Dataset Information

Variable selection in the presence of missing data: resampling and imputation.

ABSTRACT: In the presence of missing data, variable selection methods need to be tailored to missing data mechanisms and statistical approaches used for handling missing data. We focus on the mechanism of missing at random and variable selection methods that can be combined with imputation. We investigate a general resampling approach (BI-SS) that combines bootstrap imputation and stability selection, the latter of which was developed for fully observed data. The proposed approach is general and can be applied to a wide range of settings. Our extensive simulation studies demonstrate that the performance of BI-SS is the best or close to the best and is relatively insensitive to tuning parameter values in terms of variable selection, compared with several existing methods for both low-dimensional and high-dimensional problems. The proposed approach is further illustrated using two applications, one for a low-dimensional problem and the other for a high-dimensional problem.

SUBMITTER: Long Q

PROVIDER: S-EPMC5156376 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature

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Variable selection in the presence of missing data: resampling and imputation.

Long Qi Q Johnson Brent A BA

Biostatistics (Oxford, England) 20150218 3

In the presence of missing data, variable selection methods need to be tailored to missing data mechanisms and statistical approaches used for handling missing data. We focus on the mechanism of missing at random and variable selection methods that can be combined with imputation. We investigate a general resampling approach (BI-SS) that combines bootstrap imputation and stability selection, the latter of which was developed for fully observed data. The proposed approach is general and can be ap ...[more]

PMID: 25694614

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Project description:Many countries have attempted to mitigate and manage issues related to harmful algal blooms (HABs) by monitoring and predicting their occurrence. The infrequency and duration of HABs occurrence pose the challenge of data imbalance when constructing machine learning models for their prediction. Furthermore, the appropriate selection of input variables is a significant issue because of the complexities between the input and output variables. Therefore, the objective of this study was to improve the predictive performance of HABs using feature selection and data resampling. Data resampling was used to address the imbalance in the minority class data. Two machine learning models were constructed to predict algal alert levels using 10 years of meteorological, hydrodynamic, and water quality data. The improvement in model accuracy due to changes in resampling methods was more noticeable than the improvement in model accuracy due to changes in feature selection methods. Models constructed using combinations of original and synthetic data across all resampling methods demonstrated higher prediction performance for the caution level (L-1) and warning level (L-2) than models constructed using the original data. In particular, the optimal artificial neural network and random forest models constructed using combinations of original and synthetic data showed significantly improved prediction accuracy for L-1 and L-2, representing the transition from normal to bloom formation states in the training and testing steps. The test results of the optimal RF model using the original data indicated prediction accuracies of 98.8% for L0, 50.0% for L1, and 50.0% for L2. In contrast, the optimal random forest model using the Synthetic Minority Oversampling Technique-Edited Nearest Neighbor (ENN) sampling method achieved accuracies of 85.0% for L0, 85.7% for L1, and 100% for L2. Therefore, applying synthetic data can address the imbalance in the observed data and improve the detection performance of machine learning models. Reliable predictions using improved models can support the design of management practices to mitigate HABs in reservoirs and ultimately ensure safe and clean water resources.

Dataset Information

Variable selection in the presence of missing data: resampling and imputation.

Publications

Variable selection in the presence of missing data: resampling and imputation.

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