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Learning torus PCA-based classification for multiscale RNA correction with application to SARS-CoV-2 基于学习环面pca的多尺度RNA校正分类及其在SARS-CoV-2中的应用
4区 数学 Q3 STATISTICS & PROBABILITY Pub Date : 2023-03-24 DOI: 10.1093/jrsssc/qlad004
Henrik Wiechers, Benjamin Eltzner, Kanti V Mardia, Stephan F Huckemann
Abstract Three-dimensional RNA structures frequently contain atomic clashes. Usually, corrections approximate the biophysical chemistry, which is computationally intensive and often does not correct all clashes. We propose fast, data-driven reconstructions from clash-free benchmark data with two-scale shape analysis: microscopic (suites) dihedral backbone angles, mesoscopic sugar ring centre landmarks. Our analysis relates concentrated mesoscopic scale neighbourhoods to microscopic scale clusters, correcting within-suite-backbone-to-backbone clashes exploiting angular shape and size-and-shape Fréchet means. Validation shows that learned classes highly correspond with literature clusters and reconstructions are well within physical resolution. We illustrate the power of our method using cutting-edge SARS-CoV-2 RNA.
三维RNA结构经常包含原子冲突。通常,校正近似于生物物理化学,这是计算密集的,往往不能纠正所有的冲突。我们提出了快速的,数据驱动的重建从无碰撞的基准数据与双尺度形状分析:微观(套)二面体主干角,介观糖环中心地标。我们的分析将集中的介观尺度邻域与微观尺度集群联系起来,利用角形状和大小形状的fracima方法在套件内校正骨干到骨干的冲突。验证表明,学习到的类与文献簇高度对应,重构在物理分辨率范围内。我们使用尖端的SARS-CoV-2 RNA来说明我们的方法的力量。
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引用次数: 0
Bayesian model comparison for mortality forecasting 死亡率预测的贝叶斯模型比较
IF 1.6 4区 数学 Q3 STATISTICS & PROBABILITY Pub Date : 2023-03-22 DOI: 10.1093/jrsssc/qlad021
Jackie S. T. Wong, J. Forster, Peter W. F. Smith
Stochastic models are appealing for mortality forecasting in their ability to generate intervals that quantify uncertainties underlying the forecasts. We present a fully Bayesian implementation of the age-period-cohort-improvement (APCI) model with overdispersion, which is compared with the Lee–Carter model with cohorts. We show that naive prior specification can yield misleading inferences, where we propose Laplace prior as an elegant solution. We also perform model averaging to incorporate model uncertainty. Our findings indicate that the APCI model offers better fit and forecast for England and Wales data spanning 1961–2002. Our approach also allows coherent inclusion of multiple sources of uncertainty, producing well-calibrated probabilistic intervals.
随机模型在死亡率预测中很有吸引力,因为它们能够产生区间,量化预测背后的不确定性。我们提出了具有过分散的年龄-时期-队列改善(APCI)模型的完全贝叶斯实现,并将其与具有队列的Lee-Carter模型进行了比较。我们表明朴素的先验规范可以产生误导性的推论,其中我们提出拉普拉斯先验作为一个优雅的解决方案。我们还执行模型平均以纳入模型不确定性。研究结果表明,APCI模型对英格兰和威尔士1961-2002年的数据具有较好的拟合和预测效果。我们的方法还允许连贯地包含多个不确定性来源,产生校准良好的概率区间。
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引用次数: 1
Modelling intra-annual tree stem growth with a distributional regression approach for Gaussian process responses 用高斯过程响应的分布回归方法模拟年际树茎生长
IF 1.6 4区 数学 Q3 STATISTICS & PROBABILITY Pub Date : 2023-03-22 DOI: 10.1093/jrsssc/qlad015
Hannes Riebl, N. Klein, T. Kneib
High-resolution circumference dendrometers measure the irreversible growth and the reversible shrinking and swelling due to the water content of a tree stem. We propose a novel statistical method to decompose these measurements into a permanent and a temporary component, while explaining differences between the trees and years by covariates. Our model embeds Gaussian processes with parametric mean and covariance functions as response structures in a distributional regression framework with structured additive predictors. We discuss different mean and covariance functions, connections with other model classes, Markov chain Monte Carlo inference, and the efficiency of our sampling scheme.
