We introduce a sufficient graphical model by applying the recently developed nonlinear sufficient dimension reduction techniques to the evaluation of conditional independence. The graphical model is nonparametric in nature, as it does not make distributional assumptions such as the Gaussian or copula Gaussian assumptions. However, unlike a fully nonparametric graphical model, which relies on the high-dimensional kernel to characterize conditional independence, our graphical model is based on conditional independence given a set of sufficient predictors with a substantially reduced dimension. In this way we avoid the curse of dimensionality that comes with a high-dimensional kernel. We develop the population-level properties, convergence rate, and variable selection consistency of our estimate. By simulation comparisons and an analysis of the DREAM 4 Challenge data set, we demonstrate that our method outperforms the existing methods when the Gaussian or copula Gaussian assumptions are violated, and its performance remains excellent in the high-dimensional setting.
Renal cell carcinoma represents a significant global health challenge with a low survival rate. This research aimed to devise a comprehensive deep-learning model capable of predicting survival probabilities in patients with renal cell carcinoma by integrating CT imaging and clinical data and addressing the limitations observed in prior studies. The aim is to facilitate the identification of patients requiring urgent treatment. The proposed framework comprises three modules: a 3D image feature extractor, clinical variable selection, and survival prediction. The feature extractor module, based on the 3D CNN architecture, predicts the ISUP grade of renal cell carcinoma tumors linked to mortality rates from CT images. A selection of clinical variables is systematically chosen using the Spearman score and random forest importance score as criteria. A deep learning-based network, trained with discrete LogisticHazard-based loss, performs the survival prediction. Nine distinct experiments are performed, with varying numbers of clinical variables determined by different thresholds of the Spearman and importance scores. Our findings demonstrate that the proposed strategy surpasses the current literature on renal cancer prognosis based on CT scans and clinical factors. The best-performing experiment yielded a concordance index of 0.84 and an area under the curve value of 0.8 on the test cohort, which suggests strong predictive power. The multimodal deep-learning approach developed in this study shows promising results in estimating survival probabilities for renal cell carcinoma patients using CT imaging and clinical data. This may have potential implications in identifying patients who require urgent treatment, potentially improving patient outcomes. The code created for this project is available for the public on: \href{https://github.com/Balasingham-AI-Group/Survival_CTplusClinical}{GitHub}
Branch-and-bound is a typical way to solve combinatorial optimization problems. This paper proposes a graph pointer network model for learning the variable selection policy in the branch-and-bound. We extract the graph features, global features and historical features to represent the solver state. The proposed model, which combines the graph neural network and the pointer mechanism, can effectively map from the solver state to the branching variable decisions. The model is trained to imitate the classic strong branching expert rule by a designed top-k Kullback-Leibler divergence loss function. Experiments on a series of benchmark problems demonstrate that the proposed approach significantly outperforms the widely used expert-designed branching rules. Our approach also outperforms the state-of-the-art machine-learning-based branch-and-bound methods in terms of solving speed and search tree size on all the test instances. In addition, the model can generalize to unseen instances and scale to larger instances.
In this paper we propose a novel variable selection method for two-view settings, or for vector-valued supervised learning problems. Our framework is able to handle extremely large scale selection tasks, where number of data samples could be even millions. In a nutshell, our method performs variable selection by iteratively selecting variables that are highly correlated with the output variables, but which are not correlated with the previously chosen variables. To measure the correlation, our method uses the concept of projection operators and their algebra. With the projection operators the relationship, correlation, between sets of input and output variables can also be expressed by kernel functions, thus nonlinear correlation models can be exploited as well. We experimentally validate our approach, showing on both synthetic and real data its scalability and the relevance of the selected features. Keywords: Supervised variable selection, vector-valued learning, projection-valued measure, reproducing kernel Hilbert space
Cox models with time-dependent coefficients and covariates are widely used in survival analysis. In high-dimensional settings, sparse regularization techniques are employed for variable selection, but existing methods for time-dependent Cox models lack flexibility in enforcing specific sparsity patterns (i.e., covariate structures). We propose a flexible framework for variable selection in time-dependent Cox models, accommodating complex selection rules. Our method can adapt to arbitrary grouping structures, including interaction selection, temporal, spatial, tree, and directed acyclic graph structures. It achieves accurate estimation with low false alarm rates. We develop the sox package, implementing a network flow algorithm for efficiently solving models with complex covariate structures. sox offers a user-friendly interface for specifying grouping structures and delivers fast computation. Through examples, including a case study on identifying predictors of time to all-cause death in atrial fibrillation patients, we demonstrate the practical application of our method with specific selection rules.
