414 research outputs found
A classification-based framework for predicting and analyzing gene regulatory response
BACKGROUND: We have recently introduced a predictive framework for studying gene transcriptional regulation in simpler organisms using a novel supervised learning algorithm called GeneClass. GeneClass is motivated by the hypothesis that in model organisms such as Saccharomyces cerevisiae, we can learn a decision rule for predicting whether a gene is up- or down-regulated in a particular microarray experiment based on the presence of binding site subsequences ("motifs") in the gene's regulatory region and the expression levels of regulators such as transcription factors in the experiment ("parents"). GeneClass formulates the learning task as a classification problem — predicting +1 and -1 labels corresponding to up- and down-regulation beyond the levels of biological and measurement noise in microarray measurements. Using the Adaboost algorithm, GeneClass learns a prediction function in the form of an alternating decision tree, a margin-based generalization of a decision tree. METHODS: In the current work, we introduce a new, robust version of the GeneClass algorithm that increases stability and computational efficiency, yielding a more scalable and reliable predictive model. The improved stability of the prediction tree enables us to introduce a detailed post-processing framework for biological interpretation, including individual and group target gene analysis to reveal condition-specific regulation programs and to suggest signaling pathways. Robust GeneClass uses a novel stabilized variant of boosting that allows a set of correlated features, rather than single features, to be included at nodes of the tree; in this way, biologically important features that are correlated with the single best feature are retained rather than decorrelated and lost in the next round of boosting. Other computational developments include fast matrix computation of the loss function for all features, allowing scalability to large datasets, and the use of abstaining weak rules, which results in a more shallow and interpretable tree. We also show how to incorporate genome-wide protein-DNA binding data from ChIP chip experiments into the GeneClass algorithm, and we use an improved noise model for gene expression data. RESULTS: Using the improved scalability of Robust GeneClass, we present larger scale experiments on a yeast environmental stress dataset, training and testing on all genes and using a comprehensive set of potential regulators. We demonstrate the improved stability of the features in the learned prediction tree, and we show the utility of the post-processing framework by analyzing two groups of genes in yeast — the protein chaperones and a set of putative targets of the Nrg1 and Nrg2 transcription factors — and suggesting novel hypotheses about their transcriptional and post-transcriptional regulation. Detailed results and Robust GeneClass source code is available for download from
Intersection Graphs of L-Shapes and Segments in the Plane
An L-shape is the union of a horizontal and a vertical segment with a common endpoint. These come in four rotations: ⌊,⌈,⌋ and ⌉. A k-bend path is a simple path in the plane, whose direction changes k times from horizontal to vertical. If a graph admits an intersection representation in which every vertex is represented by an ⌊, an ⌊ or ⌈, a k-bend path, or a segment, then this graph is called an ⌊-graph, ⌊,⌈-graph, B k -VPG-graph or SEG-graph, respectively. Motivated by a theorem of Middendorf and Pfeiffer [Discrete Mathematics, 108(1):365–372, 1992], stating that every ⌊,⌈-graph is a SEG-graph, we investigate several known subclasses of SEG-graphs and show that they are ⌊-graphs, or B k -VPG-graphs for some small constant k. We show that all planar 3-trees, all line graphs of planar graphs, and all full subdivisions of planar graphs are ⌊-graphs. Furthermore we show that all complements of planar graphs are B 19-VPG-graphs and all complements of full subdivisions are B 2-VPG-graphs. Here a full subdivision is a graph in which each edge is subdivided at least once
Automatic Network Fingerprinting through Single-Node Motifs
Complex networks have been characterised by their specific connectivity
patterns (network motifs), but their building blocks can also be identified and
described by node-motifs---a combination of local network features. One
technique to identify single node-motifs has been presented by Costa et al. (L.
