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

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%.

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

The optimization of an assembly line layout can be modeled as a facility layout problem. Since an accurate representation of the real-world distances is essential for the validity of the optimization results, this paper compares the accuracy of the approximation of the real-world distances by the commonly used rectilinear and Euclidean distance metrics. Further, the influence of the size and aspect ratio of the machines on the approximation accuracy and the influence of the distance metrics on the solver runtime is studied. The results show the Euclidean distance metric being more accurate but extending computation time.

BackgroundReducing TB surveillance incurs significant costs, as effective control and societal impact minimization rely on robust, ongoing surveillance systems that integrate and analyze comprehensive data for prompt action. Our study supports integrating artificial intelligence (LSI) into TB and other notifiable disease monitoring frameworks to improve trackingFigure 1Binary Matrix of 125 Terms: Presence vs. Absence of Root Keywords Retrieved from the Patient ElectronicRecord for the LSI Automatic Retrieval System.Binary Matrix of 125 Terms: Presence vs. Absence of Root Keywords Retrieved from the Patient Electronic Record for the LSI Automatic Retrieval System.MethodsIn 2024, we developed a novel application within Datamart A.R.G.U.S.—Assistant for Recovery and Guarding of Urgent and Epidemiological Sentinels—a cloud-based platform hosted on AWS and developed by our team. This application integrates with hospital systems (MV) and laboratory systems (MATRIX and GAL) to enhance the surveillance of healthcare-associated infections (HAI) and notifiable diseases. Data from both hospital and outpatient care are encoded into a binary matrix of 125 terms (root keywords) extracted from patient electronic records. This matrix is then processed using Singular Value Decomposition (SVD) within an LSI-based information retrieval system (Fig. 1). In our model, each patient is represented as a point in a 125-dimensional hyperdimensional space. When projected into three-dimensional space, this framework allows for effective clustering and classification of notifiable Diseases (Fig. 2), specifically TB (Fig. 3).Figure 2:3D Visualization of High-Dimensional Data: Comparing Mandatory Notifiable Diseases versus Non-Notifiable Diseases. Both patient types are well separated in the space, enabling automatic clustering and classification.3D Visualization of High-Dimensional Data: Comparing Mandatory Notifiable Diseases versus Non-Notifiable Diseases. Both patient types are well separated in the space, enabling automatic clustering and classification.ResultsThe LSI-based matrix was constructed using data from January 2023 to February 2024, encompassing a sample of 17,895 cases (lines) across 125 presence versus absence terms, with each case classified as either a notifiable or non-notifiable disease. The 125-dimensional matrix was reduced to 28 factors using SVD. The sensitivity and specificity of the Euclidean distance were better than those of cosine similarity when automatically identifying TB cases in 1,970 independent queries (Fig. 4).Figure 3:3D Visualization of High-Dimensional Data: Comparing Tuberculosis versus Other Mandatory Notifiable Diseases versus Non-Notifiable Diseases. The three types of patients are well separated in the space, enabling automatic clustering and classification.3D Visualization of High-Dimensional Data: Comparing Tuberculosis versus Other Mandatory Notifiable Diseases versus Non-Notifiable Diseases. The three types of patients are well separated in the space, enabling automatic clustering and classification.ConclusionArtificial Intelligence (LSI), significantly enhances the surveillance of TB and other notifiable diseases by enabling real-time, automated case identification up to one day prior (D-1). This advancement allows surveillance personnel to complete their tasks more efficiently, thereby preventing outbreaks and reducing the risk of unforeseen fatalities.Figure 4:Performance Comparison of Cosine vs. Euclidean Distance Metrics in Automatically Identifying TB Cases Using LSI: Euclidean Distance Demonstrates Superior Accuracy and Has Been Integrated into Datamart A.R.G.U.S. for Real-Time Identification of TB and Other Notifiable Diseases as of the Previous Workday (D-1).Performance Comparison of Cosine vs. Euclidean Distance Metrics in Automatically Identifying TB Cases Using LSI: Euclidean Distance Demonstrates Superior Accuracy and Has Been Integrated into Datamart A.R.G.U.S. for Real-Time Identification of TB and Other Notifiable Diseases as of the Previous Workday (D-1).DisclosuresAll Authors: No reported disclosures

In this paper, we propose a feature combination, also known as feature fusion, for improving performance in content-based gastric image retrieval (CBGIR). This study provides a CBGIR system that retrieves images by combining ResNet-18 and ResNet-50 information and finally, the Euclidean distance metric is evaluated for similarity measurement. The proposed approach is also compared to different deep learning techniques such as AlexNet, VGGs (VGG-16 & VGG-19), GoogleNet, SqueezeNet, DarkNet-19 models. The proposed method was examined on the KVASIR database with 4000 images and S different classes. We get the optimum results as average precision of 95.44% and average recall of 19.09 on a scale of 20 using the proposed deep learning model and Euclidean distance metric.

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

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.

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

Decision letter for "‘Euclimatch': an R package for climate matching with Euclidean distance metrics"

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While the Euclidean distance metric is commonly utilized in most soft subspace clustering algorithms, some robust distance metrics can also be considered for soft subspace clustering. In this study, a novel soft subspace clustering algorithm called Alternative Soft Subspace Clustering (ASSC) is proposed by incorporating the alternative distance metric into the framework of entropy weighting subspace clustering. The properties of ASSC are investigated and a theoretical analysis on robustness is established accordingly. Experiments on UCI data are conducted and the experimental results show the effectiveness of the proposed algorithm.

The Recognition and Classification of Objects Based on the Modified Distance Metric