Search results for "Graphics"
showing 10 items of 1223 documents
Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting.
2015
De novo clustering is a popular technique to perform taxonomic profiling of a microbial community by grouping 16S rRNA amplicon reads into operational taxonomic units (OTUs). In this work, we introduce a new dendrogram-based OTU clustering pipeline called CRiSPy. The key idea used in CRiSPy to improve clustering accuracy is the application of an anomaly detection technique to obtain a dynamic distance cutoff instead of using the de facto value of 97 percent sequence similarity as in most existing OTU clustering pipelines. This technique works by detecting an abrupt change in the merging heights of a dendrogram. To produce the output dendrograms, CRiSPy employs the OTU hierarchical clusterin…
Tractional Motion Machines: Tangent-Managing Planar Mechanisms as Analog Computers and Educational Artifacts
2012
Concrete and virtual machines play a central role in the both Unconventional Computing (machines as computers) and in Math Education (influence of artifacts on reaching/producing abstract thought). Here we will examine some fallouts in these fields for the Tractional Motion Machines, planar mechanisms based on some devices used to plot the solutions of differential equations by the management of the tangent since the late 17th century.
Least-squares community extraction in feature-rich networks using similarity data
2021
We explore a doubly-greedy approach to the issue of community detection in feature-rich networks. According to this approach, both the network and feature data are straightforwardly recovered from the underlying unknown non-overlapping communities, supplied with a center in the feature space and intensity weight(s) over the network each. Our least-squares additive criterion allows us to search for communities one-by-one and to find each community by adding entities one by one. A focus of this paper is that the feature-space data part is converted into a similarity matrix format. The similarity/link values can be used in either of two modes: (a) as measured in the same scale so that one may …
MetNet: A two-level approach to reconstructing and comparing metabolic networks
2021
Metabolic pathway comparison and interaction between different species can detect important information for drug engineering and medical science. In the literature, proposals for reconstructing and comparing metabolic networks present two main problems: network reconstruction requires usually human intervention to integrate information from different sources and, in metabolic comparison, the size of the networks leads to a challenging computational problem. We propose to automatically reconstruct a metabolic network on the basis of KEGG database information. Our proposal relies on a two-level representation of the huge metabolic network: the first level is graph-based and depicts pathways a…
Area-Based Depth Estimation for Monochromatic Feature-Sparse Orthographic Capture
2018
With the rapid development of light field technology, depth estimation has been highlighted as one of the critical problems in the field, and a number of approaches have been proposed to extract the depth of the scene. However, depth estimation by stereo matching becomes difficult and unreliable when the captured images lack both color and feature information. In this paper, we propose a scheme that extracts robust depth from monochromatic, feature-sparse scenes recorded in orthographic sub-aperture images. Unlike approaches which rely on the rich color and texture information across the sub-aperture views, our approach is based on depth from focus techniques. First, we superimpose shifted …
Towards an Efficient Implementation of an Accurate SPH Method
2020
A modified version of the Smoothed Particle Hydrodynamics (SPH) method is considered in order to overcome the loss of accuracy of the standard formulation. The summation of Gaussian kernel functions is employed, using the Improved Fast Gauss Transform (IFGT) to reduce the computational cost, while tuning the desired accuracy in the SPH method. This technique, coupled with an algorithmic design for exploiting the performance of Graphics Processing Units (GPUs), makes the method promising, as shown by numerical experiments.
Deep Learning-Based Methods for Prostate Segmentation in Magnetic Resonance Imaging
2021
Magnetic Resonance Imaging-based prostate segmentation is an essential task for adaptive radiotherapy and for radiomics studies whose purpose is to identify associations between imaging features and patient outcomes. Because manual delineation is a time-consuming task, we present three deep-learning (DL) approaches, namely UNet, efficient neural network (ENet), and efficient residual factorized convNet (ERFNet), whose aim is to tackle the fully-automated, real-time, and 3D delineation process of the prostate gland on T2-weighted MRI. While UNet is used in many biomedical image delineation applications, ENet and ERFNet are mainly applied in self-driving cars to compensate for limited hardwar…
Total Variation Regularization in Digital Breast Tomosynthesis
2013
We developed an iterative algebraic algorithm for the reconstruction of 3D volumes from limited-angle breast projection images. Algebraic reconstruction is accelerated using the graphics processing unit. We varied a total variation (TV)-norm parameter in order to verify the influence of TV regularization on the representation of small structures in the reconstructions. The Barzilai-Borwein algorithm is used to solve the inverse reconstruction problem. The quality of our reconstructions was evaluated with the Quart Mam/Digi Phantom, which features so-called Landolt ring structures to verify perceptibility limits. The evaluation of the reconstructions was done with an automatic LR detection a…
GPU-accelerated integral imaging and full-parallax 3D display using stereo-plenoptic camera system
2019
Abstract In this paper, we propose a novel approach to produce integral images ready to be displayed onto an integral-imaging monitor. Our main contribution is the use of commercial plenoptic camera, which is arranged in a stereo configuration. Our proposed set-up is able to record the radiance, spatial and angular, information simultaneously in each different stereo position. We illustrate our contribution by composing the point cloud from a pair of captured plenoptic images, and generate an integral image from the properly registered 3D information. We have exploited the graphics processing unit (GPU) acceleration in order to enhance the integral-image computation speed and efficiency. We…
A Novel Marking Reader for Progressive Addition Lenses Based on Gabor Holography
2016
PURPOSE Progressive addition lenses (PALs) are marked with permanent engraved marks (PEMs) at standardized locations. Permanent engraved marks are very useful through the manufacturing and mounting processes, act as locator marks to re-ink the removable marks, and contain useful information about the PAL. However, PEMs are often faint and weak, obscured by scratches, partially occluded, and difficult to recognize on tinted lenses or with antireflection or scratch-resistant coatings. The aim of this article is to present a new generation of portable marking reader based on an extremely simplified concept for visualization and identification of PEMs in PALs. METHODS Permanent engraved marks o…