross-validation criterion, called the adjustable prediction error sum of squares (APRESS), is introduced and incorporated into a forward orthogonal search procedure. The main advantage of the new AOS algorithm is that the mechanism is simple and the implementation is direct and easy, and more importantly it can produce efficient model subsets for most non-linear identification problems

Model structure selection using an integrated forward orthogonal search algorithm assisted by squared correlation and mutual information

Model structure selection plays a key role in non-linear system identification. The first step in non-linear system identification is to determine which model terms should be included in the model. Once significant model terms have been determined, a model selection criterion can then be applied to select a suitable model subset. The well known Orthogonal Least Squares (OLS) type algorithms are one of the most efficient and commonly used techniques for model structure selection. However, it has been observed that the OLS type algorithms may occasionally select incorrect model terms or yield a redundant model subset in the presence of particular noise structures or input signals. A very efficient Integrated Forward Orthogonal Search (IFOS) algorithm, which is assisted by the squared correlation and mutual information, and which incorporates a Generalised Cross-Validation (GCV) criterion and hypothesis tests, is introduced to overcome these limitations in model structure selection

Model structure selection using an integrated forward orthogonal search algorithm interfered with squared correlation and mutual information

Model structure selection plays a key role in nonlinear system identification. The first step in nonlinear system identification is to determine which model terms should be included in the model. Once significant model terms have been determined, a model selection criterion can then be applied to select a suitable model subset. The well known orthogonal least squares type algorithms are one of the most efficient and commonly used techniques for model structure selection. However, it has been observed that the orthogonal least squares type algorithms may occasionally select incorrect model terms or yield a redundant model subset in the presence of particular noise structures or input signals. A very efficient integrated forward orthogonal searching (IFOS) algorithm, which is interfered with squared correlation and mutual information, and which incorporates a general cross-validation (GCV) criterion and hypothesis tests, is introduced to overcome these limitations in model structure selection

Solving the riddle of codon usage preferences: a test for translational selection

Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model

Solving the riddle of codon usage preferences: a test for translational selection

Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model