514 research outputs found
Weakly-supervised learning for image-based classification of primary melanomas into genomic immune subgroups
Determining early-stage prognostic markers and stratifying patients for effective treatment are two key challenges for improving outcomes for melanoma patients. Previous studies have used tumour transcriptome data to stratify patients into immune subgroups, which were associated with differential melanoma specific survival and potential treatment strategies. However, acquiring transcriptome data is a time-consuming and costly process. Moreover, it is not routinely used in the current clinical workflow. Here we attempt to overcome this by developing deep learning models to classify gigapixel H&E stained pathology slides, which are well established in clinical workflows, into these immune subgroups. Previous subtyping approaches have employed supervised learning which requires fully annotated data, or have only examined single genetic mutations in melanoma patients. We leverage a multiple-instance learning approach, which only requires slide-level labels and uses an attention mechanism to highlight regions of high importance to the classification. Moreover, we show that pathology-specific self-supervised models generate better representations compared to pathology-agnostic models for improving our model performance, achieving a mean AUC of 0.76 for classifying histopathology images as high or low immune subgroups. We anticipate that this method may allow us to find new biomarkers of high importance and could act as a tool for clinicians to infer the immune landscape of tumours and stratify patients, without needing to carry out additional expensive genetic tests
Nonlinear Integer Programming
Research efforts of the past fifty years have led to a development of linear
integer programming as a mature discipline of mathematical optimization. Such a
level of maturity has not been reached when one considers nonlinear systems
subject to integrality requirements for the variables. This chapter is
dedicated to this topic.
The primary goal is a study of a simple version of general nonlinear integer
problems, where all constraints are still linear. Our focus is on the
computational complexity of the problem, which varies significantly with the
type of nonlinear objective function in combination with the underlying
combinatorial structure. Numerous boundary cases of complexity emerge, which
sometimes surprisingly lead even to polynomial time algorithms.
We also cover recent successful approaches for more general classes of
problems. Though no positive theoretical efficiency results are available, nor
are they likely to ever be available, these seem to be the currently most
successful and interesting approaches for solving practical problems.
It is our belief that the study of algorithms motivated by theoretical
considerations and those motivated by our desire to solve practical instances
should and do inform one another. So it is with this viewpoint that we present
the subject, and it is in this direction that we hope to spark further
research.Comment: 57 pages. To appear in: M. J\"unger, T. Liebling, D. Naddef, G.
Nemhauser, W. Pulleyblank, G. Reinelt, G. Rinaldi, and L. Wolsey (eds.), 50
Years of Integer Programming 1958--2008: The Early Years and State-of-the-Art
Surveys, Springer-Verlag, 2009, ISBN 354068274
Walking Behavior in Technicolored GUTs
There exist two ways to obtain walk behavior: assuming a large number of
technifermions in the fundamental representation of the technicolor (TC) gauge
group, or a small number of technifermions, assuming that these fermions are in
higher-dimensional representations of the TC group. We propose a scheme to
obtain the walking behavior based on technicolored GUTs (TGUTs), where
elementary scalars with the TC degree of freedom may remain in the theory after
the GUT symmetry breaking.Comment: 11 pages, 1 figur
Nuclear Alpha-Particle Condensates
The -particle condensate in nuclei is a novel state described by a
product state of 's, all with their c.o.m. in the lowest 0S orbit. We
demonstrate that a typical -particle condensate is the Hoyle state
( MeV, state in C), which plays a crucial role for
the synthesis of C in the universe. The influence of antisymmentrization
in the Hoyle state on the bosonic character of the particle is
discussed in detail. It is shown to be weak. The bosonic aspects in the Hoyle
state, therefore, are predominant. It is conjectured that -particle
condensate states also exist in heavier nuclei, like O,
Ne, etc. For instance the state of O at MeV
is identified from a theoretical analysis as being a strong candidate of a
condensate. The calculated small width (34 keV) of ,
consistent with data, lends credit to the existence of heavier Hoyle-analogue
states. In non-self-conjugated nuclei such as B and C, we discuss
candidates for the product states of clusters, composed of 's,
triton's, and neutrons etc. The relationship of -particle condensation
in finite nuclei to quartetting in symmetric nuclear matter is investigated
with the help of an in-medium modified four-nucleon equation. A nonlinear order
parameter equation for quartet condensation is derived and solved for
particle condensation in infinite nuclear matter. The strong qualitative
difference with the pairing case is pointed out.Comment: 71 pages, 41 figures, review article, to be published in "Cluster in
Nuclei (Lecture Notes in Physics) - Vol.2 -", ed. by C. Beck,
(Springer-Verlag, Berlin, 2011
Magnetic Field Generation in Stars
Enormous progress has been made on observing stellar magnetism in stars from
the main sequence through to compact objects. Recent data have thrown into
sharper relief the vexed question of the origin of stellar magnetic fields,
which remains one of the main unanswered questions in astrophysics. In this
chapter we review recent work in this area of research. In particular, we look
at the fossil field hypothesis which links magnetism in compact stars to
magnetism in main sequence and pre-main sequence stars and we consider why its
feasibility has now been questioned particularly in the context of highly
magnetic white dwarfs. We also review the fossil versus dynamo debate in the
context of neutron stars and the roles played by key physical processes such as
buoyancy, helicity, and superfluid turbulence,in the generation and stability
of neutron star fields.
