Effective clustering of biomedical data is crucial in precision medicine, enabling accurate stratifiction of patients or samples. However, the growth in availability of high-dimensional categorical data, including `omics data, necessitates computationally efficient clustering algorithms. We present VICatMix, a variational Bayesian finite mixture model designed for the clustering of categorical data. The use of variational inference (VI) in its training allows the model to outperform competitors in term of efficiency, while maintaining high accuracy. VICatMix furthermore performs variable selection, enhancing its performance on high-dimensional, noisy data. The proposed model incorporates summarisation and model averaging to mitigate poor local optima in VI, allowing for improved estimation of the true number of clusters simultaneously with feature saliency. We demonstrate the performance of VICatMix with both simulated and real-world data, including applications to datasets from The Cancer Genome Atlas (TCGA), showing its use in cancer subtyping and driver gene discovery. We demonstrate VICatMix's utility in integrative cluster analysis with different `omics datasets, enabling the discovery of novel subtypes. \textbf{Availability:} VICatMix is freely available as an R package, incorporating C++ for faster computation, at \url{https://github.com/j-ackierao/VICatMix}.
This paper introduces a novel framework for reducing variable selection bias by balancing selection frequencies of base-learners in boosting and introduces the sgboost package in R, which implements this framework combined with sparse-group boosting. The group bias reduction algorithm employs a simulation-based approach to iteratively adjust the degrees of freedom for both individual and group base-learners, ensuring balanced selection probabilities and mitigating the tendency to over-select more complex groups. The efficacy of the group balancing algorithm is demonstrated through simulations. Sparse-group boosting offers a flexible approach for both group and individual variable selection, reducing overfitting and enhancing model interpretability for modeling high-dimensional data with natural groupings in covariates. The package uses regularization techniques based on the degrees of freedom of individual and group base-learners. Through comparisons with existing methods and demonstration of its unique functionalities, this paper provides a practical guide on utilizing sparse-group boosting in R, accompanied by code examples to facilitate its application in various research domains.
Optimization problems characterized by both discrete and continuous variables are common across various disciplines, presenting unique challenges due to their complex solution landscapes and the difficulty of navigating mixed-variable spaces effectively. To Address these challenges, we introduce a hybrid Reinforcement Learning (RL) framework that synergizes RL for discrete variable selection with Bayesian Optimization for continuous variable adjustment. This framework stands out by its strategic integration of RL and continuous optimization techniques, enabling it to dynamically adapt to the problem's mixed-variable nature. By employing RL for exploring discrete decision spaces and Bayesian Optimization to refine continuous parameters, our approach not only demonstrates flexibility but also enhances optimization performance. Our experiments on synthetic functions and real-world machine learning hyperparameter tuning tasks reveal that our method consistently outperforms traditional RL, random search, and standalone Bayesian optimization in terms of effectiveness and efficiency.
For prediction models developed on clustered data that do not account for cluster heterogeneity in model parameterization, it is crucial to use cluster-based validation to assess model generalizability on unseen clusters. This paper introduces a clustered estimator of the Network Information Criterion (NICc) to approximate leave-one-cluster-out deviance for standard prediction models with twice differentiable log-likelihood functions. The NICc serves as a fast alternative to cluster-based cross-validation. Stone (1977) proved that the Akaike Information Criterion (AIC) is asymptotically equivalent to leave-one-observation-out cross-validation for true parametric models with independent and identically distributed observations. Ripley (1996) noted that the Network Information Criterion (NIC), derived from Stone's proof, is a better approximation when the model is misspecified. For clustered data, we derived NICc by substituting the Fisher information matrix in the NIC with a clustering-adjusted estimator. The NICc imposes a greater penalty when the data exhibits stronger clustering, thereby allowing the NICc to better prevent over-parameterization. In a simulation study and an empirical example, we used standard regression to develop prediction models for clustered data with Gaussian or binomial responses. Compared to the commonly used AIC and BIC for standard regression, NICc provides a much more accurate approximation to leave-one-cluster-out deviance and results in more accurate model size and variable selection, as determined by cluster-based cross-validation, especially when the data exhibit strong clustering.
