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Search Results: 1 - 10 of 148395 matches for " John T Hogg "
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Solving Highly Constrained Search Problems with Quantum Computers
T. Hogg
Computer Science , 2011, DOI: 10.1613/jair.574
Abstract: A previously developed quantum search algorithm for solving 1-SAT problems in a single step is generalized to apply to a range of highly constrained k-SAT problems. We identify a bound on the number of clauses in satisfiability problems for which the generalized algorithm can find a solution in a constant number of steps as the number of variables increases. This performance contrasts with the linear growth in the number of steps required by the best classical algorithms, and the exponential number required by classical and quantum methods that ignore the problem structure. In some cases, the algorithm can also guarantee that insoluble problems in fact have no solutions, unlike previously proposed quantum search algorithms.
Quantum Computing and Phase Transitions in Combinatorial Search
T. Hogg
Computer Science , 1996,
Abstract: We introduce an algorithm for combinatorial search on quantum computers that is capable of significantly concentrating amplitude into solutions for some NP search problems, on average. This is done by exploiting the same aspects of problem structure as used by classical backtrack methods to avoid unproductive search choices. This quantum algorithm is much more likely to find solutions than the simple direct use of quantum parallelism. Furthermore, empirical evaluation on small problems shows this quantum algorithm displays the same phase transition behavior, and at the same location, as seen in many previously studied classical search methods. Specifically, difficult problem instances are concentrated near the abrupt change from underconstrained to overconstrained problems.
Genetic linkage map of a wild genome: genomic structure, recombination and sexual dimorphism in bighorn sheep
Jocelyn Poissant, John T Hogg, Corey S Davis, Joshua M Miller, Jillian F Maddox, David W Coltman
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-524
Abstract: Bighorn sheep population-specific maps differed slightly in contiguity but were otherwise very similar in terms of genomic structure and recombination rates. The joint analysis of the two pedigrees resulted in a highly contiguous map composed of 247 microsatellite markers distributed along all 26 autosomes and the X chromosome. The map is estimated to cover about 84% of the bighorn sheep genome and contains 240 unique positions spanning a sex-averaged distance of 3051 cM with an average inter-marker distance of 14.3 cM. Marker synteny, order, sex-averaged interval lengths and sex-averaged total map lengths were all very similar between sheep species. However, in contrast to domestic sheep, but consistent with the usual pattern for a placental mammal, recombination rates in bighorn sheep were significantly greater in females than in males (~12% difference), resulting in an autosomal female map of 3166 cM and an autosomal male map of 2831 cM. Despite differing genome-wide patterns of heterochiasmy between the sheep species, sexual dimorphism in recombination rates was correlated between orthologous intervals.We have developed a first-generation bighorn sheep linkage map that will facilitate future studies of the genetic architecture of trait variation in this species. While domestication has been hypothesized to be responsible for the elevated mean recombination rate observed in domestic sheep, our results suggest that it is a characteristic of Ovis species. However, domestication may have played a role in altering patterns of heterochiasmy. Finally, we found that interval-specific patterns of sexual dimorphism were preserved among closely related Ovis species, possibly due to the conserved position of these intervals relative to the centromeres and telomeres. This study exemplifies how transferring genomic resources from domesticated species to close wild relative can benefit evolutionary ecologists while providing insights into the evolution of genomic structure and
Stellar and Planetary Properties of K2 Campaign 1 Candidates and Validation of 17 Planets, Including a Planet Receiving Earth-like Insolation
Benjamin T. Montet,Timothy D. Morton,Daniel Foreman-Mackey,John Asher Johnson,David W. Hogg,Brendan P. Bowler,David W. Latham,Allyson Bieryla,Andrew W. Mann
Physics , 2015, DOI: 10.1088/0004-637X/809/1/25
Abstract: The extended Kepler mission, K2, is now providing photometry of new fields every three months in a search for transiting planets. In a recent study, Foreman-Mackey and collaborators presented a list of 36 planet candidates orbiting 31 stars in K2 Campaign 1. In this contribution, we present stellar and planetary properties for all systems. We combine ground-based seeing-limited survey data and adaptive optics imaging with an automated transit analysis scheme to validate 21 candidates as planets, 17 for the first time, and identify 6 candidates as likely false positives. Of particular interest is K2-18 (EPIC 201912552), a bright (K=8.9) M2.8 dwarf hosting a 2.23 \pm 0.25 R_Earth planet with T_eq = 272 \pm 15 K and an orbital period of 33 days. We also present two new open-source software packages which enable this analysis. The first, isochrones, is a flexible tool for fitting theoretical stellar models to observational data to determine stellar properties using a nested sampling scheme to capture the multimodal nature of the posterior distributions of the physical parameters of stars that may plausibly be evolved. The second is vespa, a new general-purpose procedure to calculate false positive probabilities and statistically validate transiting exoplanets.
