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arXiv 2023年

作者： Choi, Dongrak Bae, Woojung Yan, Jun Kang, Sangwook Department of Biostatistics and Bioinformatics Duke University DurhamNC United States Department of Statistics University of Florida GainesvilleFL United States Department of Statistics University of Connecticut StorrsCT United States Department of Applied Statistics Department of Statistics and Data Science Yonsei University Seoul Korea Republic of

We propose a set of goodness-of-fit tests for the semiparametric accelerated failure time (AFT) model, including an omnibus test, a link function test, and a functional form test. This set of tests is derived from a multi-parameter cumulative sum process shown to follow asymptotically a zero-mean Gaussian process. Its evaluation is based on the asymptotically equivalent perturbed version, which enables both graphical and numerical evaluations of the assumed AFT model. Empirical p-values are obtained using the Kolmogorov-type supremum test, which provides a reliable approach for estimating the significance of both proposed un-standardized and standardized test statistics. The proposed procedure is illustrated using the induced smoothed rank-based estimator but is directly applicable to other popular estimators such as non-smooth rank-based estimator or least-squares *** proposed methods are rigorously evaluated using extensive simulation experiments that demonstrate their effectiveness in maintaining a Type I error rate and detecting departures from the assumed AFT model in practical sample sizes and censoring rates. Furthermore, the proposed approach is applied to the analysis of the Primary Biliary Cirrhosis data, a widely studied dataset in survival analysis, providing further evidence of the practical usefulness of the proposed methods in real-world scenarios. To make the proposed methods more accessible to researchers, we have implemented them in the R package afttest, which is publicly available on the Comprehensive R Archieve Network. Copyright © 2023, The Authors. All rights reserved.

关键词： Model checking

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Automated selection of reliable 16S rRNA gene sequence for phylogenetic tree construction

Automated selection of reliable 16S rRNA gene sequence for p...

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The 13th International Conference on Culture Collections(ICCC 13)第13届国际菌种保藏大会

作者： Wim De Smet Paul De Vos Peter Dawyndt Bernard De Baets Department of Applied Mathematics Computer Science and StatisticsGhent UniversityBelgium BCCM/LMG bacteria collection Laboratory of MicrobiologyGhent University(LM-UGent) Belgium Department of Mathematical ModellingStatistics and BioinformaticsGhent University Gent Belgium

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REFINING THE DRIFT BARRIER HYPOTHESIS: A ROLE OF RECESSIVE GENE COUNT AND AN INHOMOGENEOUS MULLER‘S RATCHET

arXiv

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arXiv 2024年

作者： La Rocca, Luis A. Gerischer, Konrad Bovier, Anton Krawitz, Peter M. Institut for Applied Mathematics University of Bonn Endenicher Allee 60 Bonn53115 Germany Institute for Genomic Statistics and Bioinformatics University of Bonn Venusberg-Campus 1 Bonn53127 Germany

The drift-barrier hypothesis states that random genetic drift constrains the refinement of a phenotype under natural selection. The influence of effective population size and the genome-wide deleterious mutation rate were studied theoretically, and an inverse relationship between mutation rate and genome size has been observed for many species. However, the effect of the recessive gene count, an important feature of the genomic architecture, is unknown. In a Wright-Fisher model, we studied the mutation burden for a growing number of N completely recessive and lethal disease genes. Diploid individuals are represented with a binary 2 × N matrix denoting wild-type and mutated alleles. Analytic results for specific cases were complemented by simulations across a broad parameter regime for gene count, mutation and recombination rates. Simulations revealed transitions to higher mutation burden and prevalence within a few generations that were linked to the extinction of the wild-type haplotype (least-loaded class). This metastability, that is, phases of quasi-equilibrium with intermittent transitions, persists over 100 000 generations. The drift-barrier hypothesis is confirmed by a high mutation burden resulting in population collapse. Simulations showed the emergence of mutually exclusive haplotypes for a mutation rate above 0.02 lethal equivalents per generation for a genomic architecture and population size representing complex multicellular organisms such as humans. In such systems, recombination proves pivotal, preventing population collapse and maintaining a mutation burden below 10. This study advances our understanding of gene pool stability, and particularly the role of the number of recessive disorders. Insights into Muller‘s ratchet dynamics are provided, and the essential role of recombination in curbing mutation burden and stabilizing the gene pool is demonstrated. © 2024, CC BY-NC-SA.