Suppose that we first apply the Lasso to a design matrix, and then update one of its columns. In general, the signs of the Lasso coefficients may change, and there is no closed-form expression for updating the Lasso solution exactly. In this work, we propose an approximate formula for updating a debiased Lasso coefficient. We provide general nonasymptotic error bounds in terms of the norms and correlations of a given design matrix's columns, and then prove asymptotic convergence results for the case of a random design matrix with i.i.d.\ sub-Gaussian row vectors and i.i.d.\ Gaussian noise. Notably, the approximate formula is asymptotically correct for most coordinates in the proportional growth regime, under the mild assumption that each row of the design matrix is sub-Gaussian with a covariance matrix having a bounded condition number. Our proof only requires certain concentration and anti-concentration properties to control various error terms and the number of sign changes. In contrast, rigorously establishing distributional limit properties (e.g.\ Gaussian limits for the debiased Lasso) under similarly general assumptions has been considered open problem in the universality theory. As applications, we show that the approximate formula allows us to reduce the computation complexity of variable selection algorithms that require solving multiple Lasso problems, such as the conditional randomization test and a variant of the knockoff filter.
Ridge regression is an indispensable tool in big data analysis. Yet its inherent bias poses a significant and longstanding challenge, compromising both statistical efficiency and scalability across various applications. To tackle this critical issue, we introduce an iterative strategy to correct bias effectively when the dimension $p$ is less than the sample size $n$. For $p>n$, our method optimally mitigates the bias such that any remaining bias in the proposed de-biased estimator is unattainable through linear transformations of the response data. To address the remaining bias when $p>n$, we employ a Ridge-Screening (RS) method, producing a reduced model suitable for bias correction. Crucially, under certain conditions, the true model is nested within our selected one, highlighting RS as a novel variable selection approach. Through rigorous analysis, we establish the asymptotic properties and valid inferences of our de-biased ridge estimators for both $p<n$ and $p>n$, where, both $p$ and $n$ may increase towards infinity, along with the number of iterations. We further validate these results using simulated and real-world data examples. Our method offers a transformative solution to the bias challenge in ridge regression inferences across various disciplines.
Keeping the balance between electricity generation and consumption is becoming increasingly challenging and costly, mainly due to the rising share of renewables, electric vehicles and heat pumps and electrification of industrial processes. Accurate imbalance forecasts, along with reliable uncertainty estimations, enable transmission system operators (TSOs) to dispatch appropriate reserve volumes, reducing balancing costs. Further, market parties can use these probabilistic forecasts to design strategies that exploit asset flexibility to help balance the grid, generating revenue with known risks. Despite its importance, literature regarding system imbalance (SI) forecasting is limited. Further, existing methods do not focus on situations with high imbalance magnitude, which are crucial to forecast accurately for both TSOs and market parties. Hence, we propose an ensemble of C-VSNs, which are our adaptation of variable selection networks (VSNs). Each minute, our model predicts the imbalance of the current and upcoming two quarter-hours, along with uncertainty estimations on these forecasts. We evaluate our approach by forecasting the imbalance of Belgium, where high imbalance magnitude is defined as $|$SI$| > 500\,$MW (occurs 1.3% of the time in Belgium). For high imbalance magnitude situations, our model outperforms the state-of-the-art by 23.4% (in terms of continuous ranked probability score (CRPS), which evaluates probabilistic forecasts), while also attaining a 6.5% improvement in overall CRPS. Similar improvements are achieved in terms of root-mean-squared error. Additionally, we developed a fine-tuning methodology to effectively include new inputs with limited history in our model. This work was performed in collaboration with Elia (the Belgian TSO) to further improve their imbalance forecasts, demonstrating the relevance of our work.
