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View article: Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix
Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix Open
Motivation Phylogenetic reconstruction is a fundamental problem in computational biology. The Neighbor Joining (NJ) algorithm offers an efficient distance-based solution to this problem, which often serves as the foundation for more advanc…
View article: CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics
CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics Open
Motivation Copy number variations (CNVs) are common genetic alterations in tumour cells. The delineation of CNVs holds promise for enhancing our comprehension of cancer progression. Moreover, accurate inference of CNVs from single-cell seq…
View article: Cooperation in the Latent Space: The Benefits of Adding Mixture Components in Variational Autoencoders
Cooperation in the Latent Space: The Benefits of Adding Mixture Components in Variational Autoencoders Open
In this paper, we show how the mixture components cooperate when they jointly adapt to maximize the ELBO. We build upon recent advances in the multiple and adaptive importance sampling literature. We then model the mixture components using…
View article: Rapid TAURUS for Relaxation-Based Color Magnetic Particle Imaging
Rapid TAURUS for Relaxation-Based Color Magnetic Particle Imaging Open
Magnetic particle imaging (MPI) is a rapidly developing medical imaging modality that exploits the non-linear response of magnetic nanoparticles (MNPs). Color MPI widens the functionality of MPI, empowering it with the capability to distin…
View article: Partial FOV Center Imaging (PCI): A Robust X-Space Image Reconstruction for Magnetic Particle Imaging
Partial FOV Center Imaging (PCI): A Robust X-Space Image Reconstruction for Magnetic Particle Imaging Open
Magnetic Particle Imaging (MPI) is an emerging medical imaging modality that images the spatial distribution of superparamagnetic iron oxide (SPIO) nanoparticles using their nonlinear response to applied magnetic fields. In standard x-spac…
View article: Blind Source Separation for Multi-Color MPI
Blind Source Separation for Multi-Color MPI Open
In magnetic particle imaging (MPI), different magnetic nanoparticles (MNPs) in the same field-of-view can be distinguished via color-MPI techniques. Existing system-function-based techniques require extensive calibration scans, whereas x-s…
View article: Multi-dimensional Harmonic Dispersion X-space MPI
Multi-dimensional Harmonic Dispersion X-space MPI Open
In magnetic particle imaging (MPI), standard x-space reconstruction requires partial field-of-view (pFOV) processing steps: speed compensation of the received signal and gridding the non-equidistant field free point (FFP) positions to a Ca…
View article: Rapid Relaxation-Based Color MPI
Rapid Relaxation-Based Color MPI Open
Color magnetic particle imaging (MPI) techniques have recently gained popularity, with the purposes of distinguishing different nanoparticle types or nanoparticles in different environments. In this work, we extend a relaxation-based color…