Robust Ultra-High-Dimensional Variable Selection With Correlated Structure Using Group Testing
- URL: http://arxiv.org/abs/2602.07258v1
- Date: Fri, 06 Feb 2026 23:19:26 GMT
- Title: Robust Ultra-High-Dimensional Variable Selection With Correlated Structure Using Group Testing
- Authors: Wanru Guo, Juan Xie, Binbin Wang, Weicong Chen, Xiaoyi Lu, Vipin Chaudhary, Curtis Tatsuoka,
- Abstract summary: High-dimensional genomic data exhibit strong group correlation structures that challenge conventional feature selection methods.<n>We propose the Dorfman screening framework, a multi-stage procedure that forms data-driven variable groups via hierarchical clustering.
- Score: 6.702722979447597
- License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
- Abstract: Background: High-dimensional genomic data exhibit strong group correlation structures that challenge conventional feature selection methods, which often assume feature independence or rely on pre-defined pathways and are sensitive to outliers and model misspecification. Methods: We propose the Dorfman screening framework, a multi-stage procedure that forms data-driven variable groups via hierarchical clustering, performs group and within-group hypothesis testing, and refines selection using elastic net or adaptive elastic net. Robust variants incorporate OGK-based covariance estimation, rank-based correlation, and Huber-weighted regression to handle contaminated and non-normal data. Results: In simulations, Dorfman-Sparse-Adaptive-EN performed best under normal conditions, while Robust-OGK-Dorfman-Adaptive-EN showed clear advantages under data contamination, outperforming classical Dorfman and competing methods. Applied to NSCLC gene expression data for trametinib response, robust Dorfman methods achieved the lowest prediction errors and enriched recovery of clinically relevant genes. Conclusions: The Dorfman framework provides an efficient and robust approach to genomic feature selection. Robust-OGK-Dorfman-Adaptive-EN offers strong performance under both ideal and contaminated conditions and scales to ultra-high-dimensional settings, making it well suited for modern genomic biomarker discovery.
Related papers
- Reliable data clustering with Bayesian community detection [0.0]
Researchers rely on clustering similarity data to uncover modular structure.<n>Yet widely used clustering methods, such as hierarchical clustering, k-means, and WGCNA, lack principled model selection, leaving them susceptible to noise.<n>A common workaround sparsifies a correlation matrix representation to remove noise before clustering, but this extra step introduces arbitrary thresholds that can distort the structure and lead to unreliable results.
arXiv Detail & Related papers (2025-10-16T14:10:24Z) - Uncalibrated Reasoning: GRPO Induces Overconfidence for Stochastic Outcomes [55.2480439325792]
Reinforcement learning (RL) has proven remarkably effective at improving the accuracy of language models in verifiable and deterministic domains like mathematics.<n>Here, we examine if current RL methods are also effective at optimizing language models in verifiable domains with outcomes, like scientific experiments.
arXiv Detail & Related papers (2025-08-15T20:50:53Z) - A Misclassification Network-Based Method for Comparative Genomic Analysis [3.7671415694914927]
Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades.<n>In this study, we integrate AI and network science approaches to develop a comparative genomic analysis framework.
arXiv Detail & Related papers (2024-12-09T23:22:15Z) - GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models [56.63218531256961]
We introduce GenBench, a benchmarking suite specifically tailored for evaluating the efficacy of Genomic Foundation Models.
GenBench offers a modular and expandable framework that encapsulates a variety of state-of-the-art methodologies.
We provide a nuanced analysis of the interplay between model architecture and dataset characteristics on task-specific performance.
arXiv Detail & Related papers (2024-06-01T08:01:05Z) - Nonlinear Permuted Granger Causality [0.6526824510982799]
Granger causal inference is a contentious but widespread method used in fields ranging from economics to neuroscience.
To allow for out-of-sample comparison, a measure of functional connectivity is explicitly defined using permutations of the covariate set.
Performance of the permutation method is compared to penalized variable selection, naive replacement, and omission techniques via simulation.
arXiv Detail & Related papers (2023-08-11T16:44:16Z) - Variational Classification [51.2541371924591]
We derive a variational objective to train the model, analogous to the evidence lower bound (ELBO) used to train variational auto-encoders.
Treating inputs to the softmax layer as samples of a latent variable, our abstracted perspective reveals a potential inconsistency.
We induce a chosen latent distribution, instead of the implicit assumption found in a standard softmax layer.
arXiv Detail & Related papers (2023-05-17T17:47:19Z) - Less is More: Mitigate Spurious Correlations for Open-Domain Dialogue
Response Generation Models by Causal Discovery [52.95935278819512]
We conduct the first study on spurious correlations for open-domain response generation models based on a corpus CGDIALOG curated in our work.
Inspired by causal discovery algorithms, we propose a novel model-agnostic method for training and inference of response generation model.
arXiv Detail & Related papers (2023-03-02T06:33:48Z) - Inference post Selection of Group-sparse Regression Models [2.1485350418225244]
Conditional inference provides a rigorous approach to counter bias when data from automated model selections is reused for inference.
We develop in this paper a statistically consistent Bayesian framework to assess uncertainties within linear models.
Finding wide applications when genes, proteins, genetic variants, neuroimaging measurements are grouped respectively by their biological pathways, molecular functions, regulatory regions, cognitive roles, these models are selected through a useful class of group-sparse learning algorithms.
arXiv Detail & Related papers (2020-12-31T15:43:26Z) - Autoregressive Score Matching [113.4502004812927]
We propose autoregressive conditional score models (AR-CSM) where we parameterize the joint distribution in terms of the derivatives of univariable log-conditionals (scores)
For AR-CSM models, this divergence between data and model distributions can be computed and optimized efficiently, requiring no expensive sampling or adversarial training.
We show with extensive experimental results that it can be applied to density estimation on synthetic data, image generation, image denoising, and training latent variable models with implicit encoders.
arXiv Detail & Related papers (2020-10-24T07:01:24Z) - CASTLE: Regularization via Auxiliary Causal Graph Discovery [89.74800176981842]
We introduce Causal Structure Learning (CASTLE) regularization and propose to regularize a neural network by jointly learning the causal relationships between variables.
CASTLE efficiently reconstructs only the features in the causal DAG that have a causal neighbor, whereas reconstruction-based regularizers suboptimally reconstruct all input features.
arXiv Detail & Related papers (2020-09-28T09:49:38Z) - Robust Grouped Variable Selection Using Distributionally Robust
Optimization [11.383869751239166]
We propose a Distributionally Robust Optimization (DRO) formulation with a Wasserstein-based uncertainty set for selecting grouped variables under perturbations.
We prove probabilistic bounds on the out-of-sample loss and the estimation bias, and establish the grouping effect of our estimator.
We show that our formulation produces an interpretable and parsimonious model that encourages sparsity at a group level.
arXiv Detail & Related papers (2020-06-10T22:32:52Z)
This list is automatically generated from the titles and abstracts of the papers in this site.
This site does not guarantee the quality of this site (including all information) and is not responsible for any consequences.