5,719 research outputs found
Balson: Bayesian least squares optimization with nonnegative L1-Norm constraint
© 2018 IEEE. A Bayesian approach termed the BAyesian Least Squares Optimization with Nonnegative L1-norm constraint (BALSON) is proposed. The error distribution of data fitting is described by Gaussian likelihood. The parameter distribution is assumed to be a Dirichlet distribution. With the Bayes rule, searching for the optimal parameters is equivalent to finding the mode of the posterior distribution. In order to explicitly characterize the nonnegative L1-norm constraint of the parameters, we further approximate the true posterior distribution by a Dirichlet distribution. We estimate the moments of the approximated Dirichlet posterior distribution by sampling methods. Four sampling methods have been introduced and implemented. With the estimated posterior distributions, the original parameters can be effectively reconstructed in polynomial fitting problems, and the BALSON framework is found to perform better than conventional methods
A Novel Genome-Wide Association Study Approach Using Genotyping by Exome Sequencing Leads to the Identification of a Primary Open Angle Glaucoma Associated Inversion Disrupting ADAMTS17
Closed breeding populations in the dog in conjunction with advances in gene mapping and sequencing techniques facilitate mapping of autosomal recessive diseases and identification of novel disease-causing variants, often using unorthodox experimental designs. In our investigation we demonstrate successful mapping of the locus for primary open angle glaucoma in the Petit Basset Griffon Vendéen dog breed with 12 cases and 12 controls, using a novel genotyping by exome sequencing approach. The resulting genome-wide association signal was followed up by genome sequencing of an individual case, leading to the identification of an inversion with a breakpoint disrupting the ADAMTS17 gene. Genotyping of additional controls and expression analysis provide strong evidence that the inversion is disease causing. Evidence of cryptic splicing resulting in novel exon transcription as a consequence of the inversion in ADAMTS17 is identified through RNAseq experiments. This investigation demonstrates how a novel genotyping by exome sequencing approach can be used to map an autosomal recessive disorder in the dog, with the use of genome sequencing to facilitate identification of a disease-associated variant
Identification of Individual Glandular Regions Using LCWT and Machine Learning Techniques
A new approach for the segmentation of gland units in histological images is proposed with the aim of contributing to the improvement of the prostate cancer diagnosis. Clustering methods on several
colour spaces are applied to each sample in order to generate a binary
mask of the different tissue components. From the mask of lumen candidates, the Locally Constrained Watershed Transform (LCWT) is applied
as a novel gland segmentation technique never before used in this type
of images. 500 random gland candidates, both benign and pathological,
are selected to evaluate the LCWT technique providing results of Dice
coefficient of 0.85. Several shape and textural descriptors in combination
with contextual features and a fractal analysis are applied, in a novel
way, on different colour spaces achieving a total of 297 features to discern between artefacts and true glands. The most relevant features are
then selected by an exhaustive statistical analysis in terms of independence between variables and dependence with the class. 3.200 artefacts,
3.195 benign glands and 3.000 pathological glands are obtained, from a
data set of 1468 images at 10x magnification. A careful strategy of data
partition is implemented to robustly address the classification problem
between artefacts and glands. Both linear and non-linear approaches are
considered using machine learning techniques based on Support Vector
Machines (SVM) and feedforward neural networks achieving values of
sensitivity, specificity and accuracy of 0.92, 0.97 and 0.95, respectivelyThis work has been funded by the Ministry of Economy, Industry and Competitiveness under the SICAP project (DPI2016-77869-C2-1-R). The work
of Adri´an Colomer has been supported by the Spanish FPI Grant BES-2014-067889.
