Cross-validation (CV) is a popular method for model-selection. Unfortunately, it is not immediately obvious how to apply CV to unsupervised or exploratory contexts. This thesis discusses some extensions of cross-validation to unsupervised learning, specifically focusing on the problem of choosing how many principal components to keep. We introduce the latent factor model, define an objective criterion, and show how CV can be used to estimate the intrinsic dimensionality of a data set. Through both simulation and theory, we demonstrate that cross-validation is a valuable tool for unsupervised learning.
University of Alabama at Birmingham（阿拉巴马大学伯明翰分校）；Monash University（蒙纳士大学）；University of Washington（华盛顿大学）
Cross-validation (CV) is a technique used to estimate generalization error for prediction models. For pipeline modeling algorithms (i.e. modeling procedures with multiple steps), it has been recommended the entire sequence of steps be carried out during each replicate of CV to mimic the application of the entire pipeline to an external testing set. While theoretically sound, following this recommendation can lead to high computational costs when a pipeline modeling algorithm includes computationally expensive operations, e.g. imputation of missing values. There is a general belief that unsuper…
In this article, we derive concentration inequalities for the cross-validation estimate of the generalization error for empirical risk minimizers. In the general setting, we prove sanity-check bounds in the spirit of \cite{KR99} \textquotedblleft\textit{bounds showing that the worst-case error of this estimate is not much worse that of training error estimate} \textquotedblright . General loss functions and class of predictors with finite VC-dimension are considered. We closely follow the formalism introduced by \cite{DUD03} to cover a large variety of cross-validation procedures including lea…
Unsupervised Machine Learning for Scientific Discovery: Workflow and Best Practices
Department of Neuroscience, Baylor College of Medicine（神经科学系，贝勒医学院）；Department of Applied and Computational Mathematics and Statistics, University of Notre Dame（应用与计算数学和统计学系，圣母大学）；Department of Statistics, Columbia University（统计学系，哥伦比亚大学）；Zuckerman Institute & Irving Institute, Columbia University（Zuckerman研究所与Irving研究所，哥伦比亚大学）
In this article, we derive concentration inequalities for the cross-validation estimate of the generalization error for subagged estimators, both for classification and regressor. General loss functions and class of predictors with both finite and infinite VC-dimension are considered. We slightly generalize the formalism introduced by \cite{DUD03} to cover a large variety of cross-validation procedures including leave-one-out cross-validation, $k$-fold cross-validation, hold-out cross-validation (or split sample), and the leave-$\upsilon$-out cross-validation. \bigskip \noindent An interesting…
In this article, we derive concentration inequalities for the cross-validation estimate of the generalization error for stable predictors in the context of risk assessment. The notion of stability has been first introduced by \cite{DEWA79} and extended by \cite{KEA95}, \cite{BE01} and \cite{KUNIY02} to characterize class of predictors with infinite VC dimension. In particular, this covers $k$-nearest neighbors rules, bayesian algorithm (\cite{KEA95}), boosting,... General loss functions and class of predictors are considered. We use the formalism introduced by \cite{DUD03} to cover a large var…
Many clustering methods, including k-means, require the user to specify the number of clusters as an input parameter. A variety of methods have been devised to choose the number of clusters automatically, but they often rely on strong modeling assumptions. This paper proposes a data-driven approach to estimate the number of clusters based on a novel form of cross-validation. The proposed method differs from ordinary cross-validation, because clustering is fundamentally an unsupervised learning problem. Simulation and real data analysis results show that the proposed method outperforms existing…
