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Patch-Based Sparse Representation For Bacterial Detection
[article]
2019
arXiv
pre-print
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In this paper, we propose an unsupervised approach for bacterial detection in optical endomicroscopy images. ...
, corrupted by additive Gaussian noise and potentially by a sparse outlier term modelling anomalies (which are considered to be candidate bacteria). ...
SmartProbes for bacterial detection. ...
arXiv:1810.12043v2
fatcat:qxuyvedoebdade77aumgdtbtqa
Tiled sparse coding in eigenspaces for the COVID-19 diagnosis in chest X-ray images
[article]
2021
arXiv
pre-print
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In this work, we propose a classification framework based on sparse coding in order to identify the pneumonia patterns associated with different pathologies. ...
The excellent results and the pioneering use of sparse coding in this scenario evidence the applicability of this approach as an aid for clinicians in a real-world environment. ...
In this paper, we proposed a classification framework based on sparse coding to detect the pneumonia patterns caused by different pathologies. ...
arXiv:2106.14724v1
fatcat:pd5gkv7fkvde3ks3dhzupdkybm
Simplicity of Kmeans Versus Deepness of Deep Learning: A Case of Unsupervised Feature Learning with Limited Data
2015
2015 IEEE 14th International Conference on Machine Learning and Applications (ICMLA)
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Using images collected on the first day for training, on the second day for validation, and on the third day for testing Kmeans-based representation learning achieves 97% classification accuracy on the ...
We study a bio-detection application as a case study to demonstrate that Kmeans-based unsupervised feature learning can be a simple yet effective alternative to deep learning techniques for small data ...
ACKNOWLEDGMENT This research was sponsored by the National Science Foundation (NSF) under Grant Number IIS-1252648 (CAREER) and by USDA-ARS project number 8072-42000-072-00D in conjunction with the Center for ...
doi:10.1109/icmla.2015.78
dblp:conf/icmla/DundarKZHR15
fatcat:awmhng67bzclfmyfydswxm365i
A Modified Iterative Alternating Direction Minimization Algorithm for Impulse Noise Removal in Images
2014
Journal of Applied Mathematics
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A patch-based nonlocal operator and sparse representation are married in thel1-l1optimization model to be solved. ...
Simulation results demonstrate that the proposed algorithm outperforms typical denoising methods in terms of preserving edges and textures for both salt-and-pepper noise and random-valued impulse noise ...
Patch-based nonlocal operator (PANO) [27] is a linear operator to model the sparse representation of similar patches, which can be viewed as an alternative form of the block matching 3D frames. ...
doi:10.1155/2014/595782
fatcat:nlpho2xnb5hhbb2uxsklu6unuu
Cell Detection in Microscopy Images with Deep Convolutional Neural Network and Compressed Sensing
[article]
2018
arXiv
pre-print
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For the cell detection problem, the output space is the sparsely labeled pixel locations indicating cell centers. ...
Cell detection methods have evolved from employing hand-crafted features to deep learning-based techniques. ...
However, CS enables a potentially large reduction in the sampling and computation costs for sensing/reconstructing signals that are sparse or have a sparse representation under some linear transformation ...
arXiv:1708.03307v3
fatcat:dn6mzefu5jd7nphr7sjkoybmsy
Editorial: Special Section on deep image and video understanding
2017
Pattern Recognition
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On the whole, this special issue covered a number of works that highlighted the importance in using deep learning representations for image-and video-based data. ...
Given a set of image patches, weak classifiers are used for labeling purposes, which are then used to feed a DBN model for feature learning. ...
doi:10.1016/j.patcog.2016.09.001
fatcat:tdydrzgqwfc3vnrlzkutf3trqe
From photography to microbiology: Eigenbiome models for skin appearance
2015
2015 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)
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Furthermore, the use of non-negative matrix factorization allows a representation of the microbiome eigenvector as a physically plausible positive distribution of bacterial components. ...
Computational appearance provides an exciting new opportunity for integrating macroscopic imaging and microscopic biology. ...
Thus, three dimensional space is sufficient for this microbiome representation. Clustering of the eigenbiome is done based on proximity to neighbors by a simple kmeans clustering. ...
doi:10.1109/cvprw.2015.7301310
dblp:conf/cvpr/KaurDC15
fatcat:t7ch7ta6fbgunldnb7czarmq3e
Manifold-Based Visual Object Counting
2018
IEEE Transactions on Image Processing
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To address this limitation, we propose a manifold-based method for visual object counting (M-VOC), based on the manifold assumption that similar image patches share similar object densities. ...
Recently, object density based estimation method is shown to be promising for object counting as well as rough instance localization. ...