In this paper, we investigate a semiparametric regression model under the context of treatment effects via a localized neural network (LNN) approach. Due to a vast number of parameters involved, we reduce the number of effective parameters by (i) exploring the use of identification restrictions; and (ii) adopting a variable selection method based on the group-LASSO technique. Subsequently, we derive the corresponding estimation theory and propose a dependent wild bootstrap procedure to construct valid inferences accounting for the dependence of data. Finally, we validate our theoretical findings through extensive numerical studies. In an empirical study, we revisit the impacts of a tightening monetary policy action on a variety of economic variables, including short-/long-term interest rate, inflation, unemployment rate, industrial price and equity return via the newly proposed framework using a monthly dataset of the US.
Combinatorial optimization problems require an exhaustive search to find the optimal solution. A convenient approach to solving combinatorial optimization tasks in the form of Mixed Integer Linear Programs is Branch-and-Bound. Branch-and-Bound solver splits a task into two parts dividing the domain of an integer variable, then it solves them recursively, producing a tree of nested sub-tasks. The efficiency of the solver depends on the branchning heuristic used to select a variable for splitting. In the present work, we propose a reinforcement learning method that can efficiently learn the branching heuristic. We view the variable selection task as a tree Markov Decision Process, prove that the Bellman operator adapted for the tree Markov Decision Process is contracting in mean, and propose a modified learning objective for the reinforcement learning agent. Our agent requires less training data and produces smaller trees compared to previous reinforcement learning methods.
This paper considers the specification of covariance structures with tail estimates. We focus on two aspects: (i) the estimation of the VaR-CoVaR risk matrix in the case of larger number of time series observations than assets in a portfolio using quantile predictive regression models without assuming the presence of nonstationary regressors and; (ii) the construction of a novel variable selection algorithm, so-called, Feature Ordering by Centrality Exclusion (FOCE), which is based on an assumption-lean regression framework, has no tuning parameters and is proved to be consistent under general sparsity assumptions. We illustrate the usefulness of our proposed methodology with numerical studies of real and simulated datasets when modelling systemic risk in a network.
LASSO regularization is a popular regression tool to enhance the prediction accuracy of statistical models by performing variable selection through the $\ell_1$ penalty, initially formulated for the linear model and its variants. In this paper, the territory of LASSO is extended to two-layer ReLU neural networks, a fashionable and powerful nonlinear regression model. Specifically, given a neural network whose output $y$ depends only on a small subset of input $\boldsymbol{x}$, denoted by $\mathcal{S}^{\star}$, we prove that the LASSO estimator can stably reconstruct the neural network and identify $\mathcal{S}^{\star}$ when the number of samples scales logarithmically with the input dimension. This challenging regime has been well understood for linear models while barely studied for neural networks. Our theory lies in an extended Restricted Isometry Property (RIP)-based analysis framework for two-layer ReLU neural networks, which may be of independent interest to other LASSO or neural network settings. Based on the result, we advocate a neural network-based variable selection method. Experiments on simulated and real-world datasets show promising performance of the variable selection approach compared with existing techniques.
Artificial neural networks (ANNs) are powerful machine learning methods used in many modern applications such as facial recognition, machine translation, and cancer diagnostics. A common issue with ANNs is that they usually have millions or billions of trainable parameters, and therefore tend to overfit to the training data. This is especially problematic in applications where it is important to have reliable uncertainty estimates. Bayesian neural networks (BNN) can improve on this, since they incorporate parameter uncertainty. In addition, latent binary Bayesian neural networks (LBBNN) also take into account structural uncertainty by allowing the weights to be turned on or off, enabling inference in the joint space of weights and structures. In this paper, we will consider two extensions to the LBBNN method: Firstly, by using the local reparametrization trick (LRT) to sample the hidden units directly, we get a more computationally efficient algorithm. More importantly, by using normalizing flows on the variational posterior distribution of the LBBNN parameters, the network learns a more flexible variational posterior distribution than the mean field Gaussian. Experimental results show that this improves predictive power compared to the LBBNN method, while also obtaining more sparse networks. We perform two simulation studies. In the first study, we consider variable selection in a logistic regression setting, where the more flexible variational distribution leads to improved results. In the second study, we compare predictive uncertainty based on data generated from two-dimensional Gaussian distributions. Here, we argue that our Bayesian methods lead to more realistic estimates of predictive uncertainty.
