Random effect models are popular statistical models for detecting and correcting spurious sample correlations due to hidden confounders in genome-wide gene expression data. In applications where some confounding factors are known, estimating simultaneously the contribution of known and latent variance components in random effect models is a challenge that has so far relied on numerical gradient-based optimizers to maximize the likelihood function. This is unsatisfactory because the resulting solution is poorly characterized and the efficiency of the method may be suboptimal. Here we prove analytically that maximum-likelihood latent variables can always be chosen orthogonal to the known confounding factors, in other words, that maximum-likelihood latent variables explain sample covariances not already explained by known factors. Based on this result we propose a restricted maximum-likelihood method which estimates the latent variables by maximizing the likelihood on the restricted subspace orthogonal to the known confounding factors, and show that this reduces to probabilistic PCA on that subspace. The method then estimates the variance-covariance parameters by maximizing the remaining terms in the likelihood function given the latent variables, using a newly derived analytic solution for this problem. Compared to gradient-based optimizers, our method attains greater or equal likelihood values, can be computed using standard matrix operations, results in latent factors that don't overlap with any known factors, and has a runtime reduced by several orders of magnitude. Hence the restricted maximum-likelihood method facilitates the application of random effect modelling strategies for learning latent variance components to much larger gene expression datasets than possible with current methods.
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There has been a surge of interest in developing robust estimators for models with heavy-tailed data in statistics and machine learning. This paper proposes a log-truncated M-estimator for a large family of statistical regressions and establishes its excess risk bound under the condition that the data have $(1+\varepsilon)$-th moment with $\varepsilon \in (0,1]$. With an additional assumption on the associated risk function, we obtain an $\ell_2$-error bound for the estimation. Our theorems are applied to establish robust M-estimators for concrete regressions. Besides convex regressions such as quantile regression and generalized linear models, many non-convex regressions can also be fit into our theorems, we focus on robust deep neural network regressions, which can be solved by the stochastic gradient descent algorithms. Simulations and real data analysis demonstrate the superiority of log-truncated estimations over standard estimations.
Post-click conversion, as a strong signal indicating the user preference, is salutary for building recommender systems. However, accurately estimating the post-click conversion rate (CVR) is challenging due to the selection bias, i.e., the observed clicked events usually happen on users' preferred items. Currently, most existing methods utilize counterfactual learning to debias recommender systems. Among them, the doubly robust (DR) estimator has achieved competitive performance by combining the error imputation based (EIB) estimator and the inverse propensity score (IPS) estimator in a doubly robust way. However, inaccurate error imputation may result in its higher variance than the IPS estimator. Worse still, existing methods typically use simple model-agnostic methods to estimate the imputation error, which are not sufficient to approximate the dynamically changing model-correlated target (i.e., the gradient direction of the prediction model). To solve these problems, we first derive the bias and variance of the DR estimator. Based on it, a more robust doubly robust (MRDR) estimator has been proposed to further reduce its variance while retaining its double robustness. Moreover, we propose a novel double learning approach for the MRDR estimator, which can convert the error imputation into the general CVR estimation. Besides, we empirically verify that the proposed learning scheme can further eliminate the high variance problem of the imputation learning. To evaluate its effectiveness, extensive experiments are conducted on a semi-synthetic dataset and two real-world datasets. The results demonstrate the superiority of the proposed approach over the state-of-the-art methods. The code is available at //github.com/guosyjlu/MRDR-DL.
Choosing a shrinkage method can be done by selecting a penalty from a list of pre-specified penalties or by constructing a penalty based on the data. If a list of penalties for a class of linear models is given, we provide comparisons based on sample size and number of non-zero parameters under a predictive stability criterion based on data perturbation. These comparisons provide recommendations for penalty selection in a variety of settings. If the preference is to construct a penalty customized for a given problem, then we propose a technique based on genetic algorithms, again using a predictive criterion. We find that, in general, a custom penalty never performs worse than any commonly used penalties but that there are cases the custom penalty reduces to a recognizable penalty. Since penalty selection is mathematically equivalent to prior selection, our method also constructs priors. The techniques and recommendations we offer are intended for finite sample cases. In this context, we argue that predictive stability under perturbation is one of the few relevant properties that can be invoked when the true model is not known. Nevertheless, we study variable inclusion in simulations and, as part of our shrinkage selection strategy, we include oracle property considerations. In particular, we see that the oracle property typically holds for penalties that satisfy basic regularity conditions and therefore is not restrictive enough to play a direct role in penalty selection. In addition, our real data example also includes considerations merging from model mis-specification.
We study the selection of adjustment sets for estimating the interventional mean under an individualized treatment rule. We assume a non-parametric causal graphical model with, possibly, hidden variables and at least one adjustment set comprised of observable variables. Moreover, we assume that observable variables have positive costs associated with them. We define the cost of an observable adjustment set as the sum of the costs of the variables that comprise it. We show that in this setting there exist adjustment sets that are minimum cost optimal, in the sense that they yield non-parametric estimators of the interventional mean with the smallest asymptotic variance among those that control for observable adjustment sets that have minimum cost. Our results are based on the construction of a special flow network associated with the original causal graph. We show that a minimum cost optimal adjustment set can be found by computing a maximum flow on the network, and then finding the set of vertices that are reachable from the source by augmenting paths. The optimaladj Python package implements the algorithms introduced in this paper.