关键词： Genome

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Graduate Education in statistics and Data Science: The Why, When, Where, Who, and What

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statistics and Its Application 1000年第1期8卷 25-39页

作者： Marc Aerts Geert Molenberghs Olivier Thas 1Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BioStat) Hasselt University BE3590 Hasselt Belgium email: marc.aerts@uhasselt.be 2Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BioStat) KU Leuven 3000 Leuven Belgium 4Department of Applied Mathematics Computer Science and Statistics Ghent University 9000 Ghent Belgium 3National Institute for Applied Statistics Research Australia (NIASRA) University of Wollongong Keiraville New South Wales 2500 Australia

Organizing a graduate program in statistics and data science raises many questions, offering a variety of opportunities while presenting a multitude of choices. The call for graduate programs in statistics and data science is overwhelming. How does it align with other (future) study programs at the secondary and postsecondary levels? What could or should be the natural home for data science in academia? Who meets the entry criteria, and who does not? Which strategic choices inevitably play a prominent role when developing a curriculum? We share our views on the why, when, where, who and what.

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Parsimonious reconstruction of network evolution

Parsimonious reconstruction of network evolution

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Lecture Notes in Computer Science

作者： Patro, Rob Sefer, Emre Malin, Justin Marçais, Guillaume Navlakha, Saket Kingsford, Carl Center for Bioinformatics and Computational Biology University of Maryland College Park MD 20742 United States Department of Computer Science University of Maryland College Park MD 20742 United States Computational Biology Bioinformatics and Genomics Concentration Biological Sciences Graduate Program University of Maryland College Park MD 20742 United States Program in Applied Mathematics Statistics and Scientific Computation University of Maryland College Park MD 20742 United States School of Computer Science Carnegie Mellon University Pittsburgh PA 15213 United States

ISBN: (纸本)9783642230370

We consider the problem of reconstructing a maximally parsimonious history of network evolution under models that support gene duplication and loss and independent interaction gain and loss. We introduce a combinatorial framework for encoding network histories, and we give a fast procedure that, given a set of duplication histories, in practice finds network histories with close to the minimum number of interaction gain or loss events. In contrast to previous studies, our method does not require knowing the relative ordering of unrelated duplication events. Results on simulated histories suggest that common ancestral networks can be accurately reconstructed using this parsimony approach. © 2011 Springer-Verlag.

关键词： Genes

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A Flow Artist for High-Dimensional Cellular Data 33

A Flow Artist for High-Dimensional Cellular Data

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33rd IEEE International Workshop on Machine Learning for Signal Processing, MLSP 2023

作者： MacDonald, Kincaid Bhaskar, Dhananjay Thampakkul, Guy Nguyen, Nhi Zhang, Joia Perlmutter, Michael Adelstein, Ian Krishnaswamy, Smita Yale University Department of Mathematics United States Pomona College Department of Mathematics United States University of Washington Department of Statistics United States Boise State University Department of Mathematics United States Yale University Department of Computer Science United States Yale University Applied Mathematics Program United States Yale University Computational Biology and Bioinformatics Program United States

ISBN: (纸本)9798350324112

We consider the problem of embedding point cloud data sampled from an underlying manifold with an associated flow or velocity. Such data arises in many contexts where static snapshots of dynamic entities are measured, including in high-throughput biology such as single-cell transcriptomics. Existing embedding techniques either do not utilize velocity information or embed the coordinates and velocities independently, i.e., they either impose velocities on top of an existing point embedding or embed points within a prescribed vector field. Here we present FlowArtist, a neural network that embeds points while jointly learning a vector field around the points. The combination allows FlowArtist to better separate and visualize velocity-informed structures. Our results, on toy datasets and single-cell RNA velocity data, illustrate the value of utilizing coordinate and velocity information in tandem for embedding and visualizing high-dimensional data. © 2023 IEEE.

关键词： RNA

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Biconic semi-copulas with a given section

Biconic semi-copulas with a given section

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8th Conference of the European Society for Fuzzy Logic and Technology, EUSFLAT 2013

作者： Jwaid, Tarad Baets, Bernard De Meyer, Hans De Mesiar, Radko Dept. of Mathematical Modelling Statistics and Bioinformatics Ghent University Coupure 653 B-9000 Gent Belgium Dept. of Applied Mathematics Computer Science Ghent University Krijgslaan 281 S9 B-9000 Gent Belgium Dep. of Mathematics and Descriptive Geometry Slovak University of Technology Radlinského 11 813 68 Bratislava Slovakia

ISBN: (纸本)9781629932194

Inspired by the notion of biconic semi-copulas, we introduce biconic semi-copulas with a given section. Such semi-copulas are constructed by linear interpolation on segments connecting the graph of a continuous and decreasing function to the points (0, 0) and (1, 1). Special classes of biconic semi-copulas with a given section such as biconic (quasi-)copulas with a given section are considered. Some examples are also provided © 2013. The authors-Published by Atlantis Press.

关键词： Fuzzy logic

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Two-way interaction analysis of obesity trait from Korean population using generalized MDR

Two-way interaction analysis of obesity trait from Korean po...