In this report, we present an unsupervised machine learning method for determining groups of molecular systems according to similarity in their dynamics or structures using Ward's minimum variance objective function. We first apply the minimum variance clustering to a set of simulated tripeptides using the information theoretic Jensen-Shannon divergence between Markovian transition matrices in order to gain insight into how point mutations affect protein dynamics. Then, we extend the method to partition two chemoinformatic datasets according to structural similarity to motivate a train/validat…
University of Central Florida（中佛罗里达大学）；University of California San Diego（加利福尼亚大学圣迭戈分校）
Unsupervised meta-learning approaches rely on synthetic meta-tasks that are created using techniques such as random selection, clustering and/or augmentation. Unfortunately, clustering and augmentation are domain-dependent, and thus they require either manual tweaking or expensive learning. In this work, we describe an approach that generates meta-tasks using generative models. A critical component is a novel approach of sampling from the latent space that generates objects grouped into synthetic classes forming the training and validation data of a meta-task. We find that the proposed approac…
Cross-validation is the de facto standard for predictive model evaluation and selection. In proper use, it provides an unbiased estimate of a model's predictive performance. However, data sets often undergo various forms of data-dependent preprocessing, such as mean-centering, rescaling, dimensionality reduction, and outlier removal. It is often believed that such preprocessing stages, if done in an unsupervised manner (that does not incorporate the class labels or response values) are generally safe to do prior to cross-validation. In this paper, we study three commonly-practiced preprocessin…
SKADA-Bench: Benchmarking Unsupervised Domain Adaptation Methods with Realistic Validation On Diverse Modalities
École Polytechnique, IP Paris, CMAP, UMR 7641（巴黎理工学院）；Université Paris-Saclay, Inria, CEA（巴黎萨克雷大学）；Inria（法国国家信息与自动化技术研究院）；CEA（法国原子能机构）；Centre Borelli, ENS Paris-Saclay（巴黎-萨克雷大学博雷利中心）；Università degli Studi di Genova（热那亚大学）；Inria, Univ. Rennes 2, CNRS, IRISA（法国国家信息与自动化技术研究院、里昂二大学、法国国家科学研究中心、IRISA）
Determining the number of factors is essential to factor analysis. In this paper, we propose {an efficient cross validation (CV)} method to determine the number of factors in approximate factor models. The method applies CV twice, first along the directions of observations and then variables, and hence is referred to hereafter as double cross-validation (DCV). Unlike most CV methods, which are prone to overfitting, the DCV is statistically consistent in determining the number of factors when both dimension of variables and sample size are sufficiently large. Simulation studies show that DCV ha…
This article is an invited discussion of the article by Gronau and Wagenmakers (2018) that can be found at https://dx.doi.org/10.1007/s42113-018-0011-7.
Used to estimate the risk of an estimator or to perform model selection, cross-validation is a widespread strategy because of its simplicity and its apparent universality. Many results exist on the model selection performances of cross-validation procedures. This survey intends to relate these results to the most recent advances of model selection theory, with a particular emphasis on distinguishing empirical statements from rigorous theoretical results. As a conclusion, guidelines are provided for choosing the best cross-validation procedure according to the particular features of the problem…
We extend the standard Bayesian multivariate Gaussian generative data classifier by considering a generalization of the conjugate, normal-Wishart prior distribution and by deriving the hyperparameters analytically via evidence maximization. The behaviour of the optimal hyperparameters is explored in the high-dimensional data regime. The classification accuracy of the resulting generalized model is competitive with state-of-the art Bayesian discriminant analysis methods, but without the usual computational burden of cross-validation.