高分辨率周长树径计测量了由于树干含水量导致的不可逆生长和可逆收缩和膨胀。我们提出了一种新的统计方法,将这些测量分解为永久和临时成分,同时通过协变量解释树木和年份之间的差异。我们的模型将具有参数均值和协方差函数的高斯过程作为响应结构嵌入到具有结构化可加性预测因子的分布回归框架中。我们讨论了不同的均值和协方差函数,与其他模型类的联系,马尔可夫链蒙特卡罗推理,以及我们的抽样方案的效率。
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引用次数: 0
Approximately linear INGARCH models for spatio-temporal counts 时空计数的近似线性INGARCH模型
IF 1.6 4区 数学 Q3 STATISTICS & PROBABILITY Pub Date : 2023-03-16 DOI: 10.1093/jrsssc/qlad018
Malte Jahn, C. Weiß, Hee-Young Kim
Existing integer-valued generalised autoregressive conditional heteroskedasticity (INGARCH) models for spatio-temporal counts do not allow for negative parameter and autocorrelation values. Using approximately linear INGARCH models, the unified and flexible spatio-temporal (B)INGARCH framework for modelling unbounded (bounded) counts is proposed. These models combine negative dependencies with kinds of a long memory. They are easily adapted to special marginal features or cross-dependencies: When modelling precipitation data (counts of rainy hours), we account for zero-inflation, while for cloud-coverage data (counts of okta), we deal with missing data and additional cross-correlation. A copula related to the spatial error model shows an appealing performance.
现有的用于时空计数的整数值广义自回归条件异方差(INGARCH)模型不允许负参数和自相关值。利用近似线性的INGARCH模型,提出了用于无界计数建模的统一、灵活的时空INGARCH框架。这些模型将消极依赖与长期记忆相结合。它们很容易适应特殊的边缘特征或交叉依赖:当建模降水数据(降雨时数)时,我们考虑零通货膨胀,而对于云覆盖数据(okta计数),我们处理缺失数据和额外的相互关联。与空间误差模型相关的联结关系表现出令人满意的性能。
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引用次数: 3
Bayesian matrix completion for hypothesis testing. 用于假设检验的贝叶斯矩阵补全。
IF 1 4区 数学 Q3 STATISTICS & PROBABILITY Pub Date : 2023-03-15 eCollection Date: 2023-05-01 DOI: 10.1093/jrsssc/qlac005
Bora Jin, David B Dunson, Julia E Rager, David M Reif, Stephanie M Engel, Amy H Herring

We aim to infer bioactivity of each chemical by assay endpoint combination, addressing sparsity of toxicology data. We propose a Bayesian hierarchical framework which borrows information across different chemicals and assay endpoints, facilitates out-of-sample prediction of activity for chemicals not yet assayed, quantifies uncertainty of predicted activity, and adjusts for multiplicity in hypothesis testing. Furthermore, this paper makes a novel attempt in toxicology to simultaneously model heteroscedastic errors and a nonparametric mean function, leading to a broader definition of activity whose need has been suggested by toxicologists. Real application identifies chemicals most likely active for neurodevelopmental disorders and obesity.

我们的目标是通过检测终点组合来推断每种化学品的生物活性,从而解决毒理学数据稀缺的问题。我们提出了一个贝叶斯分层框架,该框架可借用不同化学品和检测终点的信息,便于对尚未检测的化学品进行样本外活性预测,量化预测活性的不确定性,并在假设检验中调整多重性。此外,本文还在毒理学方面做出了新的尝试,即同时模拟异方差误差和非参数平均函数,从而为活性下一个更宽泛的定义,毒理学家已提出了这一需求。实际应用确定了最有可能对神经发育障碍和肥胖具有活性的化学物质。
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引用次数: 0
Enumeration of regular fractional factorial designs with four-level and two-level factors 列举具有四水平和二水平因子的规则分数因子设计
IF 1.6 4区 数学 Q3 STATISTICS & PROBABILITY Pub Date : 2023-03-10 DOI: 10.1093/jrsssc/qlad031
Alexandre Bohyn, E. Schoen, P. Goos
Designs for screening experiments usually include factors with two levels only. Adding a few four-level factors allows for the inclusion of multi-level categorical factors or quantitative factors with possible quadratic or third-order effects. Three examples motivated us to generate a large catalogue of designs with two-level factors as well as four-level factors. To create the catalogue, we considered three methods. In the first method, we select designs using a search table, and in the second method, we use a procedure that selects candidate designs based on the properties of their projections into fewer factors. The third method is actually a benchmark method, in which we use a general orthogonal array enumeration algorithm. We compare the efficiencies of the new methods for generating complete sets of nonisomorphic designs. Finally, we use the most efficient method to generate a catalogue of designs with up to three four-level factors and up to 20 two-level factors for run sizes 16, 32, 64, and 128. In some cases, a complete enumeration was infeasible. For these cases, we used a bounded enumeration strategy instead. We demonstrate the usefulness of the catalogue by revisiting the motivating examples.