Big-data applications often involve a vast number of observations and features, creating new challenges for variable selection and parameter estimation. This paper presents a novel technique called ``slow kill,'' which utilizes nonconvex constrained optimization, adaptive $\ell_2$-shrinkage, and increasing learning rates. The fact that the problem size can decrease during the slow kill iterations makes it particularly effective for large-scale variable screening. The interaction between statistics and optimization provides valuable insights into controlling quantiles, stepsize, and shrinkage parameters in order to relax the regularity conditions required to achieve the desired level of statistical accuracy. Experimental results on real and synthetic data show that slow kill outperforms state-of-the-art algorithms in various situations while being computationally efficient for large-scale data.
Identifying differential equation governing dynamical system is an important problem with wide applications. Copula Entropy (CE) is a mathematical concept for measuring statistical independence in information theory. In this paper we propose a method for identifying differential equation of dynamical systems with CE. The problem is considered as a variable selection problem and solved with the previously proposed CE-based method for variable selection. The proposed method composed of two components: the difference operator and the CE estimator. Since both components can be done non-parametrically, the proposed method is therefore model-free and hyperparameter-free. The simulation experiment with the 3D Lorenz system verified the effectiveness of the proposed method.
This paper introduces a new regularized version of the robust $\tau$-regression estimator for analyzing high-dimensional datasets subject to gross contamination in the response variables and covariates. The resulting estimator, termed adaptive $\tau$-Lasso, is robust to outliers and high-leverage points. It also incorporates an adaptive $\ell_1$-norm penalty term, which enables the selection of relevant variables and reduces the bias associated with large true regression coefficients. More specifically, this adaptive $\ell_1$-norm penalty term assigns a weight to each regression coefficient. For a fixed number of predictors $p$, we show that the adaptive $\tau$-Lasso has the oracle property, ensuring both variable-selection consistency and asymptotic normality. Asymptotic normality applies only to the entries of the regression vector corresponding to the true support, assuming knowledge of the true regression vector support. We characterize its robustness by establishing the finite-sample breakdown point and the influence function. We carry out extensive simulations and observe that the class of $\tau$-Lasso estimators exhibits robustness and reliable performance in both contaminated and uncontaminated data settings. We also validate our theoretical findings on robustness properties through simulations. In the face of outliers and high-leverage points, the adaptive $\tau$-Lasso and $\tau$-Lasso estimators achieve the best performance or match the best performances of competing regularized estimators, with minimal or no loss in terms of prediction and variable selection accuracy for almost all scenarios considered in this study. Therefore, the adaptive $\tau$-Lasso and $\tau$-Lasso estimators provide attractive tools for a variety of sparse linear regression problems, particularly in high-dimensional settings and when the data is contaminated by outliers and high-leverage points.
We present a new data analysis perspective to determine variable importance regardless of the underlying learning task. Traditionally, variable selection is considered an important step in supervised learning for both classification and regression problems. The variable selection also becomes critical when costs associated with the data collection and storage are considerably high for cases like remote sensing. Therefore, we propose a new methodology to select important variables from the data by first creating dependency networks among all variables and then ranking them (i.e. nodes) by graph centrality measures. Selecting Top-$n$ variables according to preferred centrality measure will yield a strong candidate subset of variables for further learning tasks e.g. clustering. We present our tool as a Shiny app which is a user-friendly interface development environment. We also extend the user interface for two well-known unsupervised variable selection methods from literature for comparison reasons.
Subset weighted-Tempered Gibbs Sampler (wTGS) has been recently introduced by Jankowiak to reduce the computation complexity per MCMC iteration in high-dimensional applications where the exact calculation of the posterior inclusion probabilities (PIP) is not essential. However, the Rao-Backwellized estimator associated with this sampler has a high variance as the ratio between the signal dimension and the number of conditional PIP estimations is large. In this paper, we design a new subset weighted-Tempered Gibbs Sampler (wTGS) where the expected number of computations of conditional PIPs per MCMC iteration can be much smaller than the signal dimension. Different from the subset wTGS and wTGS, our sampler has a variable complexity per MCMC iteration. We provide an upper bound on the variance of an associated Rao-Blackwellized estimator for this sampler at a finite number of iterations, $T$, and show that the variance is $O\big(\big(\frac{P}{S}\big)^2 \frac{\log T}{T}\big)$ for a given dataset where $S$ is the expected number of conditional PIP computations per MCMC iteration. Experiments show that our Rao-Blackwellized estimator can have a smaller variance than its counterpart associated with the subset wTGS.