A New Look at the Easy-Hard-Easy Pattern of Combinatorial Search Difficulty
D. L. Mammen,T. Hogg
Computer Science , 1997,
Abstract: The easy-hard-easy pattern in the difficulty of combinatorial search problems as constraints are added has been explained as due to a competition between the decrease in number of solutions and increased pruning. We test the generality of this explanation by examining one of its predictions: if the number of solutions is held fixed by the choice of problems, then increased pruning should lead to a monotonic decrease in search cost. Instead, we find the easy-hard-easy pattern in median search cost even when the number of solutions is held constant, for some search methods. This generalizes previous observations of this pattern and shows that the existing theory does not explain the full range of the peak in search cost. In these cases the pattern appears to be due to changes in the size of the minimal unsolvable subproblems, rather than changing numbers of solutions.
The Aromatic Features in Very Faint Dwarf Galaxies
Ronin Wu,David W. Hogg,John Moustakas
Physics , 2009, DOI: 10.1088/0004-637X/730/2/111
Abstract: We present optical and mid-infrared photometry of a statistically complete sample of 29 very faint dwarf galaxies (M_r > -15 mag) selected from the SDSS spectroscopic sample and observed in the mid-infrared with Spitzer IRAC. This sample contains nearby (redshift z<0.005) galaxies three magnitudes fainter than previously studied samples. We compare our sample with other star-forming galaxies that have been observed with both IRAC and SDSS. We examine the relationship of the infrared color, sensitive to PAH abundance, with star-formation rates, gas-phase metallicities and radiation hardness, all estimated from optical emission lines. Consistent with studies of more luminous dwarfs, we find that the very faint dwarf galaxies show much weaker PAH emission than more luminous galaxies with similar specific star-formation rates. Unlike more luminous galaxies, we find that the very faint dwarf galaxies show no significant dependence at all of PAH emission on star-formation rate, metallicity, or radiation hardness, despite the fact that the sample spans a significant range in all of these quantities. When the very faint dwarfs in our sample are compared with more luminous (M_r ~ -18 mag) dwarfs, we find that PAH emission depends on metallicity and radiation hardness. These two parameters are correlated; we look at the PAH-metallicity relation at fixed radiation hardness and the PAH-hardness relation at fixed metallicity. This test shows that the PAH emission in dwarf galaxies depends most directly on metallicity.
Mortality in Patients with HIV-1 Infection Starting Antiretroviral Therapy in South Africa, Europe, or North America: A Collaborative Analysis of Prospective Studies
Andrew Boulle ,Michael Schomaker,Margaret T. May,Robert S. Hogg,Bryan E. Shepherd,Susana Monge,Olivia Keiser,Fiona C. Lampe,Janet Giddy,James Ndirangu,Daniela Garone,Matthew Fox,Suzanne M. Ingle,Peter Reiss,Francois Dabis,Dominique Costagliola,Antonella Castagna,Kathrin Ehren,Colin Campbell,M. John Gill,Michael Saag,Amy C. Justice,Jodie Guest,Heidi M. Crane,Matthias Egger,Jonathan A. C. Sterne
PLOS Medicine , 2014, DOI: 10.1371/journal.pmed.1001718
Abstract: Background High early mortality in patients with HIV-1 starting antiretroviral therapy (ART) in sub-Saharan Africa, compared to Europe and North America, is well documented. Longer-term comparisons between settings have been limited by poor ascertainment of mortality in high burden African settings. This study aimed to compare mortality up to four years on ART between South Africa, Europe, and North America. Methods and Findings Data from four South African cohorts in which patients lost to follow-up (LTF) could be linked to the national population register to determine vital status were combined with data from Europe and North America. Cumulative mortality, crude and adjusted (for characteristics at ART initiation) mortality rate ratios (relative to South Africa), and predicted mortality rates were described by region at 0–3, 3–6, 6–12, 12–24, and 24–48 months on ART for the period 2001–2010. Of the adults included (30,467 [South Africa], 29,727 [Europe], and 7,160 [North America]), 20,306 (67%), 9,961 (34%), and 824 (12%) were women. Patients began treatment with markedly more advanced disease in South Africa (median CD4 count 102, 213, and 172 cells/μl in South Africa, Europe, and North America, respectively). High early mortality after starting ART in South Africa occurred mainly in patients starting ART with CD4 count <50 cells/μl. Cumulative mortality at 4 