50 research outputs found
CheXpert: A Large Chest Radiograph Dataset with Uncertainty Labels and Expert Comparison
Large, labeled datasets have driven deep learning methods to achieve
expert-level performance on a variety of medical imaging tasks. We present
CheXpert, a large dataset that contains 224,316 chest radiographs of 65,240
patients. We design a labeler to automatically detect the presence of 14
observations in radiology reports, capturing uncertainties inherent in
radiograph interpretation. We investigate different approaches to using the
uncertainty labels for training convolutional neural networks that output the
probability of these observations given the available frontal and lateral
radiographs. On a validation set of 200 chest radiographic studies which were
manually annotated by 3 board-certified radiologists, we find that different
uncertainty approaches are useful for different pathologies. We then evaluate
our best model on a test set composed of 500 chest radiographic studies
annotated by a consensus of 5 board-certified radiologists, and compare the
performance of our model to that of 3 additional radiologists in the detection
of 5 selected pathologies. On Cardiomegaly, Edema, and Pleural Effusion, the
model ROC and PR curves lie above all 3 radiologist operating points. We
release the dataset to the public as a standard benchmark to evaluate
performance of chest radiograph interpretation models.
The dataset is freely available at
https://stanfordmlgroup.github.io/competitions/chexpert .Comment: Published in AAAI 201
Inferring stabilizing mutations from protein phylogenies : application to influenza hemagglutinin
One selection pressure shaping sequence evolution is the requirement that a protein fold with sufficient stability to perform its biological functions. We present a conceptual framework that explains how this requirement causes the probability that a particular amino acid mutation is fixed during evolution to depend on its effect on protein stability. We mathematically formalize this framework to develop a Bayesian approach for inferring the stability effects of individual mutations from homologous protein sequences of known phylogeny. This approach is able to predict published experimentally measured mutational stability effects (ΔΔG values) with an accuracy that exceeds both a state-of-the-art physicochemical modeling program and the sequence-based consensus approach. As a further test, we use our phylogenetic inference approach to predict stabilizing mutations to influenza hemagglutinin. We introduce these mutations into a temperature-sensitive influenza virus with a defect in its hemagglutinin gene and experimentally demonstrate that some of the mutations allow the virus to grow at higher temperatures. Our work therefore describes a powerful new approach for predicting stabilizing mutations that can be successfully applied even to large, complex proteins such as hemagglutinin. This approach also makes a mathematical link between phylogenetics and experimentally measurable protein properties, potentially paving the way for more accurate analyses of molecular evolution
Swift follow-up observations of candidate gravitational-wave transient events
We present the first multi-wavelength follow-up observations of two candidate
gravitational-wave (GW) transient events recorded by LIGO and Virgo in their
2009-2010 science run. The events were selected with low latency by the network
of GW detectors and their candidate sky locations were observed by the Swift
observatory. Image transient detection was used to analyze the collected
electromagnetic data, which were found to be consistent with background.