High-dimensional longitudinal time series data is prevalent across various real-world applications. Many such applications can be modeled as regression problems with high-dimensional time series covariates. Deep learning has been a popular and powerful tool for fitting these regression models. Yet, the development of interpretable and reproducible deep-learning models is challenging and remains underexplored. This study introduces a novel method, Deep Learning Inference using Knockoffs for Time series data (DeepLINK-T), focusing on the selection of significant time series variables in regression while controlling the false discovery rate (FDR) at a predetermined level. DeepLINK-T combines deep learning with knockoff inference to control FDR in feature selection for time series models, accommodating a wide variety of feature distributions. It addresses dependencies across time and features by leveraging a time-varying latent factor structure in time series covariates. Three key ingredients for DeepLINK-T are 1) a Long Short-Term Memory (LSTM) autoencoder for generating time series knockoff variables, 2) an LSTM prediction network using both original and knockoff variables, and 3) the application of the knockoffs framework for variable selection with FDR control. Extensive simulation studies have been conducted to evaluate DeepLINK-T's performance, showing its capability to control FDR effectively while demonstrating superior feature selection power for high-dimensional longitudinal time series data compared to its non-time series counterpart. DeepLINK-T is further applied to three metagenomic data sets, validating its practical utility and effectiveness, and underscoring its potential in real-world applications.
Social science research often hinges on the relationship between categorical variables and outcomes. We introduce CAVIAR, a novel method for embedding categorical variables that assume values in a high-dimensional ambient space but are sampled from an underlying manifold. Our theoretical and numerical analyses outline challenges posed by such categorical variables in causal inference. Specifically, dynamically varying and sparse levels can lead to violations of the Donsker conditions and a failure of the estimation functionals to converge to a tight Gaussian process. Traditional approaches, including the exclusion of rare categorical levels and principled variable selection models like LASSO, fall short. CAVIAR embeds the data into a lower-dimensional global coordinate system. The mapping can be derived from both structured and unstructured data, and ensures stable and robust estimates through dimensionality reduction. In a dataset of direct-to-consumer apparel sales, we illustrate how high-dimensional categorical variables, such as zip codes, can be succinctly represented, facilitating inference and analysis.
The popularity of transfer learning stems from the fact that it can borrow information from useful auxiliary datasets. Existing statistical transfer learning methods usually adopt a global similarity measure between the source data and the target data, which may lead to inefficiency when only partial information is shared. In this paper, we propose a novel Bayesian transfer learning method named ``CONCERT'' to allow robust partial information transfer for high-dimensional data analysis. A conditional spike-and-slab prior is introduced in the joint distribution of target and source parameters for information transfer. By incorporating covariate-specific priors, we can characterize partial similarities and integrate source information collaboratively to improve the performance on the target. In contrast to existing work, the CONCERT is a one-step procedure, which achieves variable selection and information transfer simultaneously. We establish variable selection consistency, as well as estimation and prediction error bounds for CONCERT. Our theory demonstrates the covariate-specific benefit of transfer learning. To ensure that our algorithm is scalable, we adopt the variational Bayes framework to facilitate implementation. Extensive experiments and two real data applications showcase the validity and advantage of CONCERT over existing cutting-edge transfer learning methods.
We explore the application of machine learning algorithms specifically to enhance the selection process of Russet potato clones in breeding trials by predicting their suitability for advancement. This study addresses the challenge of efficiently identifying high-yield, disease-resistant, and climate-resilient potato varieties that meet processing industry standards. Leveraging manually collected data from trials in the state of Oregon, we investigate the potential of a wide variety of state-of-the-art binary classification models. The dataset includes 1086 clones, with data on 38 attributes recorded for each clone, focusing on yield, size, appearance, and frying characteristics, with several control varieties planted consistently across four Oregon regions from 2013-2021. We conduct a comprehensive analysis of the dataset that includes preprocessing, feature engineering, and imputation to address missing values. We focus on several key metrics such as accuracy, F1-score, and Matthews correlation coefficient (MCC) for model evaluation. The top-performing models, namely a neural network classifier (Neural Net), histogram-based gradient boosting classifier (HGBC), and a support vector machine classifier (SVM), demonstrate consistent and significant results. To further validate our findings, we conduct a simulation study. By simulating different data-generating scenarios, we assess model robustness and performance through true positive, true negative, false positive, and false negative distributions, area under the receiver operating characteristic curve (AUC-ROC) and MCC. The simulation results highlight that non-linear models like SVM and HGBC consistently show higher AUC-ROC and MCC than logistic regression (LR), thus outperforming the traditional linear model across various distributions, and emphasizing the importance of model selection and tuning in agricultural trials.
