Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly
One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been improved algorithms for utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in the assembly graph structure. However, the PDBG approach faces difficulties when the variation in the insert sizes is high. To address this problem, we first transform mate-pairs into edge-pair histograms that allow one to better estimate the distance between edges in the assembly graph that represent regions linked by multiple mate-pairs. Further, we combine the ideas of mate-pair transformation and PDBGs to construct new data structures for genome assembly: pathsets and pathset graphs.
The article describes the original software tools for an experimental estimation of computational complexity of software solutions for problems on graph models of systems. The classes of the solved problems and the tools for analysis of results are listed. The method based on selection of graph models by their structural complexity is introduced.
This proceedings publication is a compilation of selected contributions from the “Third International Conference on the Dynamics of Information Systems” which took place at the University of Florida, Gainesville, February 16–18, 2011. The purpose of this conference was to bring together scientists and engineers from industry, government, and academia in order to exchange new discoveries and results in a broad range of topics relevant to the theory and practice of dynamics of information systems. Dynamics of Information Systems: Mathematical Foundation presents state-of-the art research and is intended for graduate students and researchers interested in some of the most recent discoveries in information theory and dynamical systems. Scientists in other disciplines may also benefit from the applications of new developments to their own area of study.
This volume contains a selection of contributions from the "First International Conference in Network Analysis," held at the University of Florida, Gainesville, on December 14-16, 2011. The remarkable diversity of fields that take advantage of Network Analysis makes the endeavor of gathering up-to-date material in a single compilation a useful, yet very difficult, task. The purpose of this volume is to overcome this difficulty by collecting the major results found by the participants and combining them in one easily accessible compilation.
In this paper, we present a modification of dynamic programming algorithms (DPA), which we denote as graphical algorithms (GrA). For some single machine scheduling problems, it is shown that the time complexity of the GrA is less than the time complexity of the standard DPA. Moreover, the average running time of the GrA is often essentially smaller. A GrA can also solve large-scale instances and instances, where the parameters are not integer. For some problems, GrA has a polynomial time complexity in contrast to a pseudo-polynomial complexity of a DPA.
Information systems have been developed in parallel with computer science, although information systems have roots in different disciplines including mathematics, engineering, and cybernetics. Research in information systems is by nature very interdisciplinary. As it is evidenced by the chapters in this book, dynamics of information systems has several diverse applications. The book presents the state-of-the-art work on theory and practice relevant to the dynamics of information systems. First, the book covers algorithmic approaches to numerical computations with infinite and infinitesimal numbers. Also the book presents important problems arising in service-oriented systems, such as dynamic composition, analysis of modern service-oriented information systems, and estimation of customer service times on a rail network from GPS data. After that, the book addresses the complexity of the problems arising in stochastic and distributed systems. In addition, the book discusses modulating communication for improving multi-agent learning convergence. Network issues, in particular minimum risk maximum clique problems, vulnerability of sensor networks, influence diffusion, community detection, and link prediction in social network analysis, as well as a comparative analysis of algorithms for transmission network expansion planning are described in subsequent chapters. We thank all the authors and anonymous referees for their advice and expertise in providing valuable contributions, which improved the quality of this book. Furthermore, we want to thank Springer for helping us to produce this book.
We revisit the problems of computing the maximal and the minimal non-empty suffixes of a substring of a longer text of length n, introduced by Babenko, Kolesnichenko and Starikovskaya [CPM’13]. For the minimal suffix problem we show that for any 1 ≤ τ ≤ logn there exists a linear-space data structure with(τ)query time and(nlogn/τ)preprocessing time. As a sample application, we show that this data structure can be used to compute the Lyndon decomposition of any substring of the text in(kτ)time, where k is the number of distinct factors in the decomposition. For the maximal suffix problem we give a linear-space structure with(1)query time and(n)preprocessing time, i.e., we manage to achieve both the optimal query and the optimal construction time simultaneously.
A form for an unbiased estimate of the coefficient of determination of a linear regression model is obtained. It is calculated by using a sample from a multivariate normal distribution. This estimate is proposed as an alternative criterion for a choice of regression factors.