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 feature selection


MinShap: A Modified Shapley Value Approach for Feature Selection

Zheng, Chenghui, Raskutti, Garvesh

arXiv.org Machine Learning

Feature selection is a classical problem in statistics and machine learning, and it continues to remain an extremely challenging problem especially in the context of unknown non-linear relationships with dependent features. On the other hand, Shapley values are a classic solution concept from cooperative game theory that is widely used for feature attribution in general non-linear models with highly-dependent features. However, Shapley values are not naturally suited for feature selection since they tend to capture both direct effects from each feature to the response and indirect effects through other features. In this paper, we combine the advantages of Shapley values and adapt them to feature selection by proposing \emph{MinShap}, a modification of the Shapley value framework along with a suite of other related algorithms. In particular for MinShap, instead of taking the average marginal contributions over permutations of features, considers the minimum marginal contribution across permutations. We provide a theoretical foundation motivated by the faithfulness assumption in DAG (directed acyclic graphical models), a guarantee for the Type I error of MinShap, and show through numerical simulations and real data experiments that MinShap tends to outperform state-of-the-art feature selection algorithms such as LOCO, GCM and Lasso in terms of both accuracy and stability. We also introduce a suite of algorithms related to MinShap by using the multiple testing/p-value perspective that improves performance in lower-sample settings and provide supporting theoretical guarantees.


bioLeak: Leakage-Aware Modeling and Diagnostics for Machine Learning in R

Korkmaz, Selçuk

arXiv.org Machine Learning

Data leakage remains a recurrent source of optimistic bias in biomedical machine learning studies. Standard row-wise cross-validation and globally estimated preprocessing steps are often inappropriate for data with repeated measurements, study-level heterogeneity, batch effects, or temporal dependencies. This paper describes bioLeak, an R package for constructing leakage-aware resampling workflows and for auditing fitted models for common leakage mechanisms. The package provides leakage-aware split construction, train-fold-only preprocessing, cross-validated model fitting, nested hyperparameter tuning, post hoc leakage audits, and HTML reporting. The implementation supports binary classification, multiclass classification, regression, and survival analysis, with task-specific metrics and S4 containers for splits, fits, audits, and inflation summaries. The simulation artifacts show how apparent performance changes under controlled leakage mechanisms, and the case study illustrates how guarded and leaky pipelines can yield materially different conclusions on multi-study transcriptomic data. The emphasis throughout is on software design, reproducible workflows, and interpretation of diagnostic output.


Starting Off on the Wrong Foot: Pitfalls in Data Preparation

Guo, Jiayi, Dong, Panyi, Quan, Zhiyu

arXiv.org Machine Learning

When working with real-world insurance data, practitioners often encounter challenges during the data preparation stage that can undermine the statistical validity and reliability of downstream modeling. This study illustrates that conventional data preparation procedures such as random train-test partitioning, often yield unreliable and unstable results when confronted with highly imbalanced insurance loss data. To mitigate these limitations, we propose a novel data preparation framework leveraging two recent statistical advancements: support points for representative data splitting to ensure distributional consistency across partitions, and the Chatterjee correlation coefficient for initial, non-parametric feature screening to capture feature relevance and dependence structure. We further integrate these theoretical advances into a unified, efficient framework that also incorporates missing-data handling, and embed this framework within our custom InsurAutoML pipeline. The performance of the proposed approach is evaluated using both simulated datasets and datasets often cited in the academic literature. Our findings definitively demonstrate that incorporating statistically rigorous data preparation methods not only significantly enhances model robustness and interpretability but also substantially reduces computational resource requirements across diverse insurance loss modeling tasks. This work provides a crucial methodological upgrade for achieving reliable results in high stakes insurance applications.


Safe Distributionally Robust Feature Selection under Covariate Shift

Hanada, Hiroyuki, Akahane, Satoshi, Hashimoto, Noriaki, Takeno, Shion, Takeuchi, Ichiro

arXiv.org Machine Learning

In practical machine learning, the environments encountered during the model development and deployment phases often differ, especially when a model is used by many users in diverse settings. Learning models that maintain reliable performance across plausible deployment environments is known as distributionally robust (DR) learning. In this work, we study the problem of distributionally robust feature selection (DRFS), with a particular focus on sparse sensing applications motivated by industrial needs. In practical multi-sensor systems, a shared subset of sensors is typically selected prior to deployment based on performance evaluations using many available sensors. At deployment, individual users may further adapt or fine-tune models to their specific environments. When deployment environments differ from those anticipated during development, this strategy can result in systems lacking sensors required for optimal performance. To address this issue, we propose safe-DRFS, a novel approach that extends safe screening from conventional sparse modeling settings to a DR setting under covariate shift. Our method identifies a feature subset that encompasses all subsets that may become optimal across a specified range of input distribution shifts, with finite-sample theoretical guarantees of no false feature elimination.


Kernel Feature Selection via Conditional Covariance Minimization

Neural Information Processing Systems

We propose a method for feature selection that employs kernel-based measures of independence to find a subset of covariates that is maximally predictive of the response. Building on past work in kernel dimension reduction, we show how to perform feature selection via a constrained optimization problem involving the trace of the conditional covariance operator. We prove various consistency results for this procedure, and also demonstrate that our method compares favorably with other state-of-the-art algorithms on a variety of synthetic and real data sets.


DeepPINK: reproducible feature selection in deep neural networks

Neural Information Processing Systems

Deep learning has become increasingly popular in both supervised and unsupervised machine learning thanks to its outstanding empirical performance. However, because of their intrinsic complexity, most deep learning methods are largely treated as black box tools with little interpretability. Even though recent attempts have been made to facilitate the interpretability of deep neural networks (DNNs), existing methods are susceptible to noise and lack of robustness. Therefore, scientists are justifiably cautious about the reproducibility of the discoveries, which is often related to the interpretability of the underlying statistical models. In this paper, we describe a method to increase the interpretability and reproducibility of DNNs by incorporating the idea of feature selection with controlled error rate. By designing a new DNN architecture and integrating it with the recently proposed knockoffs framework, we perform feature selection with a controlled error rate, while maintaining high power. This new method, DeepPINK (Deep feature selection using Paired-Input Nonlinear Knockoffs), is applied to both simulated and real data sets to demonstrate its empirical utility.