The problem of selecting optimal backdoor adjustment sets to estimate causal effects in graphical models with hidden and conditioned variables is addressed. Previous work has defined optimality as achieving the smallest asymptotic estimation variance and derived an optimal set for the case without hidden variables. For the case with hidden variables there can be settings where no optimal set exists and currently only a sufficient graphical optimality criterion of limited applicability has been derived. In the present work optimality is characterized as maximizing a certain adjustment information which allows to derive a necessary and sufficient graphical criterion for the existence of an optimal adjustment set and a definition and algorithm to construct it. Further, the optimal set is valid if and only if a valid adjustment set exists and has higher (or equal) adjustment information than the Adjust-set proposed in Perkovi{\'c} et al. [Journal of Machine Learning Research, 18: 1--62, 2018] for any graph. The results translate to minimal asymptotic estimation variance for a class of estimators whose asymptotic variance follows a certain information-theoretic relation. Numerical experiments indicate that the asymptotic results also hold for relatively small sample sizes and that the optimal adjustment set or minimized variants thereof often yield better variance also beyond that estimator class. Surprisingly, among the randomly created setups more than 90\% fulfill the optimality conditions indicating that also in many real-world scenarios graphical optimality may hold. Code is available as part of the python package \url{//github.com/jakobrunge/tigramite}.
Percentiles and more generally, quantiles are commonly used in various contexts to summarize data. For most distributions, there is exactly one quantile that is unbiased. For distributions like the Gaussian that have the same mean and median, that becomes the medians. There are different ways to estimate quantiles from finite samples described in the literature and implemented in statistics packages. It is possible to leverage the memory-less property of the exponential distribution and design high quality estimators that are unbiased and have low variance and mean squared errors. Naturally, these estimators out-perform the ones in statistical packages when the underlying distribution is exponential. But, they also happen to generalize well when that assumption is violated.
Implicit probabilistic models are models defined naturally in terms of a sampling procedure and often induces a likelihood function that cannot be expressed explicitly. We develop a simple method for estimating parameters in implicit models that does not require knowledge of the form of the likelihood function or any derived quantities, but can be shown to be equivalent to maximizing likelihood under some conditions. Our result holds in the non-asymptotic parametric setting, where both the capacity of the model and the number of data examples are finite. We also demonstrate encouraging experimental results.
Most of previous machine learning algorithms are proposed based on the i.i.d. hypothesis. However, this ideal assumption is often violated in real applications, where selection bias may arise between training and testing process. Moreover, in many scenarios, the testing data is not even available during the training process, which makes the traditional methods like transfer learning infeasible due to their need on prior of test distribution. Therefore, how to address the agnostic selection bias for robust model learning is of paramount importance for both academic research and real applications. In this paper, under the assumption that causal relationships among variables are robust across domains, we incorporate causal technique into predictive modeling and propose a novel Causally Regularized Logistic Regression (CRLR) algorithm by jointly optimize global confounder balancing and weighted logistic regression. Global confounder balancing helps to identify causal features, whose causal effect on outcome are stable across domains, then performing logistic regression on those causal features constructs a robust predictive model against the agnostic bias. To validate the effectiveness of our CRLR algorithm, we conduct comprehensive experiments on both synthetic and real world datasets. Experimental results clearly demonstrate that our CRLR algorithm outperforms the state-of-the-art methods, and the interpretability of our method can be fully depicted by the feature visualization.
We consider the task of learning the parameters of a {\em single} component of a mixture model, for the case when we are given {\em side information} about that component, we call this the "search problem" in mixture models. We would like to solve this with computational and sample complexity lower than solving the overall original problem, where one learns parameters of all components. Our main contributions are the development of a simple but general model for the notion of side information, and a corresponding simple matrix-based algorithm for solving the search problem in this general setting. We then specialize this model and algorithm to four common scenarios: Gaussian mixture models, LDA topic models, subspace clustering, and mixed linear regression. For each one of these we show that if (and only if) the side information is informative, we obtain parameter estimates with greater accuracy, and also improved computation complexity than existing moment based mixture model algorithms (e.g. tensor methods). We also illustrate several natural ways one can obtain such side information, for specific problem instances. Our experiments on real data sets (NY Times, Yelp, BSDS500) further demonstrate the practicality of our algorithms showing significant improvement in runtime and accuracy.
In this paper we introduce a covariance framework for the analysis of EEG and MEG data that takes into account observed temporal stationarity on small time scales and trial-to-trial variations. We formulate a model for the covariance matrix, which is a Kronecker product of three components that correspond to space, time and epochs/trials, and consider maximum likelihood estimation of the unknown parameter values. An iterative algorithm that finds approximations of the maximum likelihood estimates is proposed. We perform a simulation study to assess the performance of the estimator and investigate the influence of different assumptions about the covariance factors on the estimated covariance matrix and on its components. Apart from that, we illustrate our method on real EEG and MEG data sets. The proposed covariance model is applicable in a variety of cases where spontaneous EEG or MEG acts as source of noise and realistic noise covariance estimates are needed for accurate dipole localization, such as in evoked activity studies, or where the properties of spontaneous EEG or MEG are themselves the topic of interest, such as in combined EEG/fMRI experiments in which the correlation between EEG and fMRI signals is investigated.
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