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https://www.readbyqxmd.com/read/28732230/maximum-likelihood-optimal-and-robust-support-vector-regression-with-lncosh-loss-function
#1
Omer Karal
In this paper, a novel and continuously differentiable convex loss function based on natural logarithm of hyperbolic cosine function, namely lncosh loss, is introduced to obtain Support Vector Regression (SVR) models which are optimal in the maximum likelihood sense for the hyper-secant error distributions. Most of the current regression models assume that the distribution of error is Gaussian, which corresponds to the squared loss function and has helpful analytical properties such as easy computation and analysis...
June 30, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28729710/learning-a-health-knowledge-graph-from-electronic-medical-records
#2
Maya Rotmensch, Yoni Halpern, Abdulhakim Tlimat, Steven Horng, David Sontag
Demand for clinical decision support systems in medicine and self-diagnostic symptom checkers has substantially increased in recent years. Existing platforms rely on knowledge bases manually compiled through a labor-intensive process or automatically derived using simple pairwise statistics. This study explored an automated process to learn high quality knowledge bases linking diseases and symptoms directly from electronic medical records. Medical concepts were extracted from 273,174 de-identified patient records and maximum likelihood estimation of three probabilistic models was used to automatically construct knowledge graphs: logistic regression, naive Bayes classifier and a Bayesian network using noisy OR gates...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28728577/integrating-data-from-randomized-controlled-trials-and-observational-studies-to-predict-the-response-to-pregabalin-in-patients-with-painful-diabetic-peripheral-neuropathy
#3
Joe Alexander, Roger A Edwards, Alberto Savoldelli, Luigi Manca, Roberto Grugni, Birol Emir, Ed Whalen, Stephen Watt, Marina Brodsky, Bruce Parsons
BACKGROUND: More patient-specific medical care is expected as more is learned about variations in patient responses to medical treatments. Analytical tools enable insights by linking treatment responses from different types of studies, such as randomized controlled trials (RCTs) and observational studies. Given the importance of evidence from both types of studies, our goal was to integrate these types of data into a single predictive platform to help predict response to pregabalin in individual patients with painful diabetic peripheral neuropathy (pDPN)...
July 20, 2017: BMC Medical Research Methodology
https://www.readbyqxmd.com/read/28728369/estimation-of-heritability-and-genetic-correlation-of-body-weight-gain-and-growth-curve-parameters-in-korean-native-chicken
#4
Prabuddha Manjula, Hee-Bok Park, Dongwon Seo, Nuri Choi, Shil Jin, Sung Jin Ahn, Kang Nyeong Heo, Bo Seok Kang, Jun Heon Lee
Objective: The aim of this present study was to estimate genetic parameters for body weight gain and growth curve parameter traits in Korean Native Chicken (KNC). Methods: A total of 585 F1 chickens were used along with 88 of their F0 birds. Body weights were measured every 2 weeks from hatching to 20 weeks of age to measure weight gain at 2-week intervals. For each individual, a logistic growth curve model was fitted to the longitudinal growth dataset to obtain three growth curve parameters (α: asymptotic final body weight, β: inflection point, and γ: constant scale that was proportional to the overall growth rate)...
June 27, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28728362/estimation-of-genetic-parameters-of-the-productive-and-reproductive-traits-in-ethiopian-holstein-using-multi-trait-models
#5
Wondossen Ayalew, Mohammed Aliy, Enyew Negussie
Objective: The objective of this study was to estimate genetic parameters for productive and reproductive traits. Methods: The data included production and reproduction records of animals that have calved between 1979 and 2013. The genetic parameters were estimated using multivariate mixed models (DMU) package, fitting univariate and multivariate mixed models with average information restricted maximum likelihood (AI-REML) algorithm. Results: The estimates of heritability for milk production traits from the first three lactation records were 0...