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IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Sungyoung Lee Sohee Oh Min-Seok Kwon Seungyeoun Lee Taesung Park Interdisciplinary Program in Bioinformatics Seoul National University Seoul South Korea Department of Statistics Seoul National University Seoul South Korea Department of Applied Mathematics Sejong University Seoul South Korea

Most common complex traits such as obesity, hypertension, diabetes, and cancers are known to be associated with multiple genes, environmental factors, and epistasis. Recently, the development of advanced genotyping technologies allows us to perform the genome-wide association studies (GWAS). For detecting the effects of multiple genes on complex traits, many approaches have been proposed for GWAS. Multifactor dimensionality reduction (MDR) proposed by Ritchie et al. (2001) is one of the powerful methods for detecting epistasis, which detects high order interactions among genes. However, MDR is computationally intensive due to its requirement of testing all possible n-way combinations. Thus, it is not practically feasible to apply MDR directly to analyzing large-scale GWAS data. We propose an efficient strategy to perform MDR analysis for GWAS data. First, select a subset of genetic factors such as SNPs with some marginal significance. Second, perform MDR analysis only for the selected genetic factors. Third, provide MDR summary results through network graph. Even for the MDR analysis for the selected SNPs, a fast computing system is required. We developed our own GPU based system for the large-scale GWAS data. We applied our strategy to Korean Association REsource (KARE) (8,838 individuals with 101,837 SNPs) for detecting two-way interactions of genetic factors associated with body mass index (BMI). We identified several genes and pathways which have been known to be associated with obesity.

关键词： Obesity bioinformatics Genomics Graphics processing unit Diabetes

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ON ESTIMATION OF OPTIMAL DYNAMIC TREATMENT REGIMES WITH MULTIPLE TREATMENTS FOR SURVIVAL DATA-WITH APPLICATION TO COLORECTAL CANCER STUDY

arXiv

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arXiv 2023年

作者： Liu, Zhishuai Zhan, Zishu Liu, Jian Yi, Danhui Lin, Cunjie Yang, Yufei Department of Biostatistics & Bioinformatics Duke University United States Department of Biostatistics School of Public Health Southern Medical University China School of Statistics Renmin University of China China Center for Applied Statistics School of Statistics Renmin University of China China Xiyuan Clinical Medical College Beijing University of Chinese Medicine China

Dynamic treatment regimes (DTR) are sequential decision rules corresponding to several stages of intervention. Each rule maps patients’ covariates to optional treatments. The optimal dynamic treatment regime is the one that maximizes the mean outcome of interest if followed by the overall population. Motivated by a clinical study on advanced colorectal cancer with traditional Chinese medicine, we propose a censored C-learning (CC-learning) method to estimate the dynamic treatment regime with multiple treatments using survival data. To address the challenges of multiple stages with right censoring, we modify the backward recursion algorithm in order to adapt to the flexible number and timing of treatments. For handling the problem of multiple treatments, we propose a framework from the classification perspective by transferring the problem of optimization with multiple treatment comparisons into an example-dependent cost-sensitive classification problem. With classification and regression tree (CART) as the classifier, the CC-learning method can produce an estimated optimal DTR with good interpretability. We theoretically prove the optimality of our method and numerically evaluate its finite sample performances through simulation. With the proposed method, we identify the interpretable tree treatment regimes at each stage for the advanced colorectal cancer treatment data from Xiyuan Hospital. Copyright © 2023, The Authors. All rights reserved.

关键词： Sampling

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On the causes of outliers in Affymetrix GeneChip data

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Briefings in Functional Genomics and Proteomics 2009年第3期8卷 199-212页

作者： Upton, Graham J.G. Sanchez-Graillet, Olivia Rowsell, Joanna Arteaga-Salas, Jose M. Graham, Neil S. Stalteri, Maria A. Memon, Farhat N. May, Sean T. Harrison, Andrew P. Departmet of Applied Statistics University of Essex Colchester Essex CO4 3SQ United Kingdom Departmet of Integrative Bioinformatics University of Essex Colchester Essex CO4 3SQ Wivenhoe Park United Kingdom University of Essex Colchester Essex CO4 3SQ Wivenhoe Park United Kingdom Department of Bioinformatics Nottingham Arabidopsis Stock Centre Nottingham United Kingdom Departmet of Bioinformatics University of Essex Colchester Essex CO4 3SQ Wivenhoe Park United Kingdom Nottingham Arabidopsis Stock Centre School of Biosciences University of Nottingham Nottingham United Kingdom Department of Mathematical Sciences Department of Biological Sciences University of Essex Colchester Essex CO4 3SQ Wivenhoe Park United Kingdom

We describe various types of outliers seen in Affymetrix GeneChip data. We have been able to utilise the data in the Gene Expression Omnibus to screen GeneChips across a range of scales, from single probes, to spatially adjacent fractions of arrays, to whole arrays, to whole experiments. In this review we describe a number of causes for why some reported intensities might be misleading on GeneChips. © The Author 2009. Published by Oxford University Press.

关键词： Affymetrix Genechips Blur Degradation Outliers Probe correlations Scanners

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