Robust correlation feature selection based support vector machine approach for high dimensional datasets

Orthogonally constrained matrix factorization for robust unsupervised feature selection with local preserving

High-dimensional data expands the spatial dimension, leading to increased computational complexity and reduced generalization performance. Microarray data classification, such as diagnosing diseases like cancer, involves complex dimensions due to their genetic and biological information. To address this issue, dimension reduction is essential for these data sets. The main goal of this chapter is to provide a method for dimension reduction and classification of genetic data sets. The proposed approach comprises multiple stages. Initially, various feature ranking methods are combined to improve the robustness and stability of the feature selection process. A hybrid ranking method, which incorporates gene interactions, is integrated with a wrapper method. Subsequently, a support vector machine (SVM) is employed for classification. To address class imbalance in the training data, a solution is implemented before feeding the data into the SVM classifier. The experimental outcomes of the proposed approach, tested on five microarray databases, indicate robust feature selection with a metric ranging from 0.70 to 0.88. Additionally, the classification accuracy falls within the range of 91-96%.

Robust feature selection using label enhancement and β-precision fuzzy rough sets for multilabel fuzzy decision system

Previous chapter Next chapter Full AccessProceedings Proceedings of the 2016 SIAM International Conference on Data Mining (SDM)Robust Unsupervised Feature Selection on Networked DataJundong Li, Xia Hu, Liang Wu, and Huan LiuJundong Li, Xia Hu, Liang Wu, and Huan Liupp.387 - 395Chapter DOI:https://doi.org/10.1137/1.9781611974348.44PDFBibTexSections ToolsAdd to favoritesExport CitationTrack CitationsEmail SectionsAboutAbstract Feature selection has shown its effectiveness to prepare high-dimensional data for many data mining and machine learning tasks. Traditional feature selection algorithms are mainly based on the assumption that data instances are independent and identically distributed. However, this assumption is invalid in networked data since instances are not only associated with high dimensional features but also inherently interconnected with each other. In addition, obtaining label information for networked data is time consuming and labor intensive. Without label information to direct feature selection, it is difficult to assess the feature relevance. In contrast to the scarce label information, link information in networks are abundant and could help select relevant features. However, most networked data has a lot of noisy links, resulting in the feature selection algorithms to be less effective. To address the above mentioned issues, we propose a robust unsupervised feature selection framework NetFS for networked data, which embeds the latent representation learning into feature selection. Therefore, content information is able to help mitigate the negative effects from noisy links in learning latent representations, while good latent representations in turn can contribute to extract more meaningful features. In other words, both phases could cooperate and boost each other. Experimental results on real-world datasets demonstrate the effectiveness of the proposed framework. Previous chapter Next chapter RelatedDetails Published:2016eISBN:978-1-61197-434-8 https://doi.org/10.1137/1.9781611974348Book Series Name:ProceedingsBook Code:PRDT16Book Pages:1-867

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Robust microarray data feature selection using a correntropy based distance metric learning approach

Exploring features associated with the clinical outcome of interest is a rapidly advancing area of research. However, with contemporary sequencing technologies capable of identifying over thousands of genes per sample, there is a challenge in constructing efficient prediction models that balance accuracy and resource utilization. To address this challenge, researchers have developed feature selection methods to enhance performance, reduce overfitting, and ensure resource efficiency. However, applying feature selection models to survival analysis, particularly in clinical datasets characterized by substantial censoring and limited sample sizes, introduces unique challenges. We propose a robust ensemble feature selection approach integrated with group Lasso to identify compelling features and evaluate its performance in predicting survival outcomes. Our approach consistently outperforms established models across various criteria through extensive simulations, demonstrating low false discovery rates, high sensitivity, and high stability. Furthermore, we applied the approach to a colorectal cancer dataset from The Cancer Genome Atlas, showcasing its effectiveness by generating a composite score based on the selected genes to correctly distinguish different subtypes of the patients. In summary, our proposed approach excels in selecting impactful features from high-dimensional data, yielding better outcomes compared to contemporary state-of-the-art models.

A robust graph-based semi-supervised sparse feature selection method

Feature selection has attracted considerable attention due to the wide application of multi-label learning. However, previous methods do not fully consider the relationship between feature sets and label sets but devote attention to either of them. Furthermore, conventional multi-label learning utilizes logical labels to estimate relevance between feature sets and label sets so that the importance of corresponding labels cannot be well reflected. Additionally, numerous irrelevant and redundant labels degrade the classification performance of models. To this end, we propose a multi-label feature selection method named Robust multi-label Feature Selection with shared Label Enhanced (RLEFS). First, we obtain a robust label enhancement term by reconstructing labels from logical labels to numerical labels and imposing \(l_{2,1}\)-norm onto the label enhancement term. Second, RLEFS utilizes the robust label enhancement term to share the similar latent semantic structure between feature matrix and label matrix. Third, local structure is considered to ensure the consistency of label information during the feature selection process. Finally, we integrate the above terms into one joint learning framework, and then, a simple but effective optimization method with provable convergence is proposed to solve RLEFS. Experimental results demonstrate the classification superiority of RLEFS in comparison with seven state-of-the-art methods.

Image hashing has become a major research area due to rapid growth of image alteration techniques that can tamper digital images. The major concern of all image hashing schemes is the selection of robust features. Local Binary Pattern (LBP) is a technique that selects robust features for different image applications. This paper presents a perceptual image hashing scheme by the utilization of Noise Resistant Local Binary Pattern (NRLBP), a modified form of the LBP. The features of NRLBP are extracted from non-overlapping blocks of a gray scale image. The NRLBP is combined with Singular Value Decomposition (SVD) to provide good robustness characteristics against a number of non-malicious distortions. Another major advantage of the proposed scheme is to detect localized tampered regions. Experimental results exhibit that the proposed scheme has the capability to detect tampering as small as 3% of the image size and at the same time offers good robustness properties.

