5,144 research outputs found
Visual Feature Attribution using Wasserstein GANs
Attributing the pixels of an input image to a certain category is an
important and well-studied problem in computer vision, with applications
ranging from weakly supervised localisation to understanding hidden effects in
the data. In recent years, approaches based on interpreting a previously
trained neural network classifier have become the de facto state-of-the-art and
are commonly used on medical as well as natural image datasets. In this paper,
we discuss a limitation of these approaches which may lead to only a subset of
the category specific features being detected. To address this problem we
develop a novel feature attribution technique based on Wasserstein Generative
Adversarial Networks (WGAN), which does not suffer from this limitation. We
show that our proposed method performs substantially better than the
state-of-the-art for visual attribution on a synthetic dataset and on real 3D
neuroimaging data from patients with mild cognitive impairment (MCI) and
Alzheimer's disease (AD). For AD patients the method produces compellingly
realistic disease effect maps which are very close to the observed effects.Comment: Accepted to CVPR 201
Non-Engine Order Blade Vibration in a High Pressure Compressor
International audienceHigh amplitude levels of blade vibration have occurred on the first rotor of a multi stage high pressure compressor. The frequencies are not in resonance with harmonics of the rotor speed. The excitation is aerodynamically caused and associated with a rotating flow instability in the blade tip region of the first compressor stage. A vortex shedding mechanism can be interpreted as a rotating source to generate pressure waves. The source moves relative to the blade row at a fraction of the rotor speed, similar to the 'well known mechanism' of rotating stall. To investigate the unsteady flow field in the tip region of the rotor and its relation to the blade vibration, measurements of the pressure and velocity fluctuations in the vicinity of the blade tips are compared with blade vibrations. A calculation model of the spectral characteristics of the pressure fluctuations confirms the measured data. The effect is sensitive to aerodynamic blade loading so that a modification in the design could reduce the mechanism of the rotating excitation
Measuring cosmological bulk flows via the kinematic Sunyaev-Zeldovich effect in the upcoming cosmic microwave background maps
We propose a new method to measure the possible large-scale bulk flows in the
Universe from the cosmic microwave background (CMB) maps from the upcoming
missions, MAP and Planck. This can be done by studying the statistical
properties of the CMB temperature field at many X-ray cluster positions. At
each cluster position, the CMB temperature fluctuation will be a combination of
the Sunyaev-Zeldovich (SZ) kinematic and thermal components, the cosmological
fluctuations and the instrument noise term. When averaged over many such
clusters the last three will integrate down, whereas the first one will be
dominated by a possible bulk flow component. In particular, we propose to use
all-sky X-ray cluster catalogs that should (or could) be available soon from
X-ray satellites, and then to evaluate the dipole component of the CMB field at
the cluster positions. We show that for the MAP and Planck mission parameters
the dominant contributions to the dipole will be from the terms due to the SZ
kinematic effect produced by the bulk flow (the signal we seek) and the
instrument noise (the noise in our signal). Computing then the expected
signal-to-noise ratio for such measurement, we get that at the 95 % confidence
level the bulk flows on scales >100h^{-1} Mpc can be probed down to the
amplitude of km/sec with the MAP data and down to only 30 km/sec with
the Planck mission.Comment: Astrophysical Journal Letters, in pres
Scaling of polymers in aligned rods
We study the behavior of self avoiding polymers in a background of vertically
aligned rods that are either frozen into random positions or free to move
horizontally. We find that in both cases the polymer chains are highly
elongated, with vertical and horizontal size exponents that differ by a factor
of 3. Though these results are different than previous predictions, our results
are confirmed by detailed computer simulations.Comment: 4 pages, 4 figure
Gene identification for the cblD defect of vitamin B12 metabolism
Background Vitamin B12 (cobalamin) is an essential cofactor in several metabolic pathways. Intracellular conversion of cobalamin to its two coenzymes, adenosylcobalamin in mitochondria and methylcobalamin in the cytoplasm, is necessary for the homeostasis of methylmalonic acid and homocysteine. Nine defects of intracellular cobalamin metabolism have been defined by means of somatic complementation analysis. One of these defects, the cblD defect, can cause isolated methylmalonic aciduria, isolated homocystinuria, or both. Affected persons present with multisystem clinical abnormalities, including developmental, hematologic, neurologic, and metabolic findings. The gene responsible for the cblD defect has not been identified.
Methods We studied seven patients with the cblD defect, and skin fibroblasts from each were investigated in cell culture. Microcell-mediated chromosome transfer and refined genetic mapping were used to localize the responsible gene. This gene was transfected into cblD fibroblasts to test for the rescue of adenosylcobalamin and methylcobalamin synthesis.
Results The cblD gene was localized to human chromosome 2q23.2, and a candidate gene, designated MMADHC (methylmalonic aciduria, cblD type, and homocystinuria), was identified in this region. Transfection of wild-type MMADHC rescued the cellular phenotype, and the functional importance of mutant alleles was shown by means of transfection with mutant constructs. The predicted MMADHC protein has sequence homology with a bacterial ATP-binding cassette transporter and contains a putative cobalamin binding motif and a putative mitochondrial targeting sequence.
Conclusions Mutations in a gene we designated MMADHC are responsible for the cblD defect in vitamin B12 metabolism. Various mutations are associated with each of the three biochemical phenotypes of the disorder
Comparison of organic apricot production under all-season rain protection, seasonal rain protection and without rain protection
Comparison of organic apricot production under all-season rain protection, seasonal rain protection and without rain protection
Right for the Wrong Reason: Can Interpretable ML Techniques Detect Spurious Correlations?