years was 16.6%, 4.7%, and 15.3% in South Africa, Europe, and North America, respectively. Mortality was initially much lower in Europe and North America than South Africa, but the differences were reduced or reversed (North America) at longer durations on ART (adjusted rate ratios 0.46, 95% CI 0.37–0.58, and 1.62, 95% CI 1.27–2.05 between 24 and 48 months on ART comparing Europe and North America to South Africa). While bias due to under-ascertainment of mortality was minimised through death registry linkage, residual bias could still be present due to differing approaches to and frequency of linkage. Conclusions After accounting for under-ascertainment of mortality, with increasing duration on ART, the mortality rate on HIV treatment in South Africa declines to levels comparable to or below those described in participating North American cohorts, while substantially narrowing the differential with the European cohorts. Please see later in the article for the Editors' Summary
Highly Diverse, Poorly Studied and Uniquely Threatened by Climate Change: An Assessment of Marine Biodiversity on South Georgia's Continental Shelf
Oliver T. Hogg,David K. A. Barnes,Huw J. Griffiths
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0019795
Abstract: We attempt to quantify how significant the polar archipelago of South Georgia is as a source of regional and global marine biodiversity. We evaluate numbers of rare, endemic and range-edge species and how the faunal structure of South Georgia may respond to some of the fastest warming waters on the planet.
Extreme deconvolution: Inferring complete distribution functions from noisy, heterogeneous and incomplete observations
Jo Bovy,David W. Hogg,Sam T. Roweis
Physics , 2009, DOI: 10.1214/10-AOAS439
Abstract: We generalize the well-known mixtures of Gaussians approach to density estimation and the accompanying Expectation--Maximization technique for finding the maximum likelihood parameters of the mixture to the case where each data point carries an individual $d$-dimensional uncertainty covariance and has unique missing data properties. This algorithm reconstructs the error-deconvolved or "underlying" distribution function common to all samples, even when the individual data points are samples from different distributions, obtained by convolving the underlying distribution with the heteroskedastic uncertainty distribution of the data point and projecting out the missing data directions. We show how this basic algorithm can be extended with conjugate priors on all of the model parameters and a "split-and-merge" procedure designed to avoid local maxima of the likelihood. We demonstrate the full method by applying it to the problem of inferring the three-dimensional velocity distribution of stars near the Sun from noisy two-dimensional, transverse velocity measurements from the Hipparcos satellite.
The velocity distribution of nearby stars from Hipparcos data I. The significance of the moving groups
Jo Bovy,David W. Hogg,Sam T. Roweis
Physics , 2009, DOI: 10.1088/0004-637X/700/2/1794
Abstract: We present a three-dimensional reconstruction of the velocity distribution of nearby stars (<~ 100 pc) using a maximum likelihood density estimation technique applied to the two-dimensional tangential velocities of stars. The underlying distribution is modeled as a mixture of Gaussian components. The algorithm reconstructs the error-deconvolved distribution function, even when the individual stars have unique error and missing-data properties. We apply this technique to the tangential velocity measurements from a kinematically unbiased sample of 11,865 main sequence stars observed by the Hipparcos satellite. We explore various methods for validating the complexity of the resulting velocity distribution function, including criteria based on Bayesian model selection and how accurately our reconstruction predicts the radial velocities of a sample of stars from the Geneva-Copenhagen survey (GCS). Using this very conservative external validation test based on the GCS, we find that there is little evidence for structure in the distribution function beyond the moving groups established prior to the Hipparcos mission. This is in sharp contrast with internal tests performed here and in previous analyses, which point consistently to maximal structure in the velocity distribution. We quantify the information content of the radial velocity measurements and find that the mean amount of new information gained from a radial velocity measurement of a single star is significant. This argues for complementary radial velocity surveys to upcoming astrometric surveys.
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