Off-line analysis of the GW data alone has also established that the selected
GW events show no evidence of an astrophysical origin; one of them is
consistent with background and the other one was a test, part of a "blind
injection challenge". With this work we demonstrate the feasibility of rapid
follow-ups of GW transients and establish the sensitivity improvement joint
electromagnetic and GW observations could bring. This is a first step toward an
electromagnetic follow-up program in the regime of routine detections with the
advanced GW instruments expected within this decade. In that regime
multi-wavelength observations will play a significant role in completing the
astrophysical identification of GW sources. We present the methods and results
from this first combined analysis and discuss its implications in terms of
sensitivity for the present and future instruments.Comment: Submitted for publication 2012 May 25, accepted 2012 October 25,
published 2012 November 21, in ApJS, 203, 28 (
http://stacks.iop.org/0067-0049/203/28 ); 14 pages, 3 figures, 6 tables;
LIGO-P1100038; Science summary at
http://www.ligo.org/science/Publication-S6LVSwift/index.php ; Public access
area to figures, tables at
https://dcc.ligo.org/cgi-bin/DocDB/ShowDocument?docid=p110003
Search for gravitational waves associated with the InterPlanetary Network short gamma ray bursts
We outline the scientific motivation behind a search for gravitational waves
associated with short gamma ray bursts detected by the InterPlanetary Network
(IPN) during LIGO's fifth science run and Virgo's first science run. The IPN
localisation of short gamma ray bursts is limited to extended error boxes of
different shapes and sizes and a search on these error boxes poses a series of
challenges for data analysis. We will discuss these challenges and outline the
methods to optimise the search over these error boxes.Comment: Methods paper; Proceedings for Eduardo Amaldi 9 Conference on
Gravitational Waves, July 2011, Cardiff, U
A First Search for coincident Gravitational Waves and High Energy Neutrinos using LIGO, Virgo and ANTARES data from 2007
We present the results of the first search for gravitational wave bursts
associated with high energy neutrinos. Together, these messengers could reveal
new, hidden sources that are not observed by conventional photon astronomy,
particularly at high energy. Our search uses neutrinos detected by the
underwater neutrino telescope ANTARES in its 5 line configuration during the
period January - September 2007, which coincided with the fifth and first
science runs of LIGO and Virgo, respectively. The LIGO-Virgo data were analysed
for candidate gravitational-wave signals coincident in time and direction with
the neutrino events. No significant coincident events were observed. We place
limits on the density of joint high energy neutrino - gravitational wave
emission events in the local universe, and compare them with densities of
merger and core-collapse events.Comment: 19 pages, 8 figures, science summary page at
http://www.ligo.org/science/Publication-S5LV_ANTARES/index.php. Public access
area to figures, tables at
https://dcc.ligo.org/cgi-bin/DocDB/ShowDocument?docid=p120000
First Low-Latency LIGO+Virgo Search for Binary Inspirals and their Electromagnetic Counterparts
Aims. The detection and measurement of gravitational-waves from coalescing
neutron-star binary systems is an important science goal for ground-based
gravitational-wave detectors. In addition to emitting gravitational-waves at
frequencies that span the most sensitive bands of the LIGO and Virgo detectors,
these sources are also amongst the most likely to produce an electromagnetic
counterpart to the gravitational-wave emission. A joint detection of the
gravitational-wave and electromagnetic signals would provide a powerful new
probe for astronomy.
Methods. During the period between September 19 and October 20, 2010, the
first low-latency search for gravitational-waves from binary inspirals in LIGO
and Virgo data was conducted. The resulting triggers were sent to
electromagnetic observatories for followup. We describe the generation and
processing of the low-latency gravitational-wave triggers. The results of the
electromagnetic image analysis will be described elsewhere.
Results. Over the course of the science run, three gravitational-wave
triggers passed all of the low-latency selection cuts. Of these, one was
followed up by several of our observational partners. Analysis of the
gravitational-wave data leads to an estimated false alarm rate of once every
6.4 days, falling far short of the requirement for a detection based solely on
gravitational-wave data.Comment: 13 pages, 13 figures. For a repository of data used in the
publication, go to:
http://dcc.ligo.org/cgi-bin/DocDB/ShowDocument?docid=P1100065 Also see the
announcement for this paper on ligo.org at:
http://www.ligo.org/science/Publication-S6CBCLowLatency
Henry Versus Thompson Approach for Fixation of Proximal Third Radial Shaft Fractures: A Multicenter Study
Objective:
To compare the volar Henry and dorsal Thompson approaches with respect to outcomes and complications for proximal third radial shaft fractures.
Design:
Multicenter retrospective cohort study.
Patients/Participants:
Patients with proximal third radial shaft fractures ± associated ulna fractures (OTA/AO 2R1 ± 2U1) treated operatively at 11 trauma centers were included.
Intervention:
Patient demographics and injury, fracture, and surgical data were recorded. Final range of motion and complications of infection, neurologic injury, compartment syndrome, and malunion/nonunion were compared for volar versus dorsal approaches.
