In this paper, we present a new information-theoretic approach to image segmentation. We cast the segmentation problem as the maximization of the mutual information between the region labels and the ...image pixel intensities, subject to a constraint on the total length of the region boundaries. We assume that the probability densities associated with the image pixel intensities within each region are completely unknown a priori, and we formulate the problem based on nonparametric density estimates. Due to the nonparametric structure, our method does not require the image regions to have a particular type of probability distribution and does not require the extraction and use of a particular statistic. We solve the information-theoretic optimization problem by deriving the associated gradient flows and applying curve evolution techniques. We use level-set methods to implement the resulting evolution. The experimental results based on both synthetic and real images demonstrate that the proposed technique can solve a variety of challenging image segmentation problems. Furthermore, our method, which does not require any training, performs as good as methods based on training.
We present a source localization method based on a sparse representation of sensor measurements with an overcomplete basis composed of samples from the array manifold. We enforce sparsity by imposing ...penalties based on the /spl lscr//sub 1/-norm. A number of recent theoretical results on sparsifying properties of /spl lscr//sub 1/ penalties justify this choice. Explicitly enforcing the sparsity of the representation is motivated by a desire to obtain a sharp estimate of the spatial spectrum that exhibits super-resolution. We propose to use the singular value decomposition (SVD) of the data matrix to summarize multiple time or frequency samples. Our formulation leads to an optimization problem, which we solve efficiently in a second-order cone (SOC) programming framework by an interior point implementation. We propose a grid refinement method to mitigate the effects of limiting estimates to a grid of spatial locations and introduce an automatic selection criterion for the regularization parameter involved in our approach. We demonstrate the effectiveness of the method on simulated data by plots of spatial spectra and by comparing the estimator variance to the Crame/spl acute/r-Rao bound (CRB). We observe that our approach has a number of advantages over other source localization techniques, including increased resolution, improved robustness to noise, limitations in data quantity, and correlation of the sources, as well as not requiring an accurate initialization.
Abstract
Motivation
Identification of interactions between bioactive small molecules and target proteins is crucial for novel drug discovery, drug repurposing and uncovering off-target effects. Due ...to the tremendous size of the chemical space, experimental bioactivity screening efforts require the aid of computational approaches. Although deep learning models have been successful in predicting bioactive compounds, effective and comprehensive featurization of proteins, to be given as input to deep neural networks, remains a challenge.
Results
Here, we present a novel protein featurization approach to be used in deep learning-based compound–target protein binding affinity prediction. In the proposed method, multiple types of protein features such as sequence, structural, evolutionary and physicochemical properties are incorporated within multiple 2D vectors, which is then fed to state-of-the-art pairwise input hybrid deep neural networks to predict the real-valued compound–target protein interactions. The method adopts the proteochemometric approach, where both the compound and target protein features are used at the input level to model their interaction. The whole system is called MDeePred and it is a new method to be used for the purposes of computational drug discovery and repositioning. We evaluated MDeePred on well-known benchmark datasets and compared its performance with the state-of-the-art methods. We also performed in vitro comparative analysis of MDeePred predictions with selected kinase inhibitors’ action on cancer cells. MDeePred is a scalable method with sufficiently high predictive performance. The featurization approach proposed here can also be utilized for other protein-related predictive tasks.
Availability and implementation
The source code, datasets, additional information and user instructions of MDeePred are available at https://github.com/cansyl/MDeePred.
Supplementary information
Supplementary data are available at Bioinformatics online.
A
bstract
We present results of the Relic Axion Dark-Matter Exploratory Setup (RADES), a detector which is part of the CERN Axion Solar Telescope (CAST), searching for axion dark matter in the 34.67
...μ
eV mass range. A radio frequency cavity consisting of 5 sub-cavities coupled by inductive irises took physics data inside the CAST dipole magnet for the first time using this filter-like haloscope geometry. An exclusion limit with a 95% credibility level on the axion-photon coupling constant of g
aγ
≳ 4 × 10
−
13
GeV
−
1
over a mass range of 34
.
6738
μ
eV
< m
a
<
34
.
6771
μ
eV is set. This constitutes a significant improvement over the current strongest limit set by CAST at this mass and is at the same time one of the most sensitive direct searches for an axion dark matter candidate above the mass of 25
μ
eV. The results also demonstrate the feasibility of exploring a wider mass range around the value probed by CAST-RADES in this work using similar coherent resonant cavities.
Sparse signal representations and approximations from overcomplete dictionaries have become an invaluable tool recently. In this paper, we develop a new, heuristic, graph-structured, sparse signal ...representation algorithm for overcomplete dictionaries that can be decomposed into subdictionaries and whose dictionary elements can be arranged in a hierarchy. Around this algorithm, we construct a methodology for advanced image formation in wide-angle synthetic aperture radar (SAR), defining an approach for joint anisotropy characterization and image formation. Additionally, we develop a coordinate descent method for jointly optimizing a parameterized dictionary and recovering a sparse representation using that dictionary. The motivation is to characterize a phenomenon in wide-angle SAR that has not been given much attention before: migratory scattering centers, i.e., scatterers whose apparent spatial location depends on aspect angle. Finally, we address the topic of recovering solutions that are sparse in more than one objective domain by introducing a suitable sparsifying cost function. We encode geometric objectives into SAR image formation through sparsity in two domains, including the normal parameter space of the Hough transform.
Search for chameleons with CAST Anastassopoulos, V.; Arik, M.; Aune, S. ...
Physics letters. B,
10/2015, Volume:
749, Issue:
C
Journal Article
Peer reviewed
Open access
In this work we present a search for (solar) chameleons with the CERN Axion Solar Telescope (CAST). This novel experimental technique, in the field of dark energy research, exploits both the ...chameleon coupling to matter (βm) and to photons (βγ) via the Primakoff effect. By reducing the X-ray detection energy threshold used for axions from 1 keV to 400 eV CAST became sensitive to the converted solar chameleon spectrum which peaks around 600 eV. Even though we have not observed any excess above background, we can provide a 95% C.L. limit for the coupling strength of chameleons to photons of βγ≲1011 for 1<βm<106.
Display omitted
•Evaluation framework for coronary artery lumen segmentation and stenosis grading.•Description of the datasets and creation of reference standard is given.•Standardized evaluation ...measures are defined.•Results on current 11 submissions are presented.•Framework is open for new submissions.
Though conventional coronary angiography (CCA) has been the standard of reference for diagnosing coronary artery disease in the past decades, computed tomography angiography (CTA) has rapidly emerged, and is nowadays widely used in clinical practice. Here, we introduce a standardized evaluation framework to reliably evaluate and compare the performance of the algorithms devised to detect and quantify the coronary artery stenoses, and to segment the coronary artery lumen in CTA data. The objective of this evaluation framework is to demonstrate the feasibility of dedicated algorithms to: (1) (semi-)automatically detect and quantify stenosis on CTA, in comparison with quantitative coronary angiography (QCA) and CTA consensus reading, and (2) (semi-)automatically segment the coronary lumen on CTA, in comparison with expert’s manual annotation. A database consisting of 48 multicenter multivendor cardiac CTA datasets with corresponding reference standards are described and made available. The algorithms from 11 research groups were quantitatively evaluated and compared. The results show that (1) some of the current stenosis detection/quantification algorithms may be used for triage or as a second-reader in clinical practice, and that (2) automatic lumen segmentation is possible with a precision similar to that obtained by experts. The framework is open for new submissions through the website, at http://coronary.bigr.nl/stenoses/.
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