D. F. Costa, F. A. Rodrigues, C. C. Hilgetag, and M. Kaiser, Europhys. Lett.,
87, 1, 2009). Here, we first suggest improvements to the method including how
its parameters can be determined automatically. Such automatic routines make
high-throughput studies of many networks feasible. Second, the new routines are
validated in different network-series. Third, we provide an example of how the
method can be used to analyse network time-series. In conclusion, we provide a
robust method for systematically discovering and classifying characteristic
nodes of a network. In contrast to classical motif analysis, our approach can
identify individual components (here: nodes) that are specific to a network.
Such special nodes, as hubs before, might be found to play critical roles in
real-world networks.Comment: 16 pages (4 figures) plus supporting information 8 pages (5 figures
Adaptive structure tensors and their applications
The structure tensor, also known as second moment matrix or Förstner interest operator, is a very popular tool in image processing. Its purpose is the estimation of orientation and the local analysis of structure in general. It is based on the integration of data from a local neighborhood. Normally, this neighborhood is defined by a Gaussian window function and the structure tensor is computed by the weighted sum within this window. Some recently proposed methods, however, adapt the computation of the structure tensor to the image data. There are several ways how to do that. This article wants to give an overview of the different approaches, whereas the focus lies on the methods based on robust statistics and nonlinear diffusion. Furthermore, the dataadaptive structure tensors are evaluated in some applications. Here the main focus lies on optic flow estimation, but also texture analysis and corner detection are considered
Highlights from the Pierre Auger Observatory
The Pierre Auger Observatory is the world's largest cosmic ray observatory.
Our current exposure reaches nearly 40,000 km str and provides us with an
unprecedented quality data set. The performance and stability of the detectors
and their enhancements are described. Data analyses have led to a number of
major breakthroughs. Among these we discuss the energy spectrum and the
searches for large-scale anisotropies. We present analyses of our X
data and show how it can be interpreted in terms of mass composition. We also
describe some new analyses that extract mass sensitive parameters from the 100%
duty cycle SD data. A coherent interpretation of all these recent results opens
new directions. The consequences regarding the cosmic ray composition and the
properties of UHECR sources are briefly discussed.Comment: 9 pages, 12 figures, talk given at the 33rd International Cosmic Ray
Conference, Rio de Janeiro 201
Ultrahigh-energy neutrino follow-up of Gravitational Wave events GW150914 and GW151226 with the Pierre Auger Observatory
On September 14, 2015 the Advanced LIGO detectors observed their first
gravitational-wave (GW) transient GW150914. This was followed by a second GW
event observed on December 26, 2015. Both events were inferred to have arisen
from the merger of black holes in binary systems. Such a system may emit
neutrinos if there are magnetic fields and disk debris remaining from the
formation of the two black holes. With the surface detector array of the Pierre
Auger Observatory we can search for neutrinos with energy above 100 PeV from
point-like sources across the sky with equatorial declination from about -65
deg. to +60 deg., and in particular from a fraction of the 90% confidence-level
(CL) inferred positions in the sky of GW150914 and GW151226. A targeted search
for highly-inclined extensive air showers, produced either by interactions of
downward-going neutrinos of all flavors in the atmosphere or by the decays of
tau leptons originating from tau-neutrino interactions in the Earth's crust
(Earth-skimming neutrinos), yielded no candidates in the Auger data collected
within s around or 1 day after the coordinated universal time (UTC)
of GW150914 and GW151226, as well as in the same search periods relative to the
UTC time of the GW candidate event LVT151012. From the non-observation we
constrain the amount of energy radiated in ultrahigh-energy neutrinos from such
remarkable events.Comment: Published version. Added journal reference and DOI. Added Report
Numbe
Azimuthal asymmetry in the risetime of the surface detector signals of the Pierre Auger Observatory
The azimuthal asymmetry in the risetime of signals in Auger surface detector
stations is a source of information on shower development. The azimuthal