With the increasing power of mobile headsets and mobile networks, mobile visual search applications have gained popularity and became tractable. One of the key technologies to enable visual search are the robust and compact features, which are extracted from an image and are invariant to recapturing variations. One of the key factors for compact visual descriptors is the selection of local features. The size of the compact visual descriptors and the computational complexities of a visual search system increase with the number of features selected. In this sense, ranking the descriptors extracted from a single image according to their importance in terms of recapturing is very necessary and important. In this paper, we attack this problem by proposing a novel self-matching selection. In this method, we randomly apply an out-of-plane rotation to the target image and match the original features to the features that are extracted from the out-of-plane rotated image. The importance of the features is ranked according to the self-matching score. This method is proven to be better than other peak strength and edge strength based methods by 30% from experiments on a large database.

PurposeThis study aimed to select robust features against lung motion in a phantom study and use them as input to feature selection algorithms and machine learning classifiers in a clinical study to predict the lymphovascular invasion (LVI) of non-small cell lung cancer (NSCLC). The results of robust features were also compared with conventional techniques without considering the robustness of radiomic features.MethodsAn in-house developed lung phantom was developed with two 22mm lesion sizes based on a clinical study. A specific motor was built to simulate motion in two orthogonal directions. Lesions of both clinical and phantom studies were segmented using a Fuzzy C-means-based segmentation algorithm. After inducing motion and extracting 105 radiomic features in 4 feature sets, including shape, first-, second-, and higher-order statistics features from each region of interest (ROI) of the phantom image, statistical analyses were performed to select robust features against motion. Subsequently, these robust features and a total of 105 radiomic features were extracted from 126 clinical data. Various feature selection (FS) and multiple machine learning (ML) classifiers were implemented to predict the LVI of NSCLC, followed by comparing the results of predicting LVI using robust features with common conventional techniques not considering the robustness of radiomic features.ResultsOur results demonstrated that selecting robust features as input to FS algorithms and ML classifiers surges the sensitivity, which has a gentle negative effect on the accuracy and the area under the curve (AUC) of predictions compared with commonly used methods in 12 of 15 outcomes. The top performance of the LVI prediction was achieved by the NB classifier and RFE FS without considering the robustness of radiomic features with 95% area under the curve of AUC, 67% accuracy, and 100% sensitivity. Moreover, the top performance of the LVI prediction using robust features belonged to the NB classifier and Boruta feature selection with 92% AUC, 86% accuracy, and 100% sensitivity.ConclusionRobustness over various influential factors is critical and should be considered in a radiomic study. Selecting robust features is a solution to overcome the low reproducibility of radiomic features. Although setting robust features against motion in a phantom study has a minor negative impact on the accuracy and AUC of LVI prediction, it boosts the sensitivity of prediction to a large extent.

The impact of respiratory motion and CT pitch on the robustness of radiomics feature extraction in 4DCT lung imaging

Various supervised embedded methods have been proposed to select discriminative features from original ones, such as Feature Selection with Orthogonal Regression (FSOR) and Robust Feature Selection. Compared with embedded methods based on the least square regression, FSOR, utilizing orthogonal regression, can preserve more discriminative information in the subspace and have better performance on feature selection. However, the embedded approaches have scarcely considered the dependency among the selected feature subset. To address the defect, in this paper, we propose a two-stage (filter-embedded) feature selection technique based on Maximum Relevance Minimum Redundancy and FSOR, termed as Orthogonal Regression with Minimum Redundancy (ORMR). We compared the feature selection performance between ORMR and nine other state-of-the-art supervised feature selection methods on six benchmark datasets. The results demonstrate the advantage of ORMR method over others in choosing discriminative features with considering the redundant information among the selected feature subset.

PurposeThis study explores the application of machine learning to high-dimensional proteomics datasets for identifying Alzheimer’s disease (AD) biomarkers. AD, a neurodegenerative disorder affecting millions worldwide, necessitates early and accurate diagnosis for effective management.MethodsWe leverage Tandem Mass Tag (TMT) proteomics data from the cerebrospinal fluid (CSF) samples from the frontal cortex of patients with idiopathic normal pressure hydrocephalus (iNPH), a condition often comorbid with AD, with rare access to both lumbar and ventricular samples. Our methodology includes extensive data preprocessing to address batch effects and missing values, followed by the use of the Synthetic Minority Over-sampling Technique (SMOTE) for data augmentation to overcome the small sample size. We apply linear, and non-linear machine learning models, and ensemble methods, to compare iNPH patients with and without biomarker evidence of AD pathology (Aβ-T- or Aβ+T+) in a classification task.ResultsWe present a machine learning workflow for working with high-dimensional TMT proteomics data that addresses their inherent data characteristics. Our results demonstrate that batch effect correction has no or minor impact on the models’ performance and robust feature selection is critical for model stability and performance, especially in the high-dimensional proteomics data setting for AD diagnostics. The results further indicated that removing features with missing values produced stronger models than imputing them, and the batch effect had minimal impact on the models Our best-performing disease-progression detection model, a random forest, achieves an AUC of 0.84 (± 0.03).ConclusionWe identify several novel protein biomarkers candidates, such as FABP3 and GOT1, with potential diagnostic value for AD pathology detection, suggesting the necessity of different biomarkers for AD diagnoses for patients with iNPH, and considering different biomarkers for ventricular and lumbar CSF samples. This work underscores the importance of a meticulous machine learning process in enhancing biomarker discovery. Our study also provides insights in translating biomarkers from other central nervous system diseases like iNPH, and both ventricular and lumbar CSF samples for biomarker discovery, providing a foundation for future research and clinical applications.