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Patch-Based Sparse Representation For Bacterial Detection [article]

Ahmed Karam Eldaly, Yoann Altmann, Ahsan Akram, Antonios Perperidis, Kevin Dhaliwal, Stephen McLaughlin
2019 arXiv   pre-print
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]

Juan E. Arco and Andrés Ortiz and Javier Ramírez and Juan M Gorriz
2021 arXiv   pre-print
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

Murat Dundar, Qiang Kou, Baichuan Zhang, Yicheng He, Bartek Rajwa
2015 2015 IEEE 14th International Conference on Machine Learning and Applications (ICMLA)  
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

Di Guo, Xiaobo Qu, Meng Wu, Keshou Wu
2014 Journal of Applied Mathematics  
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]

Yao Xue, Nilanjan Ray
2018 arXiv   pre-print
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

João Paulo Papa, Ryan Farrell
2017 Pattern Recognition  
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

Parneet Kaur, Kristin J. Dana, Gabriela Oana Cula
2015 2015 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)  
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

Yi Wang, Yuexian Zou, Wenwu Wang
2018 IEEE Transactions on Image Processing  
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

Geert Litjens, Thijs Kooi, Babak Ehteshami Bejnordi, Arnaud Arindra Adiyoso Setio, Francesco Ciompi, Mohsen Ghafoorian, Jeroen A.W.M. van der Laak, Bram van Ginneken, Clara I. Sánchez
2017 Medical Image Analysis  
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

Samuel Bickel, Dani Or
2020 Nature Communications  
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

Steven A J Declerck, Christian Winter, Jonathan B Shurin, Curtis A Suttle, Blake Matthews
2012 The ISME Journal  
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

Deborah Stevens, Robert Cornmell, David Taylor, Sally G. Grimshaw, Svetlana