June 27, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28728147/efficient-maximum-likelihood-estimation-for-pedigree-data-with-the-sum-product-algorithm
#6
Alexander Engelhardt, Anna Rieger, Achim Tresch, Ulrich Mansmann
OBJECTIVE: We analyze data sets consisting of pedigrees with age at onset of colorectal cancer (CRC) as phenotype. The occurrence of familial clusters of CRC suggests the existence of a latent, inheritable risk factor. We aimed to compute the probability of a family possessing this risk factor as well as the hazard rate increase for these risk factor carriers. Due to the inheritability of this risk factor, the estimation necessitates a costly marginalization of the likelihood. METHODS: We propose an improved EM algorithm by applying factor graphs and the sum-product algorithm in the E-step...
July 21, 2017: Human Heredity
https://www.readbyqxmd.com/read/28725873/genetic-characterization-of-human-immunodeficiency-virus-type-1-transmission-in-the-middle-east-and-north-africa
#7
Malik Sallam, Gülşen Özkaya Şahin, Mikael Ingman, Anders Widell, Joakim Esbjörnsson, Patrik Medstrand
BACKGROUND: The HIV-1 spread in the Middle East and North Africa (MENA) has not been previously characterised using the phylogenetic approach. The aim of the current study was to investigate the genetic diversity and domestic transmission of HIV-1 in the MENA. METHODS: A total of 2036 HIV-1 sequences available in Genbank and collected in the MENA during 1988-2016 were used together with 715 HIV-1 reference sequences that were retrieved from Genbank based on genetic similarity with the MENA sequences...
July 2017: Heliyon
https://www.readbyqxmd.com/read/28721955/spatiotemporal-clustering-of-dengue-cases-in-thiruvananthapuram-district-kerala
#8
Joanna Sara Valson, Biju Soman
BACKGROUND: Dengue cases are increasing in Kerala since 2010. Information on clustering of cases across locations and time periods is vital for disease surveillance and timely control. OBJECTIVES: The objective is to study spatiotemporal clustering of dengue cases and their climatic and physioenvironmental correlates in Thiruvananthapuram district during 2010-2014. METHODS: Health department data on reported cases of dengue were obtained from January 2011 to June 2014...
April 2017: Indian Journal of Public Health
https://www.readbyqxmd.com/read/28721680/evaluation-of-haplotype-diversity-of-achatina-fulica-lissachatina-bowdich-from-indian-sub-continent-by-means-of-16s-rdna-sequence-and-its-phylogenetic-relationships-with-other-global-populations
#9
Vijaya Sai Ayyagari, Krupanidhi Sreerama
Achatina fulica (Lissachatina fulica) is one of the most invasive species found across the globe causing a significant damage to crops, vegetables, and horticultural plants. This terrestrial snail is native to east Africa and spread to different parts of the world by introductions. India, a hot spot for biodiversity of several endemic gastropods, has witnessed an outburst of this snail population in several parts of the country posing a serious threat to crop loss and also to human health. With an objective to evaluate the genetic diversity of this snail, we have sampled this snail from different parts of India and analyzed its haplotype diversity by means of 16S rDNA sequence information...
August 2017: 3 Biotech
https://www.readbyqxmd.com/read/28719074/influence-diagnostics-in-meta-regression-model
#10
Lei Shi, ShanShan Zuo, Dalei Yu, Xiaohua Zhou
This paper studies the influence diagnostics in meta-regression model including case deletion diagnostic and local influence analysis. We derive the subset deletion formulae for the estimation of regression coefficient and heterogeneity variance and obtain the corresponding influence measures. The DerSimonian and Laird estimation and maximum likelihood estimation methods in meta-regression are considered, respectively, to derive the results. Internal and external residual and leverage measure are defined. The local influence analysis based on case-weights perturbation scheme, responses perturbation scheme, covariate perturbation scheme, and within-variance perturbation scheme are explored...
