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Discussion of ‘Network cross-validation by edge sampling’

对《通过边抽样进行网络交叉验证》的讨论

We congratulate the authors for their exciting paper (Li et al., 2020) on the difficult problem of network model selection. The authors have proposed an interesting cross-validation procedure that selects the best network model according to the criterion ... One of the main novelties of the method is the use of matrix completion to reconstruct a full network |$\{\skew6\hat{A}_{ij}\}_{1\leq i\neq j\leq n}$| from the partial set of observations |$\{A_{ij}\}_{(i,\,j)\in\Omega}$|…

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Rejoinder: ‘Network cross-validation by edge sampling’

《基于边抽样的网络交叉验证》讨论回复

We thank the editor for organizing this discussion and giving us the opportunity to read experts’ perspectives on our work. We are grateful to all the discussants for their insightful contributions, which raise many important points and offer suggestions for potential improvements and generalizations of our method. In this rejoinder we provide some clarifications, remarks and selected numerical results in response to these comments. Lei & Lin (2020) conjecture, and we agree,…

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Discussion of ‘Network cross-validation by edge sampling’

《通过边抽样进行网络交叉验证》的讨论

We congratulate the authors for a nice contribution to the literature on model selection and assessment for complex network data. The article of Li et al. (2020) enriches the collection of tools available for network data analysis, bringing together different fields such as low-rank matrix estimation, cross-validation and network modelling. This discussion will focus on the |$V$|-fold variant of the edge sampling cross-validation method and its combination with other…

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Classification with imperfect training labels

训练标签不完美时的分类

Summary We study the effect of imperfect training data labels on the performance of classification methods. In a general setting, where the probability that an observation in the training dataset is mislabelled may depend on both the feature vector and the true label, we bound the excess risk of an arbitrary classifier trained with imperfect labels in terms of its excess risk for predicting a noisy label. This reveals conditions under which a classifier trained with…

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Estimation from cross-sectional data under a semiparametric truncation model

半参数截断模型下基于横截面数据的估计

Summary Cross-sectional sampling is often used when investigating inter-event times, resulting in left-truncated and right-censored data. In this paper, we consider a semiparametric truncation model in which the truncating variable is assumed to belong to a certain parametric family. We examine two methods of estimating both the truncation and the lifetime distributions. We obtain asymptotic representations of the estimators for the lifetime distribution and establish their…

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Network cross-validation by edge sampling

通过边抽样进行网络交叉验证

Summary While many statistical models and methods are now available for network analysis, resampling of network data remains a challenging problem. Cross-validation is a useful general tool for model selection and parameter tuning, but it is not directly applicable to networks since splitting network nodes into groups requires deleting edges and destroys some of the network structure. In this paper we propose a new network resampling strategy, based on splitting node pairs…

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Discontinuous Hamiltonian Monte Carlo for discrete parameters and discontinuous likelihoods

用于离散参数与不连续似然的非连续哈密顿蒙特卡洛

Summary Hamiltonian Monte Carlo has emerged as a standard tool for posterior computation. In this article we present an extension that can efficiently explore target distributions with discontinuous densities. Our extension in particular enables efficient sampling from ordinal parameters through the embedding of probability mass functions into continuous spaces. We motivate our approach through a theory of discontinuous Hamiltonian dynamics and develop a corresponding…

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The essential histogram

本质直方图

Summary The histogram is widely used as a simple, exploratory way of displaying data, but it is usually not clear how to choose the number and size of the bins. We construct a confidence set of distribution functions that optimally deal with the two main tasks of the histogram: estimating probabilities and detecting features such as increases and modes in the distribution. We define the essential histogram as the histogram in the confidence set with the fewest bins. Thus the…

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Lassoing eigenvalues

特征值的 Lasso 收缩

Summary The properties of penalized sample covariance matrices depend on the choice of the penalty function. In this paper, we introduce a class of nonsmooth penalty functions for the sample covariance matrix and demonstrate how their use results in a grouping of the estimated eigenvalues. We refer to the proposed method as lassoing eigenvalues, or the elasso.

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Doubly functional graphical models in high dimensions

高维双重函数型图模型

Summary We consider estimating a functional graphical model from multivariate functional observations. In functional data analysis, the classical assumption is that each function has been measured over a densely sampled grid. However, in practice the functions have often been observed, with measurement error, at a relatively small number of points. We propose a class of doubly functional graphical models to capture the evolving conditional dependence relationship among a…

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On the use of approximate Bayesian computation Markov chain Monte Carlo with inflated tolerance and post-correction

放宽容差并作事后校正的近似贝叶斯计算马尔可夫链蒙特卡洛

Summary Approximate Bayesian computation enables inference for complicated probabilistic models with intractable likelihoods using model simulations. The Markov chain Monte Carlo implementation of approximate Bayesian computation is often sensitive to the tolerance parameter: low tolerance leads to poor mixing and large tolerance entails excess bias. We propose an approach that involves using a relatively large tolerance for the Markov chain Monte Carlo sampler to ensure…

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Robust empirical Bayes small area estimation with density power divergence

基于密度幂散度的稳健经验贝叶斯小区域估计

Summary A two-stage normal hierarchical model called the Fay–Herriot model and the empirical Bayes estimator are widely used to obtain indirect and model-based estimates of means in small areas. However, the performance of the empirical Bayes estimator can be poor when the assumed normal distribution is misspecified. This article presents a simple modification that makes use of density power divergence and proposes a new robust empirical Bayes small area estimator. The mean…

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Adaptive nonparametric regression with the K-nearest neighbour fused lasso