筛选实验的设计通常只包括两个水平的因素。添加一些四级因素允许包含多级分类因素或可能具有二次或三阶效应的定量因素。三个例子促使我们产生了一个包含两级因素和四级因素的大型设计目录。为了创建目录,我们考虑了三种方法。在第一种方法中,我们使用搜索表选择设计,而在第二种方法中,我们使用基于其投影到较少因素的属性选择候选设计的过程。第三种方法实际上是一种基准方法,其中我们使用一般的正交数组枚举算法。我们比较了生成非同构设计完备集的新方法的效率。最后,我们使用最有效的方法生成一个设计目录,其中包含多达三个四水平因子和多达20个两水平因子,运行规模为16、32、64和128。在某些情况下,完整的列举是不可行的。对于这些情况,我们使用了有界枚举策略。我们通过回顾激励的例子来证明目录的有用性。
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引用次数: 0
A spatial stochastic frontier model introducing inefficiency spillovers 引入无效率溢出的空间随机前沿模型
IF 1.6 4区 数学 Q3 STATISTICS & PROBABILITY Pub Date : 2023-02-24 DOI: 10.1093/jrsssc/qlad012
Federica Galli
This paper develops a spatial Durbin stochastic frontier model for panel data introducing spillover effects in the determinants of technical efficiency (SDF-STE). The model nests several existing spatial and non-spatial stochastic frontier specifications and is estimated using maximum-likelihood techniques. Estimates are shown to be unbiased even for small sample sizes and for alternative specifications of the spatial weight matrix implementing different Monte Carlo simulations. Finally, an application to the Italian accommodation sector is provided. Empirical findings suggest the relevance of the SDF-STE model in capturing labour productivity and knowledge spillover effects.
本文建立了面板数据的空间Durbin随机前沿模型,引入了技术效率决定因素(SDF-STE)的溢出效应。该模型嵌套了几种现有的空间和非空间随机前沿规范,并使用最大似然技术进行估计。即使对于小样本量和实现不同蒙特卡罗模拟的空间权重矩阵的替代规范,估计也显示为无偏的。最后,提供了意大利住宿部门的申请。实证结果表明,SDF-STE模型在捕捉劳动生产率和知识溢出效应方面具有相关性。
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引用次数: 0
Using natural strata when examining unmeasured biases in an observational study of neurological side effects of antibiotics 在抗生素神经系统副作用的观察性研究中,使用天然地层检查未测量偏差
IF 1.6 4区 数学 Q3 STATISTICS & PROBABILITY Pub Date : 2023-02-23 DOI: 10.1093/jrsssc/qlad010
K. Brumberg, Darcy E. Ellis, D. Small, S. Hennessy, P. Rosenbaum
Fluoroquinolones are widely prescribed antibiotics that carry a US Food and Drug Administration warning about possible side-effects on the central and peripheral nervous system. We compare 436,891 patients with sinusitis treated with fluoroquinolones to two control groups treated with azithromycin or amoxicillin. In addition to looking for nervous system complications, we look for evidence of bias using outcomes for which an effect was not anticipated. The comparison uses ‘natural strata’ that form control groups proportional in size to the treated group and balance many covariates beyond those that define the strata. The main technical contribution is a new method for near-optimal construction of natural strata with multiple groups. The online supplement material contains proofs, details, and information about the R package natstrat and replication.