July 18, 2017: Research Synthesis Methods
https://www.readbyqxmd.com/read/28716740/multilocus-analysis-of-the-catfish-family-trichomycteridae-teleostei-ostariophysi-siluriformes-supporting-a-monophyletic-trichomycterinae
#11
Luz E Ochoa, Fabio F Roxo, Carlos DoNascimiento, Mark H Sabaj, Aléssio Datovo, Michael Alfaro, Claudio Oliveira
Trichomycteridae is the second most diverse family of the order Siluriformes, its members are widely distributed through the freshwaters of Central and South America, exhibiting an exceptional ecological and phenotypic disparity. The most diverse subfamily, Trichomycterinae, represented mainly by the genus Trichomycterus, historically has been recognized as non-monophyletic and various characters used to unite or divide its constituents are repeatedly called into question. No comprehensive molecular phylogenetic hypothesis regarding relationships of trichomycterids has been produced, and the present study is the first extensive phylogeny for the family Trichomycteridae, based on a multilocus dataset of three mitochondrial loci and two nuclear markers (3284 bp total)...
July 14, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28716394/validation-of-a-spanish-language-version-of-the-adhd-rating-scale-iv-in-a-spanish-sample
#12
M Vallejo-Valdivielso, C A Soutullo, P de Castro-Manglano, J J Marín-Méndez, A Díez-Suárez
OBJECTIVES: The purpose of this study is to validate a Spanish-language version of the 18-item ADHD Rating Scale-IV (ADHD-RS-IV.es) in a Spanish sample. METHODS: From a total sample of 652 children and adolescents aged 6 to 17 years (mean age was 11.14±3.27), we included 518 who met the DSM-IV-TR criteria for ADHD and 134 healthy controls. To evaluate the factorial structure, validity, and reliability of the scale, we performed a confirmatory factor analysis (CFA) using structural equation modelling on a polychoric correlation matrix and maximum likelihood estimation...
July 14, 2017: Neurología: Publicación Oficial de la Sociedad Española de Neurología
https://www.readbyqxmd.com/read/28715429/a-microscopic-simulation-model-for-pedestrian-pedestrian-and-pedestrian-vehicle-interactions-at-crosswalks
#13
Manxia Liu, Weiliang Zeng, Peng Chen, Xuyi Wu
This study aims to develop a microscopic pedestrian behavior model considering various interactions on pedestrian dynamics at crosswalks. Particularly, we take into account the evasion behavior with counter-flow pedestrians, the following behavior with leader pedestrians, and the collision avoidance behavior with vehicles. Aerial video data at one intersection in Beijing, China are extracted for model calibration. A microscopic calibration approach based on maximum likelihood estimation is applied to estimate the parameters of a modified social force model...
2017: PloS One
https://www.readbyqxmd.com/read/28715335/evolutionary-model-for-the-statistical-divergence-of-paralogous-and-orthologous-gene-pairs-generated-by-whole-genome-duplication-and-speciation
#14
Yue Zhang, Chunfang Zheng, David Sankoff
We outline a principled approach to the analysis of duplicate gene similarity distributions, based on a model integrating sequence divergence and the process of fractionation of duplicate genes resulting from whole genome duplication (WGD). This model allows us predict duplicate gene similarity distributions for series of two or three WGD, for whole genome triplication followed by a WGD, and for triplication, followed by speciation, followed by WGD. We calculate the probabilities of all possible fates of a gene pair as its two members proliferate or are lost, predicting the number of surviving pairs from each event...
July 14, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28715244/small-sample-methods-for-multilevel-modeling-a-colloquial-elucidation-of-reml-and-the-kenward-roger-correction
#15
Daniel McNeish
Studies on small sample properties of multilevel models have become increasingly prominent in the methodological literature in response to the frequency with which small sample data appear in empirical studies. Simulation results generally recommend that empirical researchers employ restricted maximum likelihood estimation (REML) with a Kenward-Roger correction with small samples in frequentist contexts to minimize small sample bias in estimation and to prevent inflation of Type-I error rates. However, simulation studies focus on recommendations for best practice, and there is little to no explanation of why traditional maximum likelihood (ML) breaks down with smaller samples, what differentiates REML from ML, or how the Kenward-Roger correction remedies lingering small sample issues...
