Advances in data collecting technologies in genomics have significantly increased the need for tools designed to study the genetic basis of many diseases. Effective statistical methods should excel in both prediction accuracy and biomarker identification. We introduce a novel approach to high-dimensional binary classification that integrates regularization with ensembling techniques. The method constructs compact ensembles of interpretable models derived by optimizing a global objective function. In medical genomics applications, the proposed approach identifies critical biomarkers overlooked by competing methods. We develop a variable importance ranking system to help researchers prioritize promising genes. The method's asymptotic properties are established, and an efficient computational algorithm is provided. Through extensive simulations across complex scenarios and analysis of cancer genomics datasets, we demonstrate strong predictive performance. Based on the numerical experiments, we offer practical guidelines for determining optimal ensemble size.
In this paper we discuss how to evaluate the differences between fitted logistic regression models across sub-populations. Our motivating example is in studying computerized diagnosis for learning disabilities, where sub-populations based on gender may or may not require separate models. In this context, significance tests for hypotheses of no difference between populations may provide perverse incentives, as larger variances and smaller samples increase the probability of not-rejecting the null. We argue that equivalence testing for a prespecified tolerance level on population differences inc…
Logistic regression is an important statistical tool for assessing the probability of an outcome based upon some predictive variables. Standard methods can only deal with precisely known data, however many datasets have uncertainties which traditional methods either reduce to a single point or completely disregarded. In this paper we show that it is possible to include these uncertainties by considering an imprecise logistic regression model using the set of possible models that can be obtained from values from within the intervals. This has the advantage of clearly expressing the epistemic un…
We propose a new algorithm called PLUTO for building logistic regression trees to binary response data. PLUTO can capture the nonlinear and interaction patterns in messy data by recursively partitioning the sample space. It fits a simple or a multiple linear logistic regression model in each partition. PLUTO employs the cyclical coordinate descent method for estimation of multiple linear logistic regression models with elastic net penalties, which allows it to deal with high-dimensional data efficiently. The tree structure comprises a graphical description of the data. Together with the logist…
In quantitative genetics, statistical modeling techniques are used to facilitate advances in the understanding of which genes underlie agronomically important traits and have enabled the use of genome-wide markers to accelerate genetic gain. The logistic regression model is a statistically optimal approach for quantitative genetics analysis of binary traits. To encourage more widespread use of the logistic model in such analyses, efforts need to be made to address separation, which occurs whenever a specific combination of predictors can perfectly predict the value of a binary trait. Data sepa…
We propose a penalized likelihood method that simultaneously fits the multinomial logistic regression model and combines subsets of the response categories. The penalty is non differentiable when pairs of columns in the optimization variable are equal. This encourages pairwise equality of these columns in the estimator, which corresponds to response category combination. We use an alternating direction method of multipliers algorithm to compute the estimator and we discuss the algorithm's convergence. Prediction and model selection are also addressed.
Compared to the conditional mean as a simple point estimator, the conditional density function is more informative to describe the distributions with multi-modality, asymmetry or heteroskedasticity. In this paper, we propose a novel parametric conditional density estimation method by showing the connection between the general density and the likelihood function of inhomogeneous Poisson process models. The maximum likelihood estimates can be obtained via weighted logistic regressions, and the computation can be significantly relaxed by combining a block-wise alternating maximization scheme and …
This paper rigorously establishes that the existence of the maximum likelihood estimate (MLE) in high-dimensional logistic regression models with Gaussian covariates undergoes a sharp `phase transition'. We introduce an explicit boundary curve $h_{\text{MLE}}$, parameterized by two scalars measuring the overall magnitude of the unknown sequence of regression coefficients, with the following property: in the limit of large sample sizes $n$ and number of features $p$ proportioned in such a way that $p/n \rightarrow κ$, we show that if the problem is sufficiently high dimensional in the sense tha…
We propose an optimal estimating equation for logistic regression with linked data while accounting for false positives. It builds on a previous solution but estimates the regression coefficients with a smaller variance, in large samples.
