Visual analysis for drum sequence transcription

A system is presented for analysing drum performance video sequences. A novel ellipse detection algorithm is introduced that automatically locates drum tops. This algorithm fits ellipses to edge clusters, and ranks them according to various fitness criteria. A background/foreground segmentation method is then used to extract the silhouette of the drummer and drum sticks. Coupled with a motion intensity feature, this allows for the detection of ‘hits’ in each of the extracted regions. In order to obtain a transcription of the performance, each of these regions is automatically labeled with the corresponding instrument class. A partial audio transcription and color cues are used to measure the compatibility between a region and its label, the Kuhn-Munkres algorithm is then employed to find the optimal labeling. Experimental results demonstrate the ability of visual analysis to enhance the performance of an audio drum transcription system

Spatiotemporal Barcodes for Image Sequence Analysis

Taking as input a time-varying sequence of two-dimensional (2D) binary images, we develop an algorithm for computing a spatiotemporal 0–barcode encoding lifetime of connected components on the image sequence over time. This information may not coincide with the one provided by the 0–barcode encoding the 0–persistent homology, since the latter does not respect the principle that it is not possible to move backwards in time. A cell complex K is computed from the given sequence, being the cells of K classified as spatial or temporal depending on whether they connect two consecutive frames or not. A spatiotemporal path is defined as a sequence of edges of K forming a path such that two edges of the path cannot connect the same two consecutive frames. In our algorithm, for each vertex v ∈ K, a spatiotemporal path from v to the “oldest” spatiotemporally-connected vertex is computed and the corresponding spatiotemporal 0–bar is added to the spatiotemporal 0–barcode.Junta de Andalucía FQM-369Ministerio de Economía y Competitividad MTM2012-3270

Revealing evolutionary constraints on proteins through sequence analysis

Statistical analysis of alignments of large numbers of protein sequences has revealed "sectors" of collectively coevolving amino acids in several protein families. Here, we show that selection acting on any functional property of a protein, represented by an additive trait, can give rise to such a sector. As an illustration of a selected trait, we consider the elastic energy of an important conformational change within an elastic network model, and we show that selection acting on this energy leads to correlations among residues. For this concrete example and more generally, we demonstrate that the main signature of functional sectors lies in the small-eigenvalue modes of the covariance matrix of the selected sequences. However, secondary signatures of these functional sectors also exist in the extensively-studied large-eigenvalue modes. Our simple, general model leads us to propose a principled method to identify functional sectors, along with the magnitudes of mutational effects, from sequence data. We further demonstrate the robustness of these functional sectors to various forms of selection, and the robustness of our approach to the identification of multiple selected traits.Comment: 37 pages, 28 figure

Fundamental principles in drawing inference from sequence analysis

Individual life courses are dynamic and can be represented as a sequence of states for some portion of their experiences. More generally, study of such sequences has been made in many fields around social science; for example, sociology, linguistics, psychology, and the conceptualisation of subjects progressing through a sequence of states is common. However, many models and sets of data allow only for the treatment of aggregates or transitions, rather than interpreting whole sequences. The temporal aspect of the analysis is fundamental to any inference about the evolution of the subjects but assumptions about time are not normally made explicit. Moreover, without a clear idea of what sequences look like, it is impossible to determine when something is not seen whether it was not actually there. Some principles are proposed which link the ideas of sequences, hypothesis, analytical framework, categorisation and representation; each one being underpinned by the consideration of time. To make inferences about sequences, one needs to: understand what these sequences represent; the hypothesis and assumptions that can be derived about sequences; identify the categories within the sequences; and data representation at each stage. These ideas are obvious in themselves but they are interlinked, imposing restrictions on each other and on the inferences which can be draw

BEAST: Bayesian evolutionary analysis by sampling trees

<p>Abstract</p> <p>Background</p> <p>The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented.</p> <p>Results</p> <p>BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at <url>http://beast-mcmc.googlecode.com/</url> under the GNU LGPL license.</p> <p>Conclusion</p> <p>BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.</p

Model selection and sensitivity analysis for sequence pattern models

In this article we propose a maximal a posteriori (MAP) criterion for model selection in the motif discovery problem and investigate conditions under which the MAP asymptotically gives a correct prediction of model size. We also investigate robustness of the MAP to prior specification and provide guidelines for choosing prior hyper-parameters for motif models based on sensitivity considerations.Comment: Published in at http://dx.doi.org/10.1214/193940307000000301 the IMS Collections (http://www.imstat.org/publications/imscollections.htm) by the Institute of Mathematical Statistics (http://www.imstat.org

Single nucleotide polymorphisms from Theobroma cacao expressed sequence tags associated with witches' broom disease in cacao

In order to increase the efficiency of cacao tree resistance to witches¿ broom disease, which is caused by Moniliophthora perniciosa (Tricholomataceae), we looked for molecular markers that could help in the selection of resistant cacao genotypes. Among the different markers useful for developing marker-assisted selection, single nucleotide polymorphisms (SNPs) constitute the most common type of sequence difference between alleles and can be easily detected by in silico analysis from expressed sequence tag libraries. We report the first detection and analysis of SNPs from cacao-M. perniciosa interaction expressed sequence tags, using bioinformatics. Selection based on analysis of these SNPs should be useful for developing cacao varieties resistant to this devastating disease. (Résumé d'auteur