氟喹诺酮类药物是一种广泛使用的抗生素,美国食品和药物管理局警告说,这种药物可能对中枢和周围神经系统产生副作用。我们比较了436,891例使用氟喹诺酮类药物治疗的鼻窦炎患者与使用阿奇霉素或阿莫西林治疗的对照组。除了寻找神经系统并发症外,我们还使用未预料到的结果寻找偏倚的证据。比较使用“自然地层”,形成与处理组成比例的对照组,并平衡定义地层之外的许多协变量。主要的技术贡献是提出了一种多群天然地层近最优施工的新方法。在线补充材料包含证据、细节和有关R包的natstrat和复制的信息。
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引用次数: 0
The importance of context in extreme value analysis with application to extreme temperatures in the USA and Greenland 语境在极端值分析中的重要性,并应用于美国和格陵兰岛的极端温度
IF 1.6 4区 数学 Q3 STATISTICS & PROBABILITY Pub Date : 2023-02-16 DOI: 10.1093/jrsssc/qlad020
D. Clarkson, E. Eastoe, A. Leeson
Statistical extreme value models allow estimation of the frequency, magnitude and spatio-temporal extent of extreme temperature events in the presence of climate change. Unfortunately, the assumptions of many standard methods are not valid for complex environmental data sets, with a realistic statistical model requiring appropriate incorporation of scientific context. We examine two case studies in which the application of routine extreme value methods result in inappropriate models and inaccurate predictions. In the first scenario, record-breaking temperatures experienced in the US in the summer of 2021 are found to exceed the maximum feasible temperature predicted from a standard extreme value analysis of pre-2021 data. Incorporating random effects into the standard methods accounts for additional variability in the model parameters, reflecting shifts in unobserved climatic drivers and permitting greater accuracy in return period prediction. The second scenario examines ice surface temperatures in Greenland. The temperature distribution is found to have a poorly-defined upper tail, with a spike in observations just below 0◦C and an unexpectedly large number of measurements above this value. A Gaussian mixture model fit to the full range of measurements improves fit and predictive abilities in the upper tail when compared to traditional extreme value methods.
统计极值模式可以在气候变化的情况下估计极端温度事件的频率、大小和时空范围。不幸的是,许多标准方法的假设对于复杂的环境数据集是无效的,一个现实的统计模型需要适当地结合科学背景。我们研究了两个案例研究,其中应用常规极值方法导致不适当的模型和不准确的预测。在第一种情况下,2021年夏季美国经历的破纪录温度被发现超过了根据2021年前数据的标准极值分析预测的最高可行温度。将随机效应纳入标准方法可以解释模式参数的额外变率,反映未观测到的气候驱动因素的变化,并使回归期预测更加准确。第二种情景考察的是格陵兰岛的冰层表面温度。温度分布被发现有一个不明确的上尾,在0℃以下的观察中有一个尖峰,在这个值以上的测量出乎意料地多。与传统的极值方法相比,高斯混合模型对整个测量范围的拟合提高了上尾的拟合和预测能力。
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引用次数: 1
Statistical calibration for infinite many future values in linear regression: simultaneous or pointwise tolerance intervals or what else? 线性回归中无限多个未来值的统计校准:同步或点公差区间或其他什么?
IF 1.6 4区 数学 Q3 STATISTICS & PROBABILITY Pub Date : 2023-02-13 DOI: 10.1093/jrsssc/qlac004
Yang Han, Yujia Sun, Lingjiao Wang, Wei Liu, F. Bretz
Statistical calibration using regression is a useful statistical tool with many applications. For confidence sets for x-values associated with infinitely many future y-values, there is a consensus in the statistical literature that the confidence sets constructed should guarantee a key property. While it is well known that the confidence sets based on the simultaneous tolerance intervals (STIs) guarantee this key property conservatively, it is desirable to construct confidence sets that satisfy this property exactly. Also, there is a misconception that the confidence sets based on the pointwise tolerance intervals (PTIs) also guarantee this property. This paper constructs the weighted simultaneous tolerance intervals (WSTIs) so that the confidence sets based on the WSTIs satisfy this property exactly if the future observations have the x-values distributed according to a known specific distribution F(⋅). Through the lens of the WSTIs, convincing counter examples are also provided to demonstrate that the confidence sets based on the PTIs do not guarantee the key property in general and so should not be used. The WSTIs have been applied to real data examples to show that the WSTIs can produce more accurate calibration intervals than STIs and PTIs.
使用回归的统计校准是一种有用的统计工具,具有许多应用。对于与无限多个未来y值相关的x值的置信集,在统计文献中有一个共识,即构造的置信集应该保证一个关键属性。众所周知,基于同步容差区间的置信集保守地保证了这一关键属性,但我们需要构造完全满足这一属性的置信集。此外,还有一种误解,认为基于点向公差区间(pti)的置信集也保证了这一特性。本文构造了加权同时容差区间(WSTIs),当未来观测值的x值按照已知的特定分布F(⋅)分布时,基于WSTIs的置信集完全满足这一性质。通过wsti的视角,还提供了令人信服的反例,以证明基于pti的置信集一般不能保证关键属性,因此不应使用。将WSTIs应用于实际数据实例,结果表明WSTIs比STIs和pti能得到更精确的标定区间。
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引用次数: 0
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Journal of the Royal Statistical Society Series C-Applied Statistics
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