Synthetic electronic health records (EHRs) that are both realistic and preserve privacy can serve as an alternative to real EHRs for machine learning (ML) modeling and statistical analysis. However, generating high-fidelity and granular electronic health record (EHR) data in its original, highly-dimensional form poses challenges for existing methods due to the complexities inherent in high-dimensional data. In this paper, we propose Hierarchical Autoregressive Language mOdel (HALO) for generating longitudinal high-dimensional EHR, which preserve the statistical properties of real EHR and can be used to train accurate ML models without privacy concerns. Our HALO method, designed as a hierarchical autoregressive model, generates a probability density function of medical codes, clinical visits, and patient records, allowing for the generation of realistic EHR data in its original, unaggregated form without the need for variable selection or aggregation. Additionally, our model also produces high-quality continuous variables in a longitudinal and probabilistic manner. We conducted extensive experiments and demonstrate that HALO can generate high-fidelity EHR data with high-dimensional disease code probabilities (d > 10,000), disease co-occurrence probabilities within visits (d > 1,000,000), and conditional probabilities across consecutive visits (d > 5,000,000) and achieve above 0.9 R2 correlation in comparison to real EHR data. This performance then enables downstream ML models trained on its synthetic data to achieve comparable accuracy to models trained on real data (0.938 AUROC with HALO data vs. 0.943 with real data). Finally, using a combination of real and synthetic data enhances the accuracy of ML models beyond that achieved by using only real EHR data.
In real-world applications of reinforcement learning, it is often challenging to obtain a state representation that is parsimonious and satisfies the Markov property without prior knowledge. Consequently, it is common practice to construct a state larger than necessary, e.g., by concatenating measurements over contiguous time points. However, needlessly increasing the dimension of the state may slow learning and obfuscate the learned policy. We introduce the notion of a minimal sufficient state in a Markov decision process (MDP) as the subvector of the original state under which the process remains an MDP and shares the same reward function as the original process. We propose a novel SEquEntial Knockoffs (SEEK) algorithm that estimates the minimal sufficient state in a system with high-dimensional complex nonlinear dynamics. In large samples, the proposed method achieves selection consistency. As the method is agnostic to the reinforcement learning algorithm being applied, it benefits downstream tasks such as policy learning. Empirical experiments verify theoretical results and show the proposed approach outperforms several competing methods regarding variable selection accuracy and regret.
In this paper, we consider the regularized multi-response regression problem where there exists some structural relation within the responses and also between the covariates and a set of modifying variables. To handle this problem, we propose MADMMplasso, a novel regularized regression method. This method is able to find covariates and their corresponding interactions, with some joint association with multiple related responses. We allow the interaction term between covariate and modifying variable to be included in a (weak) asymmetrical hierarchical manner by first considering whether the corresponding covariate main term is in the model. For parameter estimation, we develop an ADMM algorithm that allows us to implement the overlapping groups in a simple way. The results from the simulations and analysis of a pharmacogenomic screen data set show that the proposed method has an advantage in handling correlated responses and interaction effects, both with respect to prediction and variable selection performance.
In statistics, the least absolute shrinkage and selection operator (Lasso) is a regression method that performs both variable selection and regularization. There is a lot of literature available, discussing the statistical properties of the regression coefficients estimated by the Lasso method. However, there lacks a comprehensive review discussing the algorithms to solve the optimization problem in Lasso. In this review, we summarize five representative algorithms to optimize the objective function in Lasso, including the iterative shrinkage threshold algorithm (ISTA), fast iterative shrinkage-thresholding algorithms (FISTA), coordinate gradient descent algorithm (CGDA), smooth L1 algorithm (SLA), and path following algorithm (PFA). Additionally, we also compare their convergence rate, as well as their potential strengths and weakness.
This paper considers a multi-environment linear regression model in which data from multiple experimental settings are collected. The joint distribution of the response variable and covariates may vary across different environments, yet the conditional expectations of $y$ given the unknown set of important variables are invariant. Such a statistical model is related to the problem of endogeneity, causal inference, and transfer learning. The motivation behind it is illustrated by how the goals of prediction and attribution are inherent in estimating the true parameter and the important variable set. We construct a novel environment invariant linear least squares (EILLS) objective function, a multi-environment version of linear least-squares regression that leverages the above conditional expectation invariance structure and heterogeneity among different environments to determine the true parameter. Our proposed method is applicable without any additional structural knowledge and can identify the true parameter under a near-minimal identification condition. We establish non-asymptotic $\ell_2$ error bounds on the estimation error for the EILLS estimator in the presence of spurious variables. Moreover, we further show that the $\ell_0$ penalized EILLS estimator can achieve variable selection consistency in high-dimensional regimes. These non-asymptotic results demonstrate the sample efficiency of the EILLS estimator and its capability to circumvent the curse of endogeneity in an algorithmic manner without any prior structural knowledge. To the best of our knowledge, this paper is the first to realize statistically efficient invariance learning in the general linear model.