July 17, 2017: Multivariate Behavioral Research
https://www.readbyqxmd.com/read/28715231/bayesian-estimation-for-item-factor-analysis-models-with-sparse-categorical-indicators
#16
Sierra A Bainter
Psychometric models for item-level data are broadly useful in psychology. A recurring issue for estimating item factor analysis (IFA) models is low-item endorsement (item sparseness), due to limited sample sizes or extreme items such as rare symptoms or behaviors. In this paper, I demonstrate that under conditions characterized by sparseness, currently available estimation methods, including maximum likelihood (ML), are likely to fail to converge or lead to extreme estimates and low empirical power. Bayesian estimation incorporating prior information is a promising alternative to ML estimation for IFA models with item sparseness...
July 17, 2017: Multivariate Behavioral Research
https://www.readbyqxmd.com/read/28712533/dose-volume-toxicity-modeling-for-de-intensified-chemo-radiation-therapy-for-hpv-positive-oropharynx-cancer
#17
Panayiotis Mavroidis, Alex Price, David Fried, Mark Kostich, Robert Amdur, William Mendenhall, Chihray Liu, Shiva Das, Lawrence B Marks, Bhishamjit Chera
BACKGROUND AND PURPOSE: The aim is to determine the radiobiological parameters of four popular normal tissue complication probability (NTCP) models that describe the dose-response relations of salivary glands and pharyngeal constrictors to the severity of patient reported xerostomia and dysphagia, respectively 6 and 12months post chemo-radiotherapy, furthermore, to evaluate the goodness-of-fit of the NTCP models for different combinations of glands and constrictors. MATERIAL AND METHODS: Forty-three patients were treated on a prospective multi-institutional phase II study (ClinicalTrials...
July 13, 2017: Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology
https://www.readbyqxmd.com/read/28711653/highly-conserved-intragenic-hsv-2-sequences-results-from-next-generation-sequencing-of-hsv-2-ul-and-us-regions-from-genital-swabs-collected-from-3-continents
#18
Christine Johnston, Amalia Magaret, Pavitra Roychoudhury, Alexander L Greninger, Anqi Cheng, Kurt Diem, Matthew P Fitzgibbon, Meei-Li Huang, Stacy Selke, Jairam R Lingappa, Connie Celum, Keith R Jerome, Anna Wald, David M Koelle
INTRODUCTION: Understanding the variability in circulating herpes simplex virus type 2 (HSV-2) genomic sequences is critical to the development of HSV-2 vaccines. METHODS: Genital lesion swabs containing ≥ 10(7)log10 copies HSV DNA collected from Africa, the USA, and South America underwent next-generation sequencing, followed by K-mer based filtering and de novo genomic assembly. Sites of heterogeneity within coding regions in unique long and unique short (UL_US) regions were identified...
July 13, 2017: Virology
https://www.readbyqxmd.com/read/28709735/genetic-variation-and-correlated-changes-in-reproductive-performance-of-a-red-tilapia-line-selected-for-improved-growth-over-three-generations
#19
Ngo Phu Thoa, Azhar Hamzah, Nguyen Hong Nguyen
The present study examines genetic variation and correlated changes in reproductive performance traits in a red tilapia (Oreochromis spp.) population selected over three generations for improved growth. A total of 328 breeding females (offspring of 111 sires and 118 dams) had measurements of body weight prior to spawning (WBS), number of fry at hatching (NFH), total fry weight (TFW) and number of dead fry (NDF) or mortality of fry including unhatched eggs at hatching (MFH). Restricted maximum likelihood (REML) analysis in a multi-trait model showed that there are heritable genetic components for all traits studied...
July 6, 2017: Animal Reproduction Science
https://www.readbyqxmd.com/read/28707210/sparse-exploratory-factor-analysis
#20
Nickolay T Trendafilov, Sara Fontanella, Kohei Adachi
Sparse principal component analysis is a very active research area in the last decade. It produces component loadings with many zero entries which facilitates their interpretation and helps avoid redundant variables. The classic factor analysis is another popular dimension reduction technique which shares similar interpretation problems and could greatly benefit from sparse solutions. Unfortunately, there are very few works considering sparse versions of the classic factor analysis. Our goal is to contribute further in this direction...
July 13, 2017: Psychometrika
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