We present an efficient method to estimate cross-validation bandwidth parameters for kernel density estimation in very large datasets where ordinary cross-validation is rendered highly inefficient, both statistically and computationally. Our approach relies on calculating multiple cross-validation bandwidths on partitions of the data, followed by suitable scaling and averaging to return a partitioned cross-validation bandwidth for the entire dataset. The partitioned cross-validation approach produces substantial computational gains over ordinary cross-validation. We additionally show that part…
This paper develops detailed mathematical statistical theory of a new class of cross-validation techniques of local linear kernel hazards and their multiplicative bias corrections. The new class of cross-validation combines principles of local information and recent advances in indirect cross-validation. A few applications of cross-validating multiplicative kernel hazard estimation do exist in the literature. However, detailed mathematical statistical theory and small sample performance are introduced via this paper and further upgraded to our new class of best one-sided cross-validation. Best…
Cross-validation is a well-known and widely used bandwidth selection method in nonparametric regression estimation. However, this technique has two remarkable drawbacks: (i) the large variability of the selected bandwidths, and (ii) the inability to provide results in a reasonable time for very large sample sizes. To overcome these problems, bagging cross-validation bandwidths are analyzed in this paper. This approach consists in computing the cross-validation bandwidths for a finite number of subsamples and then rescaling the averaged smoothing parameters to the original sample size. Under a …
We consider the problem of bandwidth selection by cross-validation from a sequential point of view in a nonparametric regression model. Having in mind that in applications one often aims at estimation, prediction and change detection simultaneously, we investigate that approach for sequential kernel smoothers in order to base these tasks on a single statistic. We provide uniform weak laws of large numbers and weak consistency results for the cross-validated bandwidth. Extensions to weakly dependent error terms are discussed as well. The errors may be α-mixing or L2-near epoch dependent, which …
In this paper, for Lasso penalized linear regression models in high-dimensional settings, we propose a modified cross-validation method for selecting the penalty parameter. The methodology is extended to other penalties, such as Elastic Net. We conduct extensive simulation studies and real data analysis to compare the performance of the modified cross-validation method with other methods. It is shown that the popular $K$-fold cross-validation method includes many noise variables in the selected model, while the modified cross-validation works well in a wide range of coefficient and correlation…
This note corrects a mistake in the paper "consistent cross-validatory model-selection for dependent data: $hv$-block cross-validation" by Racine (2000). In his paper, he implied that the therein proposed $hv$-block cross-validation is consistent in the sense of Shao (1993). To get this intuition, he relied on the speculation that $hv$-block is a balanced incomplete block design (BIBD). This note demonstrates that this is not the case, and thus the theoretical consistency of $hv$-block remains an open question. In addition, I also provide a Python program counting the number of occurrences of …
Cross-validation is a popular non-parametric method for evaluating the accuracy of a predictive rule. The usefulness of cross-validation depends on the task we want to employ it for. In this note, I discuss a simple non-parametric setting, and find that cross-validation is asymptotically uninformative about the expected test error of any given predictive rule, but allows for asymptotically consistent model selection. The reason for this phenomenon is that the leading-order error term of cross-validation doesn't depend on the model being evaluated, and so cancels out when we compare two models.
We study the problem of selection of regularization parameter in penalized Gaussian graphical models. When the goal is to obtain the model with good predicting power, cross validation is the gold standard. We present a new estimator of Kullback-Leibler loss in Gaussian Graphical model which provides a computationally fast alternative to cross-validation. The estimator is obtained by approximating leave-one-out-cross validation. Our approach is demonstrated on simulated data sets for various types of graphs. The proposed formula exhibits superior performance, especially in the typical small sam…
It is shown that the log-likelihood of a hypothesis or model given some data is equivalent to an average of all leave-one-out cross-validation log-scores that can be calculated from all subsets of the data. This relation can be generalized to any $k$-fold cross-validation log-scores.
Cross validation residuals are well known for the ordinary least squares model. Here leave-M-out cross validation is extended to generalised least squares. The relationship between cross validation residuals and Cook's distance is demonstrated, in terms of an approximation to the difference in the generalised residual sum of squares for a model fit to all the data (training and test) and a model fit to a reduced dataset (training data only). For generalised least squares, as for ordinary least squares, there is no need to refit the model to reduced size datasets as all the values for K fold cr…
Recently many regularized estimators of large covariance matrices have been proposed, and the tuning parameters in these estimators are usually selected via cross-validation. However, there is no guideline on the number of folds for conducting cross-validation and there is no comparison between cross-validation and the methods based on bootstrap. Through extensive simulations, we suggest 10-fold cross-validation (nine-tenths for training and one-tenth for validation) be appropriate when the estimation accuracy is measured in the Frobenius norm, while 2-fold cross-validation (half for training …