We thank the anonymous reviewers and the associate editor for their helpful comments and suggestions for improving this paper. ...
doi:10.1109/tip.2018.2799328
pmid:29641404
fatcat:a4r6wf3vrjccpkt6d5g3ttmi3y
A survey on deep learning in medical image analysis
2017
Medical Image Analysis
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2017 pre-print arXiv:1702.05747v1 fatcat:zdedepkenraglidf7b4ojxcohiOther Versions
We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. ...
Open challenges and directions for future research are discussed. ...
Conference proceedings for MICCAI (including workshops), SPIE, ISBI and EMBC were searched based on titles of papers. We checked references in all selected papers and consulted colleagues. ...
doi:10.1016/j.media.2017.07.005
pmid:28778026
fatcat:esbj72ftwvbgzh6jgw367k73j4
Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes
2020
Nature Communications
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The soil aqueous-phase content and connectivity exert strong influence on bacterial diversity for each soil type and rainfall pattern. ...
The proposed heuristic model captures observed global trends of bacterial diversity in good agreement with predictions by an individual-based mechanistic model. ...
Acknowledgements We gratefully acknowledge Oskar Hagen and Minsu Kim for helpful comments on early drafts of the manuscript and critical reflection and discussion on the conceptual framework. ...
doi:10.1038/s41467-019-13966-w
pmid:31913270
pmcid:PMC6949233
fatcat:mxm6ph2ddbfldgmtva7jxqxz34
Effects of patch connectivity and heterogeneity on metacommunity structure of planktonic bacteria and viruses
2012
The ISME Journal
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for viruses. ...
Our results suggest that even a very limited exchange among local communities can alter the trajectory of bacterial and viral communities at small temporal and spatial scales. ...
We would like to thank Anita Norman and Michaela Martin for helping us with the maintenance and sampling of the mesocosms. ...
doi:10.1038/ismej.2012.138
pmid:23178674
pmcid:PMC3578570
fatcat:yufu3hli4jbcpmp2igmwpr66ly
Spatial variations in the microbial community structure and diversity of the human foot is associated with the production of odorous volatiles
2014
FEMS Microbiology Ecology
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Variations in the spatial distribution of these microbes appear to be responsible for the localized production of odour across the foot. ...
Culture-based analysis confirmed that Staphylococci were present in higher numbers than aerobic corynebacteria and Gram-positive aerobic cocci, with all species being present at much higher levels on the ...
Neil Hall and the Centre for Genomics Research (CGR), Liverpool, UK, for help with pyrosequencing of the bacterial samples. ...
doi:10.1093/femsec/fiu018
pmid:25764539
fatcat:4tkqz6ovjvbzdcrhwhd6ziez6a
Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice
2017
Proceedings of the National Academy of Sciences of the United States of America
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mice fed a polysaccharide-rich diet, and (ii) in situ hybridization and spectral imaging analysis methods that allow simultaneous detection of multiple bacterial strains at multiple spatial scales. ...
Here, we illustrate an approach for addressing this challenge, using (i) a model, defined 15-member consortium of phylogenetically diverse, sequenced human gut bacterial strains introduced into adult gnotobiotic ...
We thank David O'Donnell and Maria Karlsson for help with gnotobiotic animal husbandry; Louie Kerr for microscopy support; and Christopher Rieken, Blair Rossetti, and Liping Xun for outstanding technical ...
doi:10.1073/pnas.1711596114
pmid:29073107
pmcid:PMC5664539
fatcat:22c76pkdkranxdjhkv23aawcgu
Colonic patch and colonic SILT development are independent and differentially regulated events
2012
Mucosal Immunology
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We show that colonic patches and colonic SILTs are distinct tissues, based on their differential 1) anatomical location, 2) cellular organization, 3) developmental time frame and 4) developmental molecular ...
Detection of organized gut-associated lymphoid tissue was performed on every 10 th section (20 th section for adult colons) stained for CD4 and MAdCAM-1 in combination with either B220 or α-smooth muscle ...
doi:10.1038/mi.2012.90
pmid:22990625
pmcid:PMC3570605
fatcat:faopna3ctfcbljgqdtjr6ckxku
How Bacteria Adhere to Brushy PEG Surfaces: Clinging to Flaws and Compressing the Brush
2012
Macromolecules
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"patches" at their bases. ...
Thus, the dominant factor for bacterial repulsion was the mass of PEG in the brush. ...
This is explored in Figure 2B for the same data from Figure 2A . While the mass-based representation in Figure 2B brings the data sets closer, they do not completely collapse. ...
doi:10.1021/ma300981r
pmid:23148127
pmcid:PMC3494094
fatcat:k2mhihmgtbgfljqw2ge6nayasi
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