Accurate automated medical image recognition, including classification and segmentation, is one of the most challenging tasks in medical image analysis. Recently, deep learning methods have achieved remarkable success in medical image classification and segmentation, clearly becoming the state-of-the-art methods. However, most of these methods are unable to provide uncertainty quantification (UQ) for their output, often being overconfident, which can lead to disastrous consequences. Bayesian Deep Learning (BDL) methods can be used to quantify uncertainty of traditional deep learning methods, and thus address this issue. We apply three uncertainty quantification methods to deal with uncertainty during skin cancer image classification. They are as follows: Monte Carlo (MC) dropout, Ensemble MC (EMC) dropout and Deep Ensemble (DE). To further resolve the remaining uncertainty after applying the MC, EMC and DE methods, we describe a novel hybrid dynamic BDL model, taking into account uncertainty, based on the Three-Way Decision (TWD) theory. The proposed dynamic model enables us to use different UQ methods and different deep neural networks in distinct classification phases. So, the elements of each phase can be adjusted according to the dataset under consideration. In this study, two best UQ methods (i.e., DE and EMC) are applied in two classification phases (the first and second phases) to analyze two well-known skin cancer datasets, preventing one from making overconfident decisions when it comes to diagnosing the disease. The accuracy and the F1-score of our final solution are, respectively, 88.95% and 89.00% for the first dataset, and 90.96% and 91.00% for the second dataset. Our results suggest that the proposed TWDBDL model can be used effectively at different stages of medical image analysis.
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http://dx.doi.org/10.1016/j.compbiomed.2021.104418 | DOI Listing |
Invest Ophthalmol Vis Sci
January 2025
Institute for Applied Mathematics, University of Bonn, Bonn, Germany.
Purpose: To quantify outer retina structural changes and define novel biomarkers of inherited retinal degeneration associated with biallelic mutations in RPE65 (RPE65-IRD) in patients before and after subretinal gene augmentation therapy with voretigene neparvovec (Luxturna).
Methods: Application of advanced deep learning for automated retinal layer segmentation, specifically tailored for RPE65-IRD. Quantification of five novel biomarkers for the ellipsoid zone (EZ): thickness, granularity, reflectivity, and intensity.
Methods Mol Biol
January 2025
Stowers Institute for Medical Research, Kansas City, MO, USA.
Understanding the spatial and temporal dynamics of gene expression is crucial for unraveling molecular mechanisms underlying various biological processes. While traditional methods have offered insights into gene expression patterns, they primarily focus on mature mRNA transcripts, lacking real-time visualization of newly synthesized or nascent transcription events. Recent advancements in monitoring nascent transcription in live cells provide valuable insights into transcriptional dynamics.
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Stroke Monitoring and Diagnostic Division, AtheroPoint™, Roseville, CA, 95661, USA.
Women are disproportionately affected by chronic autoimmune diseases (AD) like systemic lupus erythematosus (SLE), scleroderma, rheumatoid arthritis (RA), and Sjögren's syndrome. Traditional evaluations often underestimate the associated cardiovascular disease (CVD) and stroke risk in women having AD. Vitamin D deficiency increases susceptibility to these conditions.
View Article and Find Full Text PDFAnal Chem
January 2025
Institute of Artificial Intelligence, Xiamen University, Xiamen, Fujian, 361005, China.
Metabolite identification from 1D H NMR spectra is a major challenge in NMR-based metabolomics. This study introduces NMRformer, a Transformer-based deep learning framework for accurate peak assignment and metabolite identification in 1D H NMR spectroscopy. Unlike traditional approaches, NMRformer interprets spectra as sequences of spectral peaks and integrates a self-attention mechanism and peak height ratios directly into the Transformer encoder layer.
View Article and Find Full Text PDFSoft Matter
January 2025
Department of Mechanical and Aerospace Engineering, University at Buffalo, Buffalo, NY 14260, USA.
Monolayer assembly of charged colloidal particles at liquid interfaces opens a new avenue for advancing the additive manufacturing of thin film materials and devices with tailored properties. In this study, we investigated the dynamics of electrosprayed colloidal particles at curved droplet interfaces through a combination of physics-based computational simulations and machine learning. We employed a novel mesh-constrained Brownian dynamics (BD) algorithm coupled with Ansys® electric field simulations to model the transport and assembly of charged particles on a non-spherical droplet surface.
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