We gratefully acknowledge the support of NVIDIA Corporation with the donation of
the Titan Xp GPU used for this researchGarcía-Pardo, JG.; Colomer, A.; Naranjo Ornedo, V.; Peñaranda, F.; Sales, MÁ. (2018). Identification of Individual Glandular Regions Using LCWT and Machine Learning Techniques. En Intelligent Data Engineering and Automated Learning – IDEAL 2018. Springer. 642-650. https://doi.org/10.1007/978-3-030-03493-1_67S642650Gleason, D.F.: Histologic grading and clinical staging of prostatic carcinoma. In: Urologic Pathology (1977)Naik, S., Doyle, S., Feldman, M., Tomaszewski, J., Madabhushi, A.: Gland segmentation and computerized gleason grading of prostate histology by integrating low-, high-level and domain specific information. In: MIAAB Workshop, pp. 1–8 (2007)Nguyen, K., Sabata, B., Jain, A.K.: Prostate cancer grading: gland segmentation and structural features. Pattern Recogn. Lett. 33(7), 951–961 (2012)Kwak, J.T., Hewitt, S.M.: Multiview boosting digital pathology analysis of prostate cancer. Comput. Methods Programs Biomed. 142, 91–99 (2017)Ren, J., Sadimin, E., Foran, D.J., Qi, X.: Computer aided analysis of prostate histopathology images to support a refined gleason grading system. In: SPIE Medical Imaging, International Society for Optics and Photonics, p. 101331V (2017)Soille, P.: Morphological Image Analysis: Principles and Applications. Springer, Berlin (2013)Nguyen, K., Sarkar, A., Jain, A.K.: Structure and context in prostatic gland segmentation and classification. In: Ayache, N., Delingette, H., Golland, P., Mori, K. (eds.) MICCAI 2012. LNCS, vol. 7510, pp. 115–123. Springer, Heidelberg (2012). https://doi.org/10.1007/978-3-642-33415-3_15Beare, R.: A locally constrained watershed transform. IEEE Trans. Pattern Anal. Mach. Intell. 28(7), 1063–1074 (2006)Gertych, A., et al.: Machine learning approaches to analyze histological images of tissues from radical prostatectomies. Comput. Med. Imaging Graph. 46, 197–208 (2015)Ojala, T., Pietikainen, M., Maenpaa, T.: Multiresolution gray-scale and rotation invariant texture classification with local binary patterns. IEEE Trans. Pattern Anal. Mach. Intell. 24(7), 971–987 (2002)Guo, Z., Zhang, L., Zhang, D.: A completed modeling of local binary pattern operator for texture classification. IEEE Trans. Image Process. 19(6), 1657–1663 (2010)Huang, P., Lee, C.: Automatic classification for pathological prostate images based on fractal analysis. IEEE Trans. Med. Imaging 28(7), 1037–1050 (2009)Ruifrok, A.C., Johnston, D.A., et al.: Quantification of histochemical staining by color deconvolution. Anal. Quant. Cytol. Histol. 23(4), 291–299 (2001
Enhanced switching stability in Ta 2 O 5 resistive RAM by fluorine doping
The effect of fluorine doping on the switching stability of Ta2O5 resistive random access memory devices is investigated. It shows that the dopant serves to increase the memory window and improve the stability of the resistive states due to the neutralization of oxygen vacancies. The ability to alter the current in the low resistance state with set current compliance coupled with large memory window makes multilevel cell switching more favorable. The devices have set and reset voltages of <1V with improved stability due to the fluorine doping. Density functional modelling shows that the incorporation of fluorine dopant atoms at the two-fold O vacancy site in the oxide network removes the defect state in the mid bandgap, lowering the overall density of defects capable of forming conductive filaments. This reduces the probability of forming alternative conducting paths and hence improves the current stability in the low resistance states. The doped devices exhibit more stable resistive states in both dc and pulsed set and reset cycles. The retention failure time is estimated to be a minimum of 2 years for F-doped devices measured by temperature accelerated and stress voltage accelerated retention failure methods
The role of nitrogen doping in ALD Ta2O5 and its influence on multilevel cell switching in RRAM
The role of nitrogen doping on the stability and memory window of resistive state switching in N-doped Ta2O5 deposited by atomic layer deposition is elucidated. Nitrogen incorporation increases the stability of resistive memory states which is attributed to neutralization of electronic defect levels associated with oxygen vacancies. The density functional simulation with screened exchange hybrid functional approximation finds that the incorporation of nitrogen dopant atoms in the oxide network removes the O vacancy midgap defect states, thus nullifying excess defects and eliminating alternative conductive paths. By effectively reducing the density of vacancy-induced defect states through N doping, 3-bit multilevel cell switching is demonstrated, consisting of eight distinctive resistive memory states achieved by either controlling the set current compliance or the maximum voltage during reset. Nitrogen doping has a threefold effect; widening the switching memory window to accommodate more intermediate states, improving the stability of states, and providing gradual reset for multi-level cell switching during reset. The N-doped Ta2O5 devices have relatively small set and reset voltages (< 1 V) with reduced variability due to doping
Direct generation of photon triplets using cascaded photon-pair sources
Non-classical states of light, such as entangled photon pairs and number
states, are essential for fundamental tests of quantum mechanics and optical
quantum technologies. The most widespread technique for creating these quantum
resources is the spontaneous parametric down-conversion (SPDC) of laser light
into photon pairs. Conservation of energy and momentum in this process, known
as phase-matching, gives rise to strong correlations which are used to produce
two-photon entanglement in various degrees of freedom. It has been a
longstanding goal of the quantum optics community to realise a source that can
produce analogous correlations in photon triplets, but of the many approaches
considered, none have been technically feasible. In this paper we report the
observation of photon triplets generated by cascaded down-conversion. Here each
triplet originates from a single pump photon, and therefore quantum
correlations will extend over all three photons in a way not achievable with
independently created photon pairs. We expect our photon-triplet source to open
up new avenues of quantum optics and become an important tool in quantum
technologies. Our source will allow experimental interrogation of novel quantum
correlations, the post-selection free generation of tripartite entanglement
without post- selection and the generation of heralded entangled-photon pairs
suitable for linear optical quantum computing. Two of the triplet photons have
a wavelength matched for optimal transmission in optical fibres, ideally suited
for three-party quantum communication. Furthermore, our results open
interesting regimes of non-linear optics, as we observe spontaneous
down-conversion pumped by single photons, an interaction also highly relevant
to optical quantum computing.Comment: 7 pages, 3 figures, 1 table; accepted by Natur
Superconductivity at the Border of Electron Localization and Itinerancy
The superconducting state of iron pnictides and chalcogenides exists at the
border of antiferromagnetic order. Consequently, these materials could provide
clues about the relationship between magnetism and unconventional
superconductivity. One explanation, motivated by the so-called bad-metal
behaviour of these materials, proposes that magnetism and superconductivity
develop out of quasi-localized magnetic moments which are generated by strong
electron-electron correlations. Another suggests that these phenomena are the
result of weakly interacting electron states that lie on nested Fermi surfaces.
