The Pearson correlation coefficient (ρ) is a commonly used measure of correlation, but it has limitations as it only measures the linear relationship between two numerical variables. The distance correlation measures all types of dependencies between random vectors and in arbitrary dimensions, not just the linear ones. In this paper, we propose a filter method that utilizes distance correlation as a criterion for feature selection in Random Forest regression. We conduct extensive simulation studies to evaluate its performance compared to existing methods under various data settings, in terms of the prediction mean squared error. The results show that our proposed method is competitive with existing methods and outperforms all other methods in high-dimensional (p≥300) nonlinearly related data sets. The applicability of the proposed method is also illustrated by two real data applications.
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http://dx.doi.org/10.3390/e25091250 | DOI Listing |
STAR Protoc
January 2025
Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Neurology Service, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA. Electronic address:
Here, we present a protocol for using Myotally, a user-friendly software for fast, automated quantification of muscle fiber size, number, and central nucleation from immunofluorescent stains of mouse skeletal muscle cross-sections. We describe steps for installing the software, preparing compatible images, finding the file path, and selecting key parameters like image quality and size limits. We also detail optional features, such as measuring mean fluorescence.
View Article and Find Full Text PDFAbdom Radiol (NY)
January 2025
Department of Radiology, Taizhou Municipal Hospital, Taizhou, Zhejiang, China.
Background: To develop and validate a clinical-radiomics model for preoperative prediction of lymphovascular invasion (LVI) in rectal cancer.
Methods: This retrospective study included data from 239 patients with pathologically confirmed rectal adenocarcinoma from two centers, all of whom underwent MRI examinations. Cases from the first center (n = 189) were randomly divided into a training set and an internal validation set at a 7:3 ratio, while cases from the second center (n = 50) constituted the external validation set.
Bioinformatics
January 2025
Department of Pathology and Department of Immunobiology, Yale School of Medicine.
Summary: With the increased reliance on multi-omics data for bulk and single cell analyses, the availability of robust approaches to perform unsupervised learning for clustering, visualization, and feature selection is imperative. We introduce nipalsMCIA, an implementation of multiple co-inertia analysis (MCIA) for joint dimensionality reduction that solves the objective function using an extension to Non-linear Iterative Partial Least Squares (NIPALS). We applied nipalsMCIA to both bulk and single cell datasets and observed significant speed-up over other implementations for data with a large sample size and/or feature dimension.
View Article and Find Full Text PDFBMC Geriatr
January 2025
Department of Cardiology, The Second Hospital & Clinical Medical School, Lanzhou University, No. 82 Cuiyingmen, Lanzhou, 730000, China.
Objective: Constructing a predictive model for the occurrence of heart disease in elderly hypertensive individuals, aiming to provide early risk identification.
Methods: A total of 934 participants aged 60 and above from the China Health and Retirement Longitudinal Study with a 7-year follow-up (2011-2018) were included. Machine learning methods (logistic regression, XGBoost, DNN) were employed to build a model predicting heart disease risk in hypertensive patients.
Sci Rep
January 2025
Department of Orthopaedics, Traditional Chinese Medical Hospital of Gansu Province, Qilihe District, Guazhou Street 418, Lanzhou, 730050,, Gansu, China.
Knee osteoarthritis (KOA) represents a progressive degenerative disorder characterized by the gradual erosion of articular cartilage. This study aimed to develop and validate biomarker-based predictive models for KOA diagnosis using machine learning techniques. Clinical data from 2594 samples were obtained and stratified into training and validation datasets in a 7:3 ratio.
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