Department of Indutrial Engineering and Operations Research, University of California, Berkeley（加州大学伯克利分校工业工程与运筹学系）
In logistic regression, it is often desirable to utilize regularization to promote sparse solutions, particularly for problems with a large number of features compared to available labels. In this paper, we present screening rules that safely remove features from logistic regression with $\ell_0-\ell_2$ regularization before solving the problem. The proposed safe screening rules are based on lower bounds from the Fenchel dual of strong conic relaxations of the logistic regression problem. Numerical experiments with real and synthetic data suggest that a high percentage of the features can be e…
Explicitly accounting for all applicable independent variables, even when the model being tested does not, is critical in testing goodness-of-fit for logistic regression. This can increase statistical power by orders of magnitude.
This is a note on logistic regression models and logistic kernel machine models. It contains derivations to some of the expressions in a paper -- SNP Set Analysis for Detecting Disease Association Using Exon Sequence Data -- submitted to BMC proceedings by these authors.
This paper infers a single parameter in non-sparse logistic regression models. By transforming the null hypothesis into a moment condition, we construct the test statistic and obtain the asymptotic null distribution. Numerical experiments show that our method performs well.
In several FICO studies logistic regression has been shown to be a very competitive technology for developing unrestricted scoring models, especially for performance metrics like ROC area. Application of logistic regression has been hampered by the lack of software to handle complex score engineering such as shape and pattern constraints. The purpose of this paper is to develop a sequential quadratic programming algorithm for score engineered logistic regression. This approach is based on a simple Taylor series expansion of minus log likelihood, which is locally quadratic. and fits in with the…
Genomic data arising from a genome-wide association study (GWAS) are often not only of large-scale, but also incomplete. A specific form of their incompleteness is missing values with non-ignorable missingness mechanism. The intrinsic complications of genomic data present significant challenges in developing an unbiased and informative procedure of phenotype-genotype association analysis by a statistical variable selection approach. In this paper we develop a coherent procedure of categorical phenotype-genotype association analysis, in the presence of missing values with non-ignorable missingn…
This study aims to show the fundamental difference between logistic regression and Bayesian classifiers in the case of exponential and unexponential families of distributions, yielding the following findings. First, the logistic regression is a less general representation of a Bayesian classifier. Second, one should suppose distributions of classes for the correct specification of logistic regression equations. Third, in specific cases, there is no difference between predicted probabilities from correctly specified generative Bayesian classifier and discriminative logistic regression.
In this paper we propose a principal component Liu-type logistic estimator by combining the principal component logistic regression estimator and Liu-type logistic estimator to overcome the multicollinearity problem. The superiority of the new estimator over some related estimators are studied under the asymptotic mean squared error matrix. A Monte Carlo simulation experiment is designed to compare the performances of the estimators using mean squared error criterion. Finally, a conclusion section is presented.
Genomic instability, the propensity of aberrations in chromosomes, plays a critical role in the development of many diseases. High throughput genotyping experiments have been performed to study genomic instability in diseases. The output of such experiments can be summarized as high dimensional binary vectors, where each binary variable records aberration status at one marker locus. It is of keen interest to understand how these aberrations interact with each other. In this paper, we propose a novel method, \texttt{LogitNet}, to infer the interactions among aberration events. The method is bas…
Logistic regression models are a popular and effective method to predict the probability of categorical response data. However inference for these models can become computationally prohibitive for large datasets. Here we adapt ideas from symbolic data analysis to summarise the collection of predictor variables into histogram form, and perform inference on this summary dataset. We develop ideas based on composite likelihoods to derive an efficient one-versus-rest approximate composite likelihood model for histogram-based random variables, constructed from low-dimensional marginal histograms obt…
Feature selection is a standard approach to understanding and modeling high-dimensional classification data, but the corresponding statistical methods hinge on tuning parameters that are difficult to calibrate. In particular, existing calibration schemes in the logistic regression framework lack any finite sample guarantees. In this paper, we introduce a novel calibration scheme for $\ell_1$-penalized logistic regression. It is based on simple tests along the tuning parameter path and is equipped with optimal guarantees for feature selection. It is also amenable to easy and efficient implement…
French National Institute for Transport and Safety Research (INRETS)（法国国家运输与安全研究所（INRETS））；Compiègne University of Technology（贡比涅技术大学）
A new approach for signal parametrization, which consists of a specific regression model incorporating a discrete hidden logistic process, is proposed. The model parameters are estimated by the maximum likelihood method performed by a dedicated Expectation Maximization (EM) algorithm. The parameters of the hidden logistic process, in the inner loop of the EM algorithm, are estimated using a multi-class Iterative Reweighted Least-Squares (IRLS) algorithm. An experimental study using simulated and real data reveals good performances of the proposed approach.