Independent information on the internal magnetic field of neutron stars will
come from future gravitational wave detections. Thus we maybe at the dawn of a
new era of exciting discoveries in compact star magnetism driven by the opening
of a new, non-electromagnetic observational window.
We also review recent advances in the theory and computation of
magnetohydrodynamic turbulence as it applies to stellar magnetism and dynamo
theory. These advances offer insight into the action of stellar dynamos as well
as processes whichcontrol the diffusive magnetic flux transport in stars.Comment: 41 pages, 7 figures. Invited review chapter on on magnetic field
generation in stars to appear in Space Science Reviews, Springe
The exposure of the hybrid detector of the Pierre Auger Observatory
The Pierre Auger Observatory is a detector for ultra-high energy cosmic rays.
It consists of a surface array to measure secondary particles at ground level
and a fluorescence detector to measure the development of air showers in the
atmosphere above the array. The "hybrid" detection mode combines the
information from the two subsystems. We describe the determination of the
hybrid exposure for events observed by the fluorescence telescopes in
coincidence with at least one water-Cherenkov detector of the surface array. A
detailed knowledge of the time dependence of the detection operations is
crucial for an accurate evaluation of the exposure. We discuss the relevance of
monitoring data collected during operations, such as the status of the
fluorescence detector, background light and atmospheric conditions, that are
used in both simulation and reconstruction.Comment: Paper accepted by Astroparticle Physic
Peabody Picture Vocabulary Test-III: Normative data for Spanish-speaking pediatric population
OBJECTIVE: To generate normative data for the Peabody Picture Vocabulary Test-III (PPVT-III) in Spanish-speaking
pediatric populations.
METHOD: The sample consisted of 4,373 healthy children from nine countries in Latin America (Chile, Cuba, Ecuador,
Honduras, Guatemala, Mexico, Paraguay, Peru, and Puerto Rico) and Spain. Each participant was administered the PPVT-III
as part of a larger neuropsychological battery. PPVT-III scores were normed using multiple linear regressions and standard
deviations of residual values. Age, age2, sex, and mean level of parental education (MLPE) were included as predictors in
the analyses.
RESULTS: The final multiple linear regression models showed main effects for age in all countries, such that scores increased
linearly as a function of age. In addition, age2 had a significant effect in all countries, except Guatemala and Paraguay. Models
showed that children whose parent(s) had a MLPE >12 years obtained higher scores compared to children whose parent(s)
had a MLPE ≤12 years in all countries, except for Cuba, Peru, and Puerto Rico. Sex affected scores for Chile, Ecuador,
Guatemala, Mexico, and Spain.
CONCLUSIONS: This is the largest Spanish-speaking pediatric normative study in the world, and it will allow neuropsychologists from these countries to have a more accurate interpretation of the PPVT-III when used in pediatric populations
Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment
This paper describes an analysis of the angular distribution of W->enu and
W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with
the ATLAS detector at the LHC in 2010, corresponding to an integrated
luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and
the missing transverse energy, the W decay angular distribution projected onto
the transverse plane is obtained and analysed in terms of helicity fractions
f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV
and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw
> 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour,
are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017
+/- 0.030, where the first uncertainties are statistical, and the second
include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables,
revised author list, matches European Journal of Physics C versio
Observation of a new chi_b state in radiative transitions to Upsilon(1S) and Upsilon(2S) at ATLAS
The chi_b(nP) quarkonium states are produced in proton-proton collisions at
the Large Hadron Collider (LHC) at sqrt(s) = 7 TeV and recorded by the ATLAS
detector. Using a data sample corresponding to an integrated luminosity of 4.4
fb^-1, these states are reconstructed through their radiative decays to
Upsilon(1S,2S) with Upsilon->mu+mu-. In addition to the mass peaks
corresponding to the decay modes chi_b(1P,2P)->Upsilon(1S)gamma, a new
structure centered at a mass of 10.530+/-0.005 (stat.)+/-0.009 (syst.) GeV is
also observed, in both the Upsilon(1S)gamma and Upsilon(2S)gamma decay modes.
This is interpreted as the chi_b(3P) system.Comment: 5 pages plus author list (18 pages total), 2 figures, 1 table,
corrected author list, matches final version in Physical Review Letter
Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS
We present the results of a search for new, heavy particles that decay at a
significant distance from their production point into a final state containing
charged hadrons in association with a high-momentum muon. The search is
conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV
and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS
detector operating at the Large Hadron Collider. Production of such particles
is expected in various scenarios of physics beyond the standard model. We
observe no signal and place limits on the production cross-section of
supersymmetric particles in an R-parity-violating scenario as a function of the
neutralino lifetime. Limits are presented for different squark and neutralino
masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final
version to appear in Physics Letters
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