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A new method for computing the projection median, its influence curve and techniques for the production of projected quantile plots.

ABSTRACT: This article introduces a new formulation of, and method of computation for, the projection median. Additionally, we explore its behaviour on a specific bivariate set up, providing the first theoretical result on form of the influence curve for the projection median, accompanied by numerical simulations. Via new simulations we comprehensively compare our performance with an established method for computing the projection median, as well as other existing multivariate medians. We focus on answering questions about accuracy and computational speed, whilst taking into account the underlying dimensionality. Such considerations are vitally important in situations where the data set is large, or where the operations have to be repeated many times and some well-known techniques are extremely computationally expensive. We briefly describe our associated R package that includes our new methods and novel functionality to produce animated multidimensional projection quantile plots, and also exhibit its use on some high-dimensional data examples.

SUBMITTER: Chen F

PROVIDER: S-EPMC7205268 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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A new method for computing the projection median, its influence curve and techniques for the production of projected quantile plots.

Chen Fan F Nason Guy G

PloS one 20200507 5

This article introduces a new formulation of, and method of computation for, the projection median. Additionally, we explore its behaviour on a specific bivariate set up, providing the first theoretical result on form of the influence curve for the projection median, accompanied by numerical simulations. Via new simulations we comprehensively compare our performance with an established method for computing the projection median, as well as other existing multivariate medians. We focus on answeri ...[more]

PMID: 32379826

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Project description:BackgroundComputing the distance between two RNA secondary structures can contribute in understanding the functional relationship between them. When used repeatedly, such a procedure may lead to finding a query RNA structure of interest in a database of structures. Several methods are available for computing distances between RNAs represented as strings or graphs, but none utilize the RNA representation with dot plots. Since dot plots are essentially digital images, there is a clear motivation to devise an algorithm for computing the distance between dot plots based on image processing methods.ResultsWe have developed a new metric dubbed 'DoPloCompare', which compares two RNA structures. The method is based on comparing dot plot diagrams that represent the secondary structures. When analyzing two diagrams and motivated by image processing, the distance is based on a combination of histogram correlations and a geometrical distance measure. We introduce, describe, and illustrate the procedure by two applications that utilize this metric on RNA sequences. The first application is the RNA design problem, where the goal is to find the nucleotide sequence for a given secondary structure. Examples where our proposed distance measure outperforms others are given. The second application locates peculiar point mutations that induce significant structural alternations relative to the wild type predicted secondary structure. The approach reported in the past to solve this problem was tested on several RNA sequences with known secondary structures to affirm their prediction, as well as on a data set of ribosomal pieces. These pieces were computationally cut from a ribosome for which an experimentally derived secondary structure is available, and on each piece the prediction conveys similarity to the experimental result. Our newly proposed distance measure shows benefit in this problem as well when compared to standard methods used for assessing the distance similarity between two RNA secondary structures.ConclusionInspired by image processing and the dot plot representation for RNA secondary structure, we have managed to provide a conceptually new and potentially beneficial metric for comparing two RNA secondary structures. We illustrated our approach on the RNA design problem, as well as on an application that utilizes the distance measure to detect conformational rearranging point mutations in an RNA sequence.

Dataset Information

A new method for computing the projection median, its influence curve and techniques for the production of projected quantile plots.

Publications

A new method for computing the projection median, its influence curve and techniques for the production of projected quantile plots.

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