This article develops the theoretical framework needed to study the multinomial logistic regression model for complex sample design with pseudo minimum phi-divergence estimators. Through a numerical example and simulation study new estimators are proposed for the parameter of the logistic regression model with overdispersed multinomial distributions for the response variables, the pseudo minimum Cressie-Read divergence estimators, as well as new estimators for the intra-cluster correlation coefficient. The results show that the Binder's method for the intra-cluster correlation coefficient exhi…
We obtain new mathematical properties of the exponentiated odd log-logistic family of distributions, and of its special case named the exponentiated odd log-logistic Weibull, and its log transformed. A new location and scale regression model is constructed, and some simulations are carried out to verify the behavior of the maximum likelihood estimators, and of the modified deviance-based residuals. The methodology is applied to the Japanese-Brazilian emigration data.
This paper looks at effects, due to the boundary, on inference in logistic regression. It shows that first -- and, indeed, higher -- order asymptotic results are not uniform across the model. Near the boundary, effects such as high skewness, discreteness and collinearity dominate, any of which could render inference based on asymptotic normality suspect. A highly interpretable diagnostic tool is proposed allowing the analyst to check if the boundary is going to have an appreciable effect on standard inferential techniques.
In many applications, linear models fit the data poorly. This article studies an appealing alternative, the generalized regression model. This model only assumes that there exists an unknown monotonically increasing link function connecting the response $Y$ to a single index $X^Tβ^*$ of explanatory variables $X\in\mathbb{R}^d$. The generalized regression model is flexible and covers many widely used statistical models. It fits the data generating mechanisms well in many real problems, which makes it useful in a variety of applications where regression models are regularly employed. In low dime…
In order to overcome multicollinearity, we propose a stochastic restricted Liu-type max- imum likelihood estimator by incorporating Liu-type maximum likelihood estimator (Inan and Erdo- gan, 2013) to the logistic regression model when the linear restrictions are stochastic. We also discuss the properties of the new estimator. Moreover, we give a method to choose the biasing parameter in the new estimator. Finally, a simulation study is given to show the performance of the new estimator.
We consider Bayesian logistic regression models with group-structured covariates. In high-dimensional settings, it is often assumed that only small portion of groups are significant, thus consistent group selection is of significant importance. While consistent frequentist group selection methods have been proposed, theoretical properties of Bayesian group selection methods for logistic regression models have not been investigated yet. In this paper, we consider a hierarchical group spike and slab prior for logistic regression models in high-dimensional settings. Under mild conditions, we esta…
Consider a set of categorical variables $\mathcal{P}$ where at least one, denoted by $Y$, is binary. The log-linear model that describes the counts in the resulting contingency table implies a specific logistic regression model, with the binary variable as the outcome. Extending results in Christensen (1997), by also considering the case where factors present in the contingency table disappear from the logistic regression model, we prove that the Maximum Likelihood Estimate (MLE) for the parameters of the logistic regression equals the MLE for the corresponding parameters of the log-linear mod…
Recently, a very attractive logistic regression inference method for exponential family Gibbs spatial point processes was introduced. We combined it with the technique of quadratic tangential variational approximation and derived a new Bayesian technique for analysing spatial point patterns. The technique is described in detail, and demonstrated on numerical examples.
