1,810 research outputs found
RNF: a general framework to evaluate NGS read mappers
Aligning reads to a reference sequence is a fundamental step in numerous
bioinformatics pipelines. As a consequence, the sensitivity and precision of
the mapping tool, applied with certain parameters to certain data, can
critically affect the accuracy of produced results (e.g., in variant calling
applications). Therefore, there has been an increasing demand of methods for
comparing mappers and for measuring effects of their parameters.
Read simulators combined with alignment evaluation tools provide the most
straightforward way to evaluate and compare mappers. Simulation of reads is
accompanied by information about their positions in the source genome. This
information is then used to evaluate alignments produced by the mapper.
Finally, reports containing statistics of successful read alignments are
created.
In default of standards for encoding read origins, every evaluation tool has
to be made explicitly compatible with the simulator used to generate reads. In
order to solve this obstacle, we have created a generic format RNF (Read Naming
Format) for assigning read names with encoded information about original
positions.
Futhermore, we have developed an associated software package RNF containing
two principal components. MIShmash applies one of popular read simulating tools
(among DwgSim, Art, Mason, CuReSim etc.) and transforms the generated reads
into RNF format. LAVEnder evaluates then a given read mapper using simulated
reads in RNF format. A special attention is payed to mapping qualities that
serve for parametrization of ROC curves, and to evaluation of the effect of
read sample contamination
Graph Isomorphism and the Lasserre Hierarchy
In this paper we show lower bounds for a certain large class of algorithms
solving the Graph Isomorphism problem, even on expander graph instances.
Spielman [25] shows an algorithm for isomorphism of strongly regular expander
graphs that runs in time exp(O(n^(1/3)) (this bound was recently improved to
expf O(n^(1/5) [5]). It has since been an open question to remove the
requirement that the graph be strongly regular. Recent algorithmic results show
that for many problems the Lasserre hierarchy works surprisingly well when the
underlying graph has expansion properties. Moreover, recent work of Atserias
and Maneva [3] shows that k rounds of the Lasserre hierarchy is a
generalization of the k-dimensional Weisfeiler-Lehman algorithm for Graph
Isomorphism. These two facts combined make the Lasserre hierarchy a good
candidate for solving graph isomorphism on expander graphs. Our main result
rules out this promising direction by showing that even Omega(n) rounds of the
Lasserre semidefinite program hierarchy fail to solve the Graph Isomorphism
problem even on expander graphs.Comment: 22 pages, 3 figures, submitted to CC
Visualizing dimensionality reduction of systems biology data
One of the challenges in analyzing high-dimensional expression data is the
detection of important biological signals. A common approach is to apply a
dimension reduction method, such as principal component analysis. Typically,
after application of such a method the data is projected and visualized in the
new coordinate system, using scatter plots or profile plots. These methods
provide good results if the data have certain properties which become visible
in the new coordinate system and which were hard to detect in the original
coordinate system. Often however, the application of only one method does not
suffice to capture all important signals. Therefore several methods addressing
different aspects of the data need to be applied. We have developed a framework
for linear and non-linear dimension reduction methods within our visual
analytics pipeline SpRay. This includes measures that assist the interpretation
of the factorization result. Different visualizations of these measures can be
combined with functional annotations that support the interpretation of the
results. We show an application to high-resolution time series microarray data
in the antibiotic-producing organism Streptomyces coelicolor as well as to
microarray data measuring expression of cells with normal karyotype and cells
with trisomies of human chromosomes 13 and 21
Versatile Markovian models for networks with asymmetric TCP sources
In this paper we use Stochastic Petri Nets (SPNs) to study the interaction of multiple TCP sources that share one or two buffers, thereby considerably extending earlier work. We first consider two sources sharing a buffer and investigate the consequences of two popular assumptions for the loss process in terms of fairness and link utilization. The results obtained by our model are in agreement with existing analytic models or are closer to results obtained by ns-2 simulations. We then study a network consisting of three sources and two buffers and provide evidence that link sharing is approximately minimum-potential-delay-fair in case of equal round-trip times. \u
Existence of a Meromorphic Extension of Spectral Zeta Functions on Fractals
We investigate the existence of the meromorphic extension of the spectral
zeta function of the Laplacian on self-similar fractals using the classical
results of Kigami and Lapidus (based on the renewal theory) and new results of
Hambly and Kajino based on the heat kernel estimates and other probabilistic
techniques. We also formulate conjectures which hold true in the examples that
have been analyzed in the existing literature
Projective Techniques and Functional Integration
A general framework for integration over certain infinite dimensional spaces
is first developed using projective limits of a projective family of compact
Hausdorff spaces. The procedure is then applied to gauge theories to carry out
integration over the non-linear, infinite dimensional spaces of connections
modulo gauge transformations. This method of evaluating functional integrals
can be used either in the Euclidean path integral approach or the Lorentzian
canonical approach. A number of measures discussed are diffeomorphism invariant
and therefore of interest to (the connection dynamics version of) quantum
general relativity. The account is pedagogical; in particular prior knowledge
of projective techniques is not assumed. (For the special JMP issue on
Functional Integration, edited by C. DeWitt-Morette.)Comment: 36 pages, latex, no figures, Preprint CGPG/94/10-
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