One-sided cross-validation (OSCV) is a bandwidth selection method initially introduced by Hart and Yi (1998) in the context of smooth regression functions. Mart\'ınez-Miranda et al. (2009) developed a version of OSCV for smooth density functions. This article extends the method for nonsmooth densities. It also introduces the fully robust OSCV modification that produces consistent OSCV bandwidths for both smooth and nonsmooth cases. Practical implementations of the OSCV method for smooth and nonsmooth densities are discussed. One of the considered cross-validation kernels has potential for impr…
Cross-validation is one of the most popular model selection methods in statistics and machine learning. Despite its wide applicability, traditional cross validation methods tend to select overfitting models, due to the ignorance of the uncertainty in the testing sample. We develop a new, statistically principled inference tool based on cross-validation that takes into account the uncertainty in the testing sample. This new method outputs a set of highly competitive candidate models containing the best one with guaranteed probability. As a consequence, our method can achieve consistent variable…
One of the common goals of time series analysis is to use the observed series to inform predictions for future observations. In the absence of any actual new data to predict, cross-validation can be used to estimate a model's future predictive accuracy, for instance, for the purpose of model comparison or selection. Exact cross-validation for Bayesian models is often computationally expensive, but approximate cross-validation methods have been developed, most notably methods for leave-one-out cross-validation (LOO-CV). If the actual prediction task is to predict the future given the past, LOO-…
In this paper we provide insight into the empirical properties of indirect cross-validation (ICV), a new method of bandwidth selection for kernel density estimators. First, we describe the method and report on the theoretical results used to develop a practical-purpose model for certain ICV parameters. Next, we provide a detailed description of a numerical study which shows that the ICV method usually outperforms least squares cross-validation (LSCV) in finite samples. One of the major advantages of ICV is its increased stability compared to LSCV. Two real data examples show the benefit of usi…
Cross-validation is frequently used for model selection in a variety of applications. However, it is difficult to apply cross-validation to mixed effects models (including nonlinear mixed effects models or NLME models) due to the fact that cross-validation requires "out-of-sample" predictions of the outcome variable, which cannot be easily calculated when random effects are present. We describe two novel variants of cross-validation that can be applied to nonlinear mixed effects models. One variant, where out-of-sample predictions are based on post hoc estimates of the random effects, can be u…
While many statistical models and methods are now available for network analysis, resampling network data remains a challenging problem. Cross-validation is a useful general tool for model selection and parameter tuning, but is not directly applicable to networks since splitting network nodes into groups requires deleting edges and destroys some of the network structure. Here we propose a new network resampling strategy based on splitting node pairs rather than nodes applicable to cross-validation for a wide range of network model selection tasks. We provide a theoretical justification for our…
Cross-validation can be used to measure a model's predictive accuracy for the purpose of model comparison, averaging, or selection. Standard leave-one-out cross-validation (LOO-CV) requires that the observation model can be factorized into simple terms, but a lot of important models in temporal and spatial statistics do not have this property or are inefficient or unstable when forced into a factorized form. We derive how to efficiently compute and validate both exact and approximate LOO-CV for any Bayesian non-factorized model with a multivariate normal or Student-t distribution on the outcom…
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 cross-validation averaged over all values of $p$ and all held-out test sets when using the log posterior predictive probability as the scoring rule. Moreover, the log poster…
We investigate the accuracy of the two most common estimators for the maximum expected value of a general set of random variables: a generalization of the maximum sample average, and cross validation. No unbiased estimator exists and we show that it is non-trivial to select a good estimator without knowledge about the distributions of the random variables. We investigate and bound the bias and variance of the aforementioned estimators and prove consistency. The variance of cross validation can be significantly reduced, but not without risking a large bias. The bias and variance of different va…
K-fold cross-validation (CV) with squared error loss is widely used for evaluating predictive models, especially when strong distributional assumptions cannot be taken. However, CV with squared error loss is not free from distributional assumptions, in particular in cases involving non-i.i.d. data. This paper analyzes CV for correlated data. We present a criterion for suitability of standard CV in presence of correlations. When this criterion does not hold, we introduce a bias corrected cross-validation estimator which we term $CV_c,$ that yields an unbiased estimate of prediction error in man…
Efficient Cross-Validation for Sparse Linear Regression
Department of Analytics, Marketing and Operations, Imperial Business School, London, UK（分析、营销与运营系，帝国商务学院，伦敦，英国）；Department of Industrial and Systems Engineering, Viterbi School of Engineering, University of Southern California, CA（工业与系统工程系，维特比工程学院，美国南加州大学，CA）
