33,233 research outputs found
Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study
Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons
Designing Algorithms for Optimization of Parameters of Functioning of Intelligent System for Radionuclide Myocardial Diagnostics
The influence of the number of complex components of Fast Fourier transformation in analyzing the polar maps of radionuclide examination of myocardium at rest and stress on the functional efficiency of the system of diagnostics of pathologies of myocardium was explored, and there were defined their optimum values in the information sense, which allows increasing the efficiency of the algorithms of forming the diagnostic decision rules by reducing the capacity of the dictionary of features of recognition.The information-extreme sequential cluster algorithms of the selection of the dictionary of features, which contains both quantitative and category features were developed and the results of their work were compared. The modificatios of the algorithms of the selection of the dictionary were suggested, which allows increasing both the search speed of the optimal in the information sense dictionary and reducing its capacity by 40 %. We managed to get the faultless by the training matrix decision rules, the accuracy of which is in the exam mode asymptotically approaches the limit.It was experimentally confirmed that the implementation of the proposed algorithm of the diagnosing system training has allowed to reduce the minimum representative volume of the training matrix from 300 to 81 vectors-implementations of the classes of recognition of the functional myocardium state
A Framework for Developing Real-Time OLAP algorithm using Multi-core processing and GPU: Heterogeneous Computing
The overwhelmingly increasing amount of stored data has spurred researchers
seeking different methods in order to optimally take advantage of it which
mostly have faced a response time problem as a result of this enormous size of
data. Most of solutions have suggested materialization as a favourite solution.
However, such a solution cannot attain Real- Time answers anyhow. In this paper
we propose a framework illustrating the barriers and suggested solutions in the
way of achieving Real-Time OLAP answers that are significantly used in decision
support systems and data warehouses
Compressive Mining: Fast and Optimal Data Mining in the Compressed Domain
Real-world data typically contain repeated and periodic patterns. This
suggests that they can be effectively represented and compressed using only a
few coefficients of an appropriate basis (e.g., Fourier, Wavelets, etc.).
However, distance estimation when the data are represented using different sets
of coefficients is still a largely unexplored area. This work studies the
optimization problems related to obtaining the \emph{tightest} lower/upper
bound on Euclidean distances when each data object is potentially compressed
using a different set of orthonormal coefficients. Our technique leads to
tighter distance estimates, which translates into more accurate search,
learning and mining operations \textit{directly} in the compressed domain.
We formulate the problem of estimating lower/upper distance bounds as an
optimization problem. We establish the properties of optimal solutions, and
leverage the theoretical analysis to develop a fast algorithm to obtain an
\emph{exact} solution to the problem. The suggested solution provides the
tightest estimation of the -norm or the correlation. We show that typical
data-analysis operations, such as k-NN search or k-Means clustering, can
operate more accurately using the proposed compression and distance
reconstruction technique. We compare it with many other prevalent compression
and reconstruction techniques, including random projections and PCA-based
techniques. We highlight a surprising result, namely that when the data are
highly sparse in some basis, our technique may even outperform PCA-based
compression.
The contributions of this work are generic as our methodology is applicable
to any sequential or high-dimensional data as well as to any orthogonal data
transformation used for the underlying data compression scheme.Comment: 25 pages, 20 figures, accepted in VLD
- …