Here we address the issue by comparing the newly discovered alkaline iron
selenide superconductors, which exhibit no Fermi-surface nesting, to their iron
pnictide counterparts. We show that the strong-coupling approach leads to
similar pairing amplitudes in these materials, despite their different Fermi
surfaces. We also find that the pairing amplitudes are largest at the boundary
between electronic localization and itinerancy, suggesting that new
superconductors might be found in materials with similar characteristics.Comment: Version of the published manuscript prior to final journal-editting.
Main text (23 pages, 4 figures) + Supplementary Information (14 pages, 7
figures, 3 tables). Calculation on the single-layer FeSe is added.
Enhancement of the pairing amplitude in the vicinity of the Mott transition
is highlighted. Published version is at
http://www.nature.com/ncomms/2013/131115/ncomms3783/full/ncomms3783.htm
Demon-like Algorithmic Quantum Cooling and its Realization with Quantum Optics
The simulation of low-temperature properties of many-body systems remains one
of the major challenges in theoretical and experimental quantum information
science. We present, and demonstrate experimentally, a universal cooling method
which is applicable to any physical system that can be simulated by a quantum
computer. This method allows us to distill and eliminate hot components of
quantum states, i.e., a quantum Maxwell's demon. The experimental
implementation is realized with a quantum-optical network, and the results are
in full agreement with theoretical predictions (with fidelity higher than
0.978). These results open a new path for simulating low-temperature properties
of physical and chemical systems that are intractable with classical methods.Comment: 7 pages, 5 figures, plus supplementarity material
In silico genotyping of the maize nested association mapping population
Nested Association Mapping (NAM) has been proposed as a means to combine the power of linkage mapping with the resolution of association mapping. It is enabled through sequencing or array genotyping of parental inbred lines while using low-cost, low-density genotyping technologies for their segregating progenies. For purposes of data analyses of NAM populations, parental genotypes at a large number of Single Nucleotide Polymorphic (SNP) loci need to be projected to their segregating progeny. Herein we demonstrate how approximately 0.5 million SNPs that have been genotyped in 26 parental lines of the publicly available maize NAM population can be projected onto their segregating progeny using only 1,106 SNP loci that have been genotyped in both the parents and their 5,000 progeny. The challenge is to estimate both the genotype and genetic location of the parental SNP genotypes in segregating progeny. Both challenges were met by estimating their expected genotypic values conditional on observed flanking markers through the use of both physical and linkage maps. About 90%, of 500,000 genotyped SNPs from the maize HapMap project, were assigned linkage map positions using linear interpolation between the maize Accessioned Gold Path (AGP) and NAM linkage maps. Of these, almost 70% provided high probability estimates of genotypes in almost 5,000 recombinant inbred lines
Evanescent light-matter Interactions in Atomic Cladding Wave Guides
Alkali vapors, and in particular rubidium, are being used extensively in
several important fields of research such as slow and stored light non-linear
optics3 and quantum computation. Additionally, the technology of alkali vapors
plays a major role in realizing myriad industrial applications including for
example atomic clocks magentometers8 and optical frequency stabilization.
Lately, there is a growing effort towards miniaturizing traditional
centimeter-size alkali vapor cells. Owing to the significant reduction in
device dimensions, light matter interactions are greatly enhanced, enabling new
functionalities due to the low power threshold needed for non-linear
interactions. Here, taking advantage of the mature Complimentary
Metal-Oxide-Semiconductor (CMOS) compatible platform of silicon photonics, we
construct an efficient and flexible platform for tailored light vapor
interactions on a chip. Specifically, we demonstrate light matter interactions
in an atomic cladding wave guide (ACWG), consisting of CMOS compatible silicon
nitride nano wave-guide core with a Rubidium (Rb) vapor cladding. We observe
the highly efficient interaction of the electromagnetic guided mode with the
thermal Rb cladding. The nature of such interactions is explained by a model
which predicts the transmission spectrum of the system taking into account
Doppler and transit time broadening. We show, that due to the high confinement
of the optical mode (with a mode area of 0.3{\lambda}2), the Rb absorption
saturates at powers in the nW regime.Comment: 10 Pages 4 Figures. 1 Supplementar
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