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作者：Chiarucci, Alessandro; Di Biase, Rosa Maria; Fattorini, Lorenzo; Marcheselli, Marzia; Pisani, Caterina
作者单位：University of Bologna; Tuscia University; University of Siena
摘要：The lists of species obtained by purposive sampling by field ecologists can be used to improve the sample-based estimation of species richness. A new estimator is here proposed as a modification of the difference estimator in which the species inclusion probabilities are estimated by means of the species frequencies from incidence data. If the species list used to support the estimation is complete the estimator guesses the true richness without error. In the case of incomplete lists, the esti...
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作者：Johnson, Leah R.; Gramacy, Robert B.; Cohen, Jeremy; Mordecai, Erin; Murdock, Courtney; Rohr, Jason; Ryan, Sadie J.; Stewart-Ibarra, Anna M.; Weikel, Daniel
作者单位：Virginia Polytechnic Institute & State University; State University System of Florida; University of South Florida; Stanford University; University System of Georgia; University of Georgia; University System of Georgia; University of Georgia; State University System of Florida; University of Florida; State University System of Florida; University of Florida; State University of New York (SUNY) System; SUNY Upstate Medical University; State University of New York (SUNY) System; SUNY Upstate Medical University; University of Michigan System; University of Michigan
摘要：In 2015 the US federal government sponsored a dengue forecasting competition using historical case data from Iquitos, Peru and San Juan, Puerto Rico. Competitors were evaluated on several aspects of out-of-sample forecasts including the targets of peak week, peak incidence during that week, and total season incidence across each of several seasons. Our team was one of the winners of that competition, outperforming other teams in multiple targets/locales. In this paper we report on our methodol...
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作者：Randolph, Timothy W.; Zhao, Sen; Copeland, Wade; Hullar, Meredith; Shojaie, Ali
作者单位：Fred Hutchinson Cancer Center; University of Washington; University of Washington Seattle
摘要：The analysis of human microbiome data is often based on dimensionreduced graphical displays and clusterings derived from vectors of microbial abundances in each sample. Common to these ordination methods is the use of biologically motivated definitions of similarity. Principal coordinate analysis, in particular, is often performed using ecologically defined distances, allowing analyses to incorporate context-dependent, non-Euclidean structure. In this paper, we go beyond dimension-reduced ordi...
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作者：Weber, Sebastian; Gelman, Andrew; Lee, Daniel; Betancourt, Michael; Vehtari, Aki; Racine-Poon, Amy
作者单位：Novartis; Columbia University; Aalto University
摘要：Throughout the different phases of a drug development program, randomized trials are used to establish the tolerability, safety and efficacy of a candidate drug. At each stage one aims to optimize the design of future studies by extrapolation from the available evidence at the time. This includes collected trial data and relevant external data. However, relevant external data are typically available as averages only, for example, from trials on alternative treatments reported in the literature...
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作者：Caye, Kevin; Jay, Flora; Michel, Olivier; Francois, Olivier
作者单位：Centre National de la Recherche Scientifique (CNRS); CNRS - Institute for Engineering & Systems Sciences (INSIS); Communaute Universite Grenoble Alpes; Institut National Polytechnique de Grenoble; Universite Grenoble Alpes (UGA); Centre National de la Recherche Scientifique (CNRS); CNRS - Institute of Ecology & Environment (INEE); Universite Paris Saclay; Communaute Universite Grenoble Alpes; Institut National Polytechnique de Grenoble; Universite Grenoble Alpes (UGA); Centre National de la Recherche Scientifique (CNRS); CNRS - Institute for Information Sciences & Technologies (INS2I)
摘要：Accurately evaluating the distribution of genetic ancestry across geographic space is one of the main questions addressed by evolutionary biologists. This question has been commonly addressed through the application of Bayesian estimation programs allowing their users to estimate individual admixture proportions and allele frequencies among putative ancestral populations. Following the explosion of high-throughput sequencing technologies, several algorithms have been proposed to cope with comp...
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作者：Hwang, Youngdeok; Lu, Siyuan; Kim, Jae-Kwang
作者单位：Sungkyunkwan University (SKKU); International Business Machines (IBM); IBM USA; Iowa State University; Korea Advanced Institute of Science & Technology (KAIST)
摘要：Accurately forecasting solar power using the data from multiple sources is an important but challenging problem. Our goal is to combine two different physics model forecasting outputs with real measurements from an automated monitoring network so as to better predict solar power in a timely manner. To this end, we propose a new approach of analyzing large-scale multilevel models with great computational efficiency requiring minimum monitoring and intervention. This approach features a division...
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作者：Rodriguez-Girondo, Mar; Salo, Perttu; Burzykowski, Tomasz; Perola, Markus; Houwing-Duistermaat, Jeanine; Mertens, Bart
作者单位：Leiden University - Excl LUMC; Leiden University; Leiden University Medical Center (LUMC); Finland National Institute for Health & Welfare; Hasselt University; University of Leeds
摘要：Enriching existing predictive models with new biomolecular markers is an important task in the new multi-omic era. Clinical studies increasingly include new sets of omic measurements which may prove their added value in terms of predictive performance. We introduce a two-step approach for the assessment of the added predictive ability of omic predictors, based on sequential double cross-validation and regularized regression models. We propose several performance indices to summarize the two-st...
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作者：Ding, Ying; Li, Ying Grace; Liu, Yushi; Ruberg, Stephen J.; Hsu, Jason C.
作者单位：Pennsylvania Commonwealth System of Higher Education (PCSHE); University of Pittsburgh; Eli Lilly; Lilly Research Laboratories; University System of Ohio; Ohio State University
摘要：Our research is for finding SNPs that are predictive of treatment efficacy, to decide which subgroup (with enhanced treatment efficacy) to target in drug development. Testing SNPs for lack of association with treatment outcome is inherently challenging, because any linkage disequilibrium between a noncausal SNP with a causal SNP, however small, makes the zero-null (no association) hypothesis technically false. Control of Type I error rate in testing such null hypotheses are therefore difficult...
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作者：Tang, Yunfan; Ma, Li; Nicolae, Dan L.
作者单位：University of Chicago; Duke University
摘要：In this paper, we introduce the phylogenetic scan test (PhyloScan) for investigating cross-group differences in microbiome compositions using the Dirichlet-tree multinomial (DTM) model. DTM models the microbiome data through a cascade of independent local DMs on the internal nodes of the phylogenetic tree. Each of the local DMs captures the count distributions of a certain number of operational taxonomic units at a given resolution. Since distributional differences tend to occur in clusters al...
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作者：Chiquet, Julien; Mariadassou, Mahendra; Robin, Stephane
作者单位：Universite Paris Saclay; INRAE; AgroParisTech; INRAE; Universite Paris Saclay
摘要：Many application domains, such as ecology or genomics, have to deal with multivariate non-Gaussian observations. A typical example is the joint observation of the respective abundances of a set of species in a series of sites aiming to understand the covariations between these species. The Gaussian setting provides a canonical way to model such dependencies but does not apply in general. We consider here the multivariate exponential family framework for which we introduce a generic model with ...