Recovering dynamical equations from observed noisy data is the central challenge of system identification. We develop a statistical mechanics approach to analyze sparse equation discovery algorithms, which typically balance data fit and parsimony via hyperparameter tuning. In this framework, statistical mechanics offers tools to analyze the interplay between complexity and fitness similarly to that of entropy and energy in physical systems. To establish this analogy, we define the hyperparameter optimization procedure as a two-level Bayesian inference problem that separates variable selection from coefficient inference and enables the computation of the posterior parameter distribution in closed form. Our approach provides uncertainty quantification, crucial in the low-data limit that is frequently encountered in real-world applications. A key advantage of employing statistical mechanical concepts, such as free energy and the partition function, is to connect the large data limit to thermodynamic limit and characterize the sparsity- and noise-induced phase transitions that delineate correct from incorrect identification. We thus provide a method for closed-loop inference, estimating the noise in a given model and checking if the model is tolerant to that noise amount. This perspective of sparse equation discovery is versatile and can be adapted to various other equation discovery algorithms.
We propose AFTNet, a novel network-constraint survival analysis method based on the Weibull accelerated failure time (AFT) model solved by a penalized likelihood approach for variable selection and estimation. When using the log-linear representation, the inference problem becomes a structured sparse regression problem for which we explicitly incorporate the correlation patterns among predictors using a double penalty that promotes both sparsity and grouping effect. Moreover, we establish the theoretical consistency for the AFTNet estimator and present an efficient iterative computational algorithm based on the proximal gradient descent method. Finally, we evaluate AFTNet performance both on synthetic and real data examples.
Deep networks are increasingly applied to a wide variety of data, including data with high-dimensional predictors. In such analysis, variable selection can be needed along with estimation/model building. Many of the existing deep network studies that incorporate variable selection have been limited to methodological and numerical developments. In this study, we consider modeling/estimation using the conditional Wasserstein Generative Adversarial networks. Group Lasso penalization is applied for variable selection, which may improve model estimation/prediction, interpretability, stability, etc. Significantly advancing from the existing literature, the analysis of censored survival data is also considered. We establish the convergence rate for variable selection while considering the approximation error, and obtain a more efficient distribution estimation. Simulations and the analysis of real experimental data demonstrate satisfactory practical utility of the proposed analysis.
Large Language Models (LLMs) demonstrate ever-increasing abilities in mathematical and algorithmic tasks, yet their geometric reasoning skills are underexplored. We investigate LLMs' abilities in constructive geometric problem-solving one of the most fundamental steps in the development of human mathematical reasoning. Our work reveals notable challenges that the state-of-the-art LLMs face in this domain despite many successes in similar areas. LLMs exhibit biases in target variable selection and struggle with 2D spatial relationships, often misrepresenting and hallucinating objects and their placements. To this end, we introduce a framework that formulates an LLMs-based multi-agents system that enhances their existing reasoning potential by conducting an internal dialogue. This work underscores LLMs' current limitations in geometric reasoning and improves geometric reasoning capabilities through self-correction, collaboration, and diverse role specializations.