Main Outcome:
The main outcome was difference in complications between patients treated with volar versus dorsal approach.
Results:
At an average follow-up of 292 days, 202 patients (range, 18–84 years) with proximal third radial shaft fractures were followed through union or nonunion. One hundred fifty-five patients were fixed via volar and 47 via dorsal approach. Patients treated via dorsal approach had fractures that were on average 16 mm more proximal than those approached volarly, which did not translate to more screw fixation proximal to the fracture. Complications occurred in 11% of volar and 21% of dorsal approaches with no statistical difference.
Conclusions:
There was no statistical difference in complication rates between volar and dorsal approaches. Specifically, fixation to the level of the tuberosity is safely accomplished via the volar approach. This series demonstrates the safety of the volar Henry approach for proximal third radial shaft fractures
Einstein@Home all-sky search for periodic gravitational waves in LIGO S5 data
This paper presents results of an all-sky searches for periodic gravitational
waves in the frequency range [50, 1190] Hz and with frequency derivative ranges
of [-2 x 10^-9, 1.1 x 10^-10] Hz/s for the fifth LIGO science run (S5). The
novelty of the search lies in the use of a non-coherent technique based on the
Hough-transform to combine the information from coherent searches on timescales
of about one day. Because these searches are very computationally intensive,
they have been deployed on the Einstein@Home distributed computing project
infrastructure. The search presented here is about a factor 3 more sensitive
than the previous Einstein@Home search in early S5 LIGO data. The
post-processing has left us with eight surviving candidates. We show that
deeper follow-up studies rule each of them out. Hence, since no statistically
significant gravitational wave signals have been detected, we report upper
limits on the intrinsic gravitational wave amplitude h0. For example, in the
0.5 Hz-wide band at 152.5 Hz, we can exclude the presence of signals with h0
greater than 7.6 x 10^-25 with a 90% confidence level.Comment: 29 pages, 14 figures, 6 tables. Science summary page at
http://www.ligo.org/science/Publication-FullS5EatH/index.php ; Public access
area to figures and tables at
https://dcc.ligo.org/cgi-bin/DocDB/ShowDocument?docid=p120002
The characterization of Virgo data and its impact on gravitational-wave searches
Between 2007 and 2010 Virgo collected data in coincidence with the LIGO and
GEO gravitational-wave (GW) detectors. These data have been searched for GWs
emitted by cataclysmic phenomena in the universe, by non-axisymmetric rotating
neutron stars or from a stochastic background in the frequency band of the
detectors. The sensitivity of GW searches is limited by noise produced by the
detector or its environment. It is therefore crucial to characterize the
various noise sources in a GW detector. This paper reviews the Virgo detector
noise sources, noise propagation, and conversion mechanisms which were
identified in the three first Virgo observing runs. In many cases, these
investigations allowed us to mitigate noise sources in the detector, or to
selectively flag noise events and discard them from the data. We present
examples from the joint LIGO-GEO-Virgo GW searches to show how well noise
transients and narrow spectral lines have been identified and excluded from the
Virgo data. We also discuss how detector characterization can improve the
astrophysical reach of gravitational-wave searches.Comment: 50 pages, 12 figures, 5 table
Upper limits on a stochastic gravitational-wave background using LIGO and Virgo interferometers at 600-1000 Hz
A stochastic background of gravitational waves is expected to arise from a
superposition of many incoherent sources of gravitational waves, of either
cosmological or astrophysical origin. This background is a target for the
current generation of ground-based detectors. In this article we present the
first joint search for a stochastic background using data from the LIGO and
Virgo interferometers. In a frequency band of 600-1000 Hz, we obtained a 95%
upper limit on the amplitude of , of , assuming a value of the Hubble parameter
of . These new limits are a factor of seven better than the
previous best in this frequency band.Comment: 29 pages, 6 figures. For a repository of data used in the
publication, please see
https://dcc.ligo.org/cgi-bin/DocDB/ShowDocument?docid=22210. Also see the
announcement for this paper at
http://www.ligo.org/science/Publication-S5VSR1StochIso