While deep neural network models offer unmatched classification performance,
they are prone to learning spurious correlations in the data. Such dependencies
on confounding information can be difficult to detect using performance metrics
if the test data comes from the same distribution as the training data.
Interpretable ML methods such as post-hoc explanations or inherently
interpretable classifiers promise to identify faulty model reasoning. However,
there is mixed evidence whether many of these techniques are actually able to
do so. In this paper, we propose a rigorous evaluation strategy to assess an
explanation technique's ability to correctly identify spurious correlations.
Using this strategy, we evaluate five post-hoc explanation techniques and one
inherently interpretable method for their ability to detect three types of
artificially added confounders in a chest x-ray diagnosis task. We find that
the post-hoc technique SHAP, as well as the inherently interpretable Attri-Net
provide the best performance and can be used to reliably identify faulty model
behavior
Fine-scale spatial and temporal acoustic occurrence of island-associated odontocetes near a mid-oceanic atoll in the northern Indian Ocean
© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Panicker, D., Baumgartner, M. F., & Stafford, K. M. Fine-scale spatial and temporal acoustic occurrence of island-associated odontocetes near a mid-oceanic atoll in the northern Indian Ocean. Marine Ecology Progress Series, 683, (2022): 195–208, https://doi.org/10.3354/meps13947.Temporal patterns of oceanic predators can provide valuable information on both lunar and diel influences not just on the distributions of these predators, but also on prey patches that are often difficult to study. Mid-oceanic island chains in the northern Indian Ocean have high odontocete occurrence, but the ecology of these animals is not well characterized. We investigated fine-scale spatial and temporal patterns of island-associated odontocetes using passive acoustic monitoring from January 2019 to January 2020 around Kavaratti Island, Lakshadweep, India. Based on opportunistic recordings in the presence of odontocetes, the majority of the detected whistles were likely made by spinner dolphins Stenella longirostris. We identified a resident population whose whistle occurrence was significantly influenced by month, site, and diel and lunar cycles. More acoustic detections were made in the northeast monsoon month of November and fewer during pre-monsoon and southwest monsoon periods. Distinct day-night differences along with fine-scale temporal variability were also observed, suggesting that delphinids use nearshore waters as a daytime resting habitat. Odontocete detections were highest during the new moon period and lowest during the first quarter phase. Detection rates were higher on the south side of the island. Our study shows that solar and lunar cycles modulate odontocete vocal occurrence, presumably through influences on their prey. Similarities of odontocete occurrence around Lakshadweep to other mid-oceanic island chains suggests that an island-associated micronekton community may exist around Lakshadweep that may also be important to other pelagic species targeted by local fisheries.Funding was provided by the Office of Naval Research Marine Mammal Biology Program, USA, under grant N000141812795.
We thank Ajith Kumar, the National Centre for Biological Sciences and Idrees Babu for in-country support
SonoNet: Real-Time Detection and Localisation of Fetal Standard Scan Planes in Freehand Ultrasound
Identifying and interpreting fetal standard scan planes during 2D ultrasound
mid-pregnancy examinations are highly complex tasks which require years of
training. Apart from guiding the probe to the correct location, it can be
equally difficult for a non-expert to identify relevant structures within the
image. Automatic image processing can provide tools to help experienced as well
as inexperienced operators with these tasks. In this paper, we propose a novel
method based on convolutional neural networks which can automatically detect 13
fetal standard views in freehand 2D ultrasound data as well as provide a
localisation of the fetal structures via a bounding box. An important
contribution is that the network learns to localise the target anatomy using
weak supervision based on image-level labels only. The network architecture is
designed to operate in real-time while providing optimal output for the
localisation task. We present results for real-time annotation, retrospective
frame retrieval from saved videos, and localisation on a very large and
challenging dataset consisting of images and video recordings of full clinical
anomaly screenings. We found that the proposed method achieved an average
F1-score of 0.798 in a realistic classification experiment modelling real-time
detection, and obtained a 90.09% accuracy for retrospective frame retrieval.
Moreover, an accuracy of 77.8% was achieved on the localisation task.Comment: 12 pages, 8 figures, published in IEEE Transactions in Medical
Imagin
Multi-Atlas Segmentation using Partially Annotated Data: Methods and Annotation Strategies
Multi-atlas segmentation is a widely used tool in medical image analysis,
providing robust and accurate results by learning from annotated atlas
datasets. However, the availability of fully annotated atlas images for
training is limited due to the time required for the labelling task.
Segmentation methods requiring only a proportion of each atlas image to be
labelled could therefore reduce the workload on expert raters tasked with
annotating atlas images. To address this issue, we first re-examine the
labelling problem common in many existing approaches and formulate its solution
in terms of a Markov Random Field energy minimisation problem on a graph
connecting atlases and the target image. This provides a unifying framework for
multi-atlas segmentation. We then show how modifications in the graph
configuration of the proposed framework enable the use of partially annotated
atlas images and investigate different partial annotation strategies. The
proposed method was evaluated on two Magnetic Resonance Imaging (MRI) datasets
for hippocampal and cardiac segmentation. Experiments were performed aimed at
(1) recreating existing segmentation techniques with the proposed framework and
(2) demonstrating the potential of employing sparsely annotated atlas data for
multi-atlas segmentation
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