Matrix completion estimators are employed in causal panel data models to regulate the rank of the underlying factor model using nuclear norm minimization. This convex optimization problem enables concurrent regularization of a potentially high-dimensional set of covariates to shrink the model size. For valid finite sample inference, we adopt a permutation-based approach and prove its validity for any treatment assignment mechanism. Simulations illustrate the consistency of the proposed estimator in parameter estimation and variable selection. An application to public health policies in Germany demonstrates the data-driven model selection feature on empirical data and finds no effect of travel restrictions on the containment of severe Covid-19 infections.
In this paper, we introduce a kNN-based regression method that synergizes the scalability and adaptability of traditional non-parametric kNN models with a novel variable selection technique. This method focuses on accurately estimating the conditional mean and variance of random response variables, thereby effectively characterizing conditional distributions across diverse scenarios.Our approach incorporates a robust uncertainty quantification mechanism, leveraging our prior estimation work on conditional mean and variance. The employment of kNN ensures scalable computational efficiency in predicting intervals and statistical accuracy in line with optimal non-parametric rates. Additionally, we introduce a new kNN semi-parametric algorithm for estimating ROC curves, accounting for covariates. For selecting the smoothing parameter k, we propose an algorithm with theoretical guarantees.Incorporation of variable selection enhances the performance of the method significantly over conventional kNN techniques in various modeling tasks. We validate the approach through simulations in low, moderate, and high-dimensional covariate spaces. The algorithm's effectiveness is particularly notable in biomedical applications as demonstrated in two case studies. Concluding with a theoretical analysis, we highlight the consistency and convergence rate of our method over traditional kNN models, particularly when the underlying regression model takes values in a low-dimensional space.
The Na\"ive Bayes has proven to be a tractable and efficient method for classification in multivariate analysis. However, features are usually correlated, a fact that violates the Na\"ive Bayes' assumption of conditional independence, and may deteriorate the method's performance. Moreover, datasets are often characterized by a large number of features, which may complicate the interpretation of the results as well as slow down the method's execution. In this paper we propose a sparse version of the Na\"ive Bayes classifier that is characterized by three properties. First, the sparsity is achieved taking into account the correlation structure of the covariates. Second, different performance measures can be used to guide the selection of features. Third, performance constraints on groups of higher interest can be included. Our proposal leads to a smart search, which yields competitive running times, whereas the flexibility in terms of performance measure for classification is integrated. Our findings show that, when compared against well-referenced feature selection approaches, the proposed sparse Na\"ive Bayes obtains competitive results regarding accuracy, sparsity and running times for balanced datasets. In the case of datasets with unbalanced (or with different importance) classes, a better compromise between classification rates for the different classes is achieved.
Adversarial training has been proposed to protect machine learning models against adversarial attacks. This paper focuses on adversarial training under $\ell_\infty$-perturbation, which has recently attracted much research attention. The asymptotic behavior of the adversarial training estimator is investigated in the generalized linear model. The results imply that the asymptotic distribution of the adversarial training estimator under $\ell_\infty$-perturbation could put a positive probability mass at $0$ when the true parameter is $0$, providing a theoretical guarantee of the associated sparsity-recovery ability. Alternatively, a two-step procedure is proposed -- adaptive adversarial training, which could further improve the performance of adversarial training under $\ell_\infty$-perturbation. Specifically, the proposed procedure could achieve asymptotic variable-selection consistency and unbiasedness. Numerical experiments are conducted to show the sparsity-recovery ability of adversarial training under $\ell_\infty$-perturbation and to compare the empirical performance between classic adversarial training and adaptive adversarial training.
Forecasts play a central role in decision making under uncertainty. After a brief review of the general issues, this paper considers ways of using high-dimensional data in forecasting. We consider selecting variables from a known active set, known knowns, using Lasso and OCMT, and approximating unobserved latent factors, known unknowns, by various means. This combines both sparse and dense approaches. We demonstrate the various issues involved in variable selection in a high-dimensional setting with an application to forecasting UK inflation at different horizons over the period 2020q1-2023q1. This application shows both the power of parsimonious models and the importance of allowing for global variables.