In this paper, we propose a new method remMap -- REgularized Multivariate regression for identifying MAster Predictors -- for fitting multivariate response regression models under the high-dimension-low-sample-size setting. remMap is motivated by investigating the regulatory relationships among different biological molecules based on multiple types of high dimensional genomic data. Particularly, we are interested in studying the influence of DNA copy number alterations on RNA transcript levels. For this purpose, we model the dependence of the RNA expression levels on DNA copy numbers through m…
Logistic regression has been widely applied in the field of biomedical research for a long time. In some applications, covariates of interest have a natural structure, such as being a matrix, at the time of collection. The rows and columns of the covariate matrix then have certain physical meanings, and they must contain useful information regarding the response. If we simply stack the covariate matrix as a vector and fit the conventional logistic regression model, relevant information can be lost, and the problem of inefficiency will arise. Motivated from these reasons, we propose in this pap…
Objective: To investigate the impact of different logistic regression estimators applied to RDS samples obtained by simulation and real data. Methods: Four simulated populations were created combining different connectivity models, levels of clusterization and infection processes. Each subject in the population received two attributes, only one of them related to the infection process. From each population, RDS samples with different sizes were obtained. Similarly, RDS samples were obtained from a real-world dataset. Three logistic regression estimators were applied to assess the association b…
Consider a set of categorical variables where at least one of them is binary. The log-linear model that describes the counts in the resulting contingency table implies a specific logistic regression model, with the binary variable as the outcome. Within the Bayesian framework, the $g$-prior and mixtures of $g$-priors are commonly assigned to the parameters of a generalized linear model. We prove that assigning a $g$-prior (or a mixture of $g$-priors) to the parameters of a certain log-linear model designates a $g$-prior (or a mixture of $g$-priors) on the parameters of the corresponding logist…
A new family of minimum distance estimators for binary logistic regression models based on $ϕ$-divergence measures is introduced. The so called "pseudo minimum phi-divergence estimator"(PM$ϕ$E) family is presented as an extension of "minimum phi-divergence estimator" (M$ϕ$E) for general sample survey designs and contains, as a particular case, the pseudo maximum likelihood estimator (PMLE) considered in Roberts et al. \cite{r}. Through a simulation study it is shown that some PM$ϕ$Es have a better behaviour, in terms of efficiency, than the PMLE.
We introduce Bayesian additive regression trees (BART) for log-linear models including multinomial logistic regression and count regression with zero-inflation and overdispersion. BART has been applied to nonparametric mean regression and binary classification problems in a range of settings. However, existing applications of BART have been limited to models for Gaussian "data", either observed or latent. This is primarily because efficient MCMC algorithms are available for Gaussian likelihoods. But while many useful models are naturally cast in terms of latent Gaussian variables, many others …
This paper derives a new family of estimators, namely the minimum density power divergence estimators, as a robust generalization of the maximum likelihood estimator for the polytomous logistic regression model. Based on these estimators, a family of Wald-type test statistics for linear hypotheses is introduced. Robustness properties of both the proposed estimators and the test statistics are theoretically studied through the classical influence function analysis. Appropriate real life examples are presented to justify the requirement of suitable robust statistical procedures in place of the l…
Recently, graph (network) data is an emerging research area in artificial intelligence, machine learning and statistics. In this work, we are interested in whether node's labels (people's responses) are affected by their neighbor's features (friends' characteristics). We propose a novel latent logistic regression model to describe the network dependence with binary responses. The key advantage of our proposed model is that a latent binary indicator is introduced to indicate whether a node is susceptible to the influence of its neighbour. A score-type test is proposed to diagnose the existence …
A new approach for feature extraction from time series is proposed in this paper. This approach consists of a specific regression model incorporating a discrete hidden logistic process. The model parameters are estimated by the maximum likelihood method performed by a dedicated Expectation Maximization (EM) algorithm. The parameters of the hidden logistic process, in the inner loop of the EM algorithm, are estimated using a multi-class Iterative Reweighted Least-Squares (IRLS) algorithm. A piecewise regression algorithm and its iterative variant have also been considered for comparisons. An ex…
Logistic regression models for binomial responses are routinely used in statistical practice. However, the maximum likelihood estimate may not exist due to data separability. We address this issue by considering a conjugate prior penalty which always produces finite estimates. Such a specification has a clear Bayesian interpretation and enjoys several invariance properties, making it an appealing prior choice. We show that the proposed method leads to an accurate approximation of the reduced-bias approach of Firth (1993), resulting in estimators with smaller asymptotic bias than the maximum-li…
In this letter, we consider the problem of field estimation using binary measurements. Previous work has formulated the problem as a parameter estimation problem, with the parameter estimation carried out in an online manner using sequential Monte Carlo techniques. In the current work, we consider an alternative approach to the parameter estimation based on online logistic regression. The developed algorithm is less computationally intensive than the sequential Monte Carlo approach, while having more reliable estimation performance.