asymmetry is due to a combination of the longitudinal evolution of the shower
and geometrical effects related to the angles of incidence of the particles
into the detectors. The magnitude of the effect depends upon the zenith angle
and state of development of the shower and thus provides a novel observable,
, sensitive to the mass composition of cosmic rays
above eV. By comparing measurements with predictions from
shower simulations, we find for both of our adopted models of hadronic physics
(QGSJETII-04 and EPOS-LHC) an indication that the mean cosmic-ray mass
increases slowly with energy, as has been inferred from other studies. However,
the mass estimates are dependent on the shower model and on the range of
distance from the shower core selected. Thus the method has uncovered further
deficiencies in our understanding of shower modelling that must be resolved
before the mass composition can be inferred from .Comment: Replaced with published version. Added journal reference and DO
Reconstruction of inclined air showers detected with the Pierre Auger Observatory
We describe the method devised to reconstruct inclined cosmic-ray air showers
with zenith angles greater than detected with the surface array of
the Pierre Auger Observatory. The measured signals at the ground level are
fitted to muon density distributions predicted with atmospheric cascade models
to obtain the relative shower size as an overall normalization parameter. The
method is evaluated using simulated showers to test its performance. The energy
of the cosmic rays is calibrated using a sub-sample of events reconstructed
with both the fluorescence and surface array techniques. The reconstruction
method described here provides the basis of complementary analyses including an
independent measurement of the energy spectrum of ultra-high energy cosmic rays
using very inclined events collected by the Pierre Auger Observatory.Comment: 27 pages, 19 figures, accepted for publication in Journal of
Cosmology and Astroparticle Physics (JCAP
A search for point sources of EeV photons
Measurements of air showers made using the hybrid technique developed with
the fluorescence and surface detectors of the Pierre Auger Observatory allow a
sensitive search for point sources of EeV photons anywhere in the exposed sky.
A multivariate analysis reduces the background of hadronic cosmic rays. The
search is sensitive to a declination band from -85{\deg} to +20{\deg}, in an
energy range from 10^17.3 eV to 10^18.5 eV. No photon point source has been
detected. An upper limit on the photon flux has been derived for every
direction. The mean value of the energy flux limit that results from this,
assuming a photon spectral index of -2, is 0.06 eV cm^-2 s^-1, and no celestial
direction exceeds 0.25 eV cm^-2 s^-1. These upper limits constrain scenarios in
which EeV cosmic ray protons are emitted by non-transient sources in the
Galaxy.Comment: 28 pages, 10 figures, accepted for publication in The Astrophysical
Journa
Calibration of the Logarithmic-Periodic Dipole Antenna (LPDA) Radio Stations at the Pierre Auger Observatory using an Octocopter
An in-situ calibration of a logarithmic periodic dipole antenna with a
frequency coverage of 30 MHz to 80 MHz is performed. Such antennas are part of
a radio station system used for detection of cosmic ray induced air showers at
the Engineering Radio Array of the Pierre Auger Observatory, the so-called
Auger Engineering Radio Array (AERA). The directional and frequency
characteristics of the broadband antenna are investigated using a remotely
piloted aircraft (RPA) carrying a small transmitting antenna. The antenna
sensitivity is described by the vector effective length relating the measured
voltage with the electric-field components perpendicular to the incoming signal
direction. The horizontal and meridional components are determined with an
overall uncertainty of 7.4^{+0.9}_{-0.3} % and 10.3^{+2.8}_{-1.7} %
respectively. The measurement is used to correct a simulated response of the
frequency and directional response of the antenna. In addition, the influence
of the ground conductivity and permittivity on the antenna response is
simulated. Both have a negligible influence given the ground conditions
measured at the detector site. The overall uncertainties of the vector
effective length components result in an uncertainty of 8.8^{+2.1}_{-1.3} % in
the square root of the energy fluence for incoming signal directions with
zenith angles smaller than 60{\deg}.Comment: Published version. Updated online abstract only. Manuscript is
unchanged with respect to v2. 39 pages, 15 figures, 2 table
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