利用 K 近邻融合套索的自适应非参数回归

Summary The fused lasso, also known as total-variation denoising, is a locally adaptive function estimator over a regular grid of design points. In this article, we extend the fused lasso to settings in which the points do not occur on a regular grid, leading to a method for nonparametric regression. This approach, which we call the $K$-nearest-neighbours fused lasso, involves computing the $K$-nearest-neighbours graph of the design points and then performing the fused lasso…

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On the marginal likelihood and cross-validation

边际似然与交叉验证的关系

Summary In Bayesian statistics, the marginal likelihood, also known as the evidence, is used to evaluate model fit as it quantifies the joint probability of the data under the prior. In contrast, non-Bayesian models are typically compared using cross-validation on held-out data, either through $k$-fold partitioning or leave-$p$-out subsampling. We show that the marginal likelihood is formally equivalent to exhaustive leave-$p$-out crossvalidation averaged over all values of $p$…

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Ensemble estimation and variable selection with semiparametric regression models

半参数回归模型的集成估计与变量选择

Summary We consider scenarios in which the likelihood function for a semiparametric regression model factors into separate components, with an efficient estimator of the regression parameter available for each component. An optimal weighted combination of the component estimators, named an ensemble estimator, may be employed as an overall estimate of the regression parameter, and may be fully efficient under uncorrelatedness conditions. This approach is useful when the full…

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‘Variance estimation in the particle filter’

《粒子滤波中的方差估计》勘误

Biometrika (2018), 105, pp. 609–25. There are missing curly braces in (4), which should read The displays in Remark 1 should consequently be changed to and In addition the sentence immediately after (5) should be changed to: Observe the resemblance between the right-hand sides of (4) and (5): the role of |$X_{i}$| is played by |$\sum_{j:E_{n}^{j}=i}\varphi(\zeta_{n}^{j})$|⁠, the sum of |$\varphi$| evaluated at the descendants of |$\zeta_{0}^{i}$|⁠. The consequences of this…

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Bayesian constraint relaxation

贝叶斯约束松弛

Summary Prior information often takes the form of parameter constraints. Bayesian methods include such information through prior distributions having constrained support. By using posterior sampling algorithms, one can quantify uncertainty without relying on asymptotic approximations. However, sharply constrained priors are not necessary in some settings and tend to limit modelling scope to a narrow set of distributions that are tractable computationally. We propose to…

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Model-free approach to quantifying the proportion of treatment effect explained by a surrogate marker

无模型方法量化替代标志物解释的治疗效应比例

Summary In randomized clinical trials, the primary outcome, $Y$, often requires long-term follow-up and/or is costly to measure. For such settings, it is desirable to use a surrogate marker, $S$, to infer the treatment effect on $Y$, $\Delta$. Identifying such an $S$ and quantifying the proportion of treatment effect on $Y$ explained by the effect on $S$ are thus of great importance. Most existing methods for quantifying the proportion of treatment effect are model based and…

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Consistent community detection in multi-layer network data

多层网络数据中的一致社区检测

Summary We consider multi-layer network data where the relationships between pairs of elements are reflected in multiple modalities, and may be described by multivariate or even high-dimensional vectors. Under the multi-layer stochastic block model framework we derive consistency results for a least squares estimation of memberships. Our theorems show that, as compared to single-layer community detection, a multi-layer network provides much richer information that allows for…

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Multisample estimation of bacterial composition matrices in metagenomics data

宏基因组数据中细菌组成矩阵的多样本估计

Summary Metagenomics sequencing is routinely applied to quantify bacterial abundances in microbiome studies, where bacterial composition is estimated based on the sequencing read counts. Due to limited sequencing depth and DNA dropouts, many rare bacterial taxa might not be captured in the final sequencing reads, which results in many zero counts. Naive composition estimation using count normalization leads to many zero proportions, which tend to result in inaccurate…

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A conditional density estimation partition model using logistic Gaussian processes

利用逻辑高斯过程的条件密度分区估计模型

Summary Conditional density estimation seeks to model the distribution of a response variable conditional on covariates. We propose a Bayesian partition model using logistic Gaussian processes to perform conditional density estimation. The partition takes the form of a Voronoi tessellation and is learned from the data using a reversible jump Markov chain Monte Carlo algorithm. The methodology models data in which the density changes sharply throughout the covariate space,…

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Regularized calibrated estimation of propensity scores with model misspecification and high-dimensional data

模型误设与高维数据下倾向得分的正则化校准估计

Summary Propensity scores are widely used with inverse probability weighting to estimate treatment effects in observational studies. We study calibrated estimation as an alternative to maximum likelihood estimation for fitting logistic propensity score models. We show that, with possible model misspecification, minimizing the expected calibration loss underlying the calibrated estimators involves reducing both the expected likelihood loss and a measure of relative errors…

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Bayesian sparse multiple regression for simultaneous rank reduction and variable selection

同时实现降秩与变量选择的贝叶斯稀疏多响应回归

Summary We develop a Bayesian methodology aimed at simultaneously estimating low-rank and row-sparse matrices in a high-dimensional multiple-response linear regression model. We consider a carefully devised shrinkage prior on the matrix of regression coefficients which obviates the need to specify a prior on the rank, and shrinks the regression matrix towards low-rank and row-sparse structures. We provide theoretical support to the proposed methodology by proving minimax…

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Measurement errors in the binary instrumental variable model

二元工具变量模型中的测量误差

Summary Instrumental variable methods can identify causal effects even when the treatment and outcome are confounded. We study the problem of imperfect measurements of the binary instrumental variable, treatment and outcome. We first consider nondifferential measurement errors, that is, the mismeasured variable does not depend on other variables given its true value. We show that the measurement error of the instrumental variable does not bias the estimate, that the…

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