Fully robust versions of the elastic net estimator are introduced for linear and logistic regression. The algorithms to compute the estimators are based on the idea of repeatedly applying the non-robust classical estimators to data subsets only. It is shown how outlier-free subsets can be identified efficiently, and how appropriate tuning parameters for the elastic net penalties can be selected. A final reweighting step improves the efficiency of the estimators. Simulation studies compare with non-robust and other competing robust estimators and reveal the superiority of the newly proposed met…
Firth-type logistic regression has become a standard approach for the analysis of binary outcomes with small samples. Whereas it reduces the bias in maximum likelihood estimates of coefficients, bias towards 1/2 is introduced in the predicted probabilities. The stronger the imbalance of the outcome, the more severe is the bias in the predicted probabilities. We propose two simple modifications of Firth-type logistic regression resulting in unbiased predicted probabilities. The first corrects the predicted probabilities by a post-hoc adjustment of the intercept. The other is based on an alterna…
An accurately identified maximum tolerated dose (MTD) serves as the cornerstone of successful subsequent phases in oncology drug development. Bayesian logistic regression model (BLRM) is a popular and versatile model-based dose-finding design. However, BLRM with original overdose control strategy has been reported to be safe but "excessively conservative". In this manuscript, we investigate the reason for conservativeness and point out that a major reason could be the lack of appropriate underdose control. We propose designs that balance overdose and underdose control to improve the performanc…
This paper describes a method for a model-based analysis of clinical safety data called multivariate Bayesian logistic regression (MBLR). Parallel logistic regression models are fit to a set of medically related issues, or response variables, and MBLR allows information from the different issues to "borrow strength" from each other. The method is especially suited to sparse response data, as often occurs when fine-grained adverse events are collected from subjects in studies sized more for efficacy than for safety investigations. A combined analysis of data from multiple studies can be perform…
We apply the cyclic coordinate descent algorithm of Friedman, Hastie and Tibshirani (2010) to the fitting of a conditional logistic regression model with lasso ($\ell_1$) and elastic net penalties. The sequential strong rules of Tibshirani et al (2012) are also used in the algorithm and it is shown that these offer a considerable speed up over the standard coordinate descent algorithm with warm starts. Once implemented, the algorithm is used in simulation studies to compare the variable selection and prediction performance of the conditional logistic regression model against that of its uncond…
Bivariate observations of binary and ordinal data arise frequently and require a bivariate modelling approach in cases where one is interested in aspects of the marginal distributions as separate outcomes along with the association between the two. We consider methods for constructing such bivariate models with logistic marginals and propose a model based on the Ali-Mikhail-Haq bivariate logistic distribution. We motivate the model as an extension of that based on the Gumbel type 2 distribution as considered by other authors and as a bivariate extension of the logistic distribution which prese…
