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Classification-based pathway analysis using GPNet with novel P-value computation.
Brief Bioinform
November 2024
Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC 27101, United States.
Pathway analysis plays a critical role in bioinformatics, enabling researchers to identify biological pathways associated with various conditions by analyzing gene expression data. However, the rise of large, multi-center datasets has highlighted limitations in traditional methods like Over-Representation Analysis (ORA) and Functional Class Scoring (FCS), which struggle with low signal-to-noise ratios (SNR) and large sample sizes. To tackle these challenges, we use a deep learning-based classification method, Gene PointNet, and a novel $P$-value computation approach leveraging the confusion matrix to address pathway analysis tasks.
View Article and Find Full Text PDFSpherical harmonics texture extraction for versatile analysis of biological objects.
PLoS Comput Biol
January 2025
European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany.
The characterization of phenotypes in cells or organisms from microscopy data largely depends on differences in the spatial distribution of image intensity. Multiple methods exist for quantifying the intensity distribution - or image texture - across objects in natural images. However, many of these texture extraction methods do not directly adapt to 3D microscopy data.
View Article and Find Full Text PDFOne-minute sit-to-stand test: Reference values for the Chilean population.
PLoS One
January 2025
Blanquerna School of Health Sciences, Global Research on Wellbeing (GRoW), Ramon Llull University, Barcelona, Spain.
Introduction: The one-minute sit to stand test (1min-STST) is a field test used to assess functional capacity. It is easily implementable and of significant clinical utility; however, no reference values are currently available for the Chilean population. The objective of this study was to establish reference values for the 1min-STST in a healthy Chilean population.
View Article and Find Full Text PDFEvaluation of interspecies correlation estimation models to increase taxonomic diversity while reducing reliance on animal testing for chemicals evaluated under the Toxic Substances Control Act.
Integr Environ Assess Manag
January 2025
Office of Chemical Safety Office Pollution Prevention, Office of Pollution Prevention and Toxics, US Environmental Protection Agency, Washington, DC, United States.
The U.S. Environmental Protection Agency is committed to the implementation of new approach methodologies (NAMs) to enhance the scientific basis for chemical hazard assessments.
View Article and Find Full Text PDFDiagnostic Decision-Making Variability Between Novice and Expert Optometrists for Glaucoma: Comparative Analysis to Inform AI System Design.
JMIR Med Inform
January 2025
Department of Systems Design Engineering, Faculty of Engineering, University of Waterloo, Waterloo, ON, Canada.
Background: While expert optometrists tend to rely on a deep understanding of the disease and intuitive pattern recognition, those with less experience may depend more on extensive data, comparisons, and external guidance. Understanding these variations is important for developing artificial intelligence (AI) systems that can effectively support optometrists with varying degrees of experience and minimize decision inconsistencies.
Objective: The main objective of this study is to identify and analyze the variations in diagnostic decision-making approaches between novice and expert optometrists.
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