315 research outputs found
NegBio: a high-performance tool for negation and uncertainty detection in radiology reports
Negative and uncertain medical findings are frequent in radiology reports,
but discriminating them from positive findings remains challenging for
information extraction. Here, we propose a new algorithm, NegBio, to detect
negative and uncertain findings in radiology reports. Unlike previous
rule-based methods, NegBio utilizes patterns on universal dependencies to
identify the scope of triggers that are indicative of negation or uncertainty.
We evaluated NegBio on four datasets, including two public benchmarking corpora
of radiology reports, a new radiology corpus that we annotated for this work,
and a public corpus of general clinical texts. Evaluation on these datasets
demonstrates that NegBio is highly accurate for detecting negative and
uncertain findings and compares favorably to a widely-used state-of-the-art
system NegEx (an average of 9.5% improvement in precision and 5.1% in
F1-score).Comment: Final version. Accepted for publication in AMIA 2018 Informatics
Summit. 9 pages, 2 figures, 4 table
DeepLesion: Automated Deep Mining, Categorization and Detection of Significant Radiology Image Findings using Large-Scale Clinical Lesion Annotations
Extracting, harvesting and building large-scale annotated radiological image
datasets is a greatly important yet challenging problem. It is also the
bottleneck to designing more effective data-hungry computing paradigms (e.g.,
deep learning) for medical image analysis. Yet, vast amounts of clinical
annotations (usually associated with disease image findings and marked using
arrows, lines, lesion diameters, segmentation, etc.) have been collected over
several decades and stored in hospitals' Picture Archiving and Communication
Systems. In this paper, we mine and harvest one major type of clinical
annotation data - lesion diameters annotated on bookmarked images - to learn an
effective multi-class lesion detector via unsupervised and supervised deep
Convolutional Neural Networks (CNN). Our dataset is composed of 33,688
bookmarked radiology images from 10,825 studies of 4,477 unique patients. For
every bookmarked image, a bounding box is created to cover the target lesion
based on its measured diameters. We categorize the collection of lesions using
an unsupervised deep mining scheme to generate clustered pseudo lesion labels.
Next, we adopt a regional-CNN method to detect lesions of multiple categories,
regardless of missing annotations (normally only one lesion is annotated,
despite the presence of multiple co-existing findings). Our integrated mining,
categorization and detection framework is validated with promising empirical
results, as a scalable, universal or multi-purpose CAD paradigm built upon
abundant retrospective medical data. Furthermore, we demonstrate that detection
accuracy can be significantly improved by incorporating pseudo lesion labels
(e.g., Liver lesion/tumor, Lung nodule/tumor, Abdomen lesions, Chest lymph node
and others). This dataset will be made publicly available (under the open
science initiative)
ChestX-ray8: Hospital-scale Chest X-ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases
The chest X-ray is one of the most commonly accessible radiological
examinations for screening and diagnosis of many lung diseases. A tremendous
number of X-ray imaging studies accompanied by radiological reports are
accumulated and stored in many modern hospitals' Picture Archiving and
Communication Systems (PACS). On the other side, it is still an open question
how this type of hospital-size knowledge database containing invaluable imaging
informatics (i.e., loosely labeled) can be used to facilitate the data-hungry
deep learning paradigms in building truly large-scale high precision
computer-aided diagnosis (CAD) systems.
In this paper, we present a new chest X-ray database, namely "ChestX-ray8",
which comprises 108,948 frontal-view X-ray images of 32,717 unique patients
with the text-mined eight disease image labels (where each image can have
multi-labels), from the associated radiological reports using natural language
processing. Importantly, we demonstrate that these commonly occurring thoracic
diseases can be detected and even spatially-located via a unified
weakly-supervised multi-label image classification and disease localization
framework, which is validated using our proposed dataset. Although the initial
quantitative results are promising as reported, deep convolutional neural
network based "reading chest X-rays" (i.e., recognizing and locating the common
disease patterns trained with only image-level labels) remains a strenuous task
for fully-automated high precision CAD systems. Data download link:
https://nihcc.app.box.com/v/ChestXray-NIHCCComment: CVPR 2017 spotlight;V1: CVPR submission+supplementary; V2: Statistics
and benchmark results on published ChestX-ray14 dataset are updated in
Appendix B V3: Minor correction V4: new data download link upated:
https://nihcc.app.box.com/v/ChestXray-NIHCC V5: Update benchmark results on
the published data split in the appendi
Molecular orbital tomography beyond the plane wave approximation
The use of plane wave approximation in molecular orbital tomography via
high-order harmonic generation has been questioned since it was proposed, owing
to the fact that it ignores the essential property of the continuum wave
function. To address this problem, we develop a theory to retrieve the valence
molecular orbital directly utilizing molecular continuum wave function which
takes into account the influence of the parent ion field on the continuum
electrons. By transforming this wave function into momentum space, we show that
the mapping from the relevant molecular orbital to the high-order harmonic
spectra is still invertible. As an example, the highest orbital of
is successfully reconstructed and it shows good agreement with
the \emph{ab initio} orbital. Our work clarifies the long-standing controversy
and strengthens the theoretical basis of molecular orbital tomography
Probing rotational wave-packet dynamics with the structural minimum in high-order harmonic spectra
We investigate the alignment-dependent high-order harmonic spectrum generated
from nonadiabatically aligned molecules around the first half rotational
revival. It is found that the evolution of the molecular alignment is encoded
in the structural minima. To reveal the relation between the molecular
alignment and the structural minimum in the high-order harmonic spectrum, we
perform an analysis based on the two-center interference model. Our analysis
shows that the structural minimum position depends linearly on the inverse of
the alignment parameter . This linear relation indicates the
possibility of probing the rotational wave-packet dynamics by measuring the
spectral minima
Interference of high-order harmonics generated from molecules at different alignment angles
We theoretically investigate the interference effect of high-order harmonics
generated from molecules at different alignment angles. It is shown that the
interference of the harmonic emissions from molecules aligned at different
angles can significantly modulate the spectra and result in the anomalous
harmonic cutoffs observed in a recent experiment [ Nature Phys. 7, 822 (2011)
]. The shift of the spectral minimum position with decreasing the degree of
alignment is also explained by the interference effect of the harmonic
emissions.Comment: 6 pages,5 figures,journa
Influence of large permanent dipoles on molecular orbital tomography
The influence of large permanent dipoles on molecular orbital tomography via
high-order harmonic generation (HHG) is investigated in this work. It is found
that, owing to the modification of the angle-dependent ionization rate
resulting from the Stark shift, the one-side-recollision condition for the
tomographic imaging can not be satisfied even with the few-cycle driving
pulses. To overcome this problem, we employ a tailored driving pulse by adding
a weak low-frequency pulse to the few-cycle laser pulse to control the HHG
process and the recollision of the continuum electrons are effectively
restricted to only one side of the core. Then we carried out the orbital
reconstruction in both the length and velocity forms. The results show that,
the orbital structure can only be successfully reproduced by using the dipole
matrix elements projected perpendicular to the permanent dipole in both forms.Comment: 14 pages, 7 figure
Tomographic reconstruction of molecular orbitals with twofold mirror antisymmetry: overcoming the nodal plane problem
We propose a new method to overcome the nodal plane problem for the
tomographic reconstruction of molecular orbitals with twofold mirror
antisymmetry in the length form based on high-order harmonic generation. It is
shown that, by carrying out the reconstruction procedure in the rotating
laboratory frame using the component of the dipole moment parallel to the
electron recollision direction, the nodal plane problem is avoided and the
target orbital is successfully reconstructed. Moreover, it is found that, the
proposed method can completely avoid the additional artificial lobes found in
the results from the traditional method in the velocity form and therefore
provides a more reliable reproduction of the target orbital.Comment: 4 figure
The selection rules of high harmonic generation: the symmetries of molecules and laser fields
The selection rules of high harmonic generation (HHG) are investigated using
three-dimensional time-dependent density functional theory (TDDFT). From the
harmonic spectra obtained with various real molecules and different forms of
laser fields, several factors that contribute to selection rules are revealed.
Extending the targets to stereoscopic molecules, it is shown that the allowed
harmonics are dependent on the symmetries of the projections of molecules. For
laser fields, the symmetries contributing to the selection rules are discussed
according to Lissajous figures and their dynamical directivities. All the
phenomena are explained by the symmetry of the full time-dependent Hamiltonian
under a combined transformation. We present a systematic study on the selection
rules and propose an intuitive method for the judgment of allowed harmonic
orders, which can be extended to more complex molecules and various forms of
laser pulses
Time-dependent population imaging for solid high harmonic generation
We propose an intuitive method, called time-dependent population imaging
(TDPI), to map the dynamical processes of high harmonic generation (HHG) in
solids by solving the time-dependent Schr\"{o}dinger equation (TDSE). It is
shown that the real-time dynamical characteristics of HHG in solids, such as
the instantaneous photon energies of emitted harmonics, can be read directly
from the energy-resolved population oscillations of electrons in the TDPIs.
Meanwhile, the short and long trajectories of solid HHG are illustrated clearly
from TDPI. By using the TDPI, we also investigate the effects of
carrier-envelope phase (CEP) in few-cycle pulses and intuitively demonstrate
the HHG dynamics driven by two-color fields. Our results show that the TDPI
provides a powerful tool to study the ultrafast dynamics in strong fields for
various laser-solid configurations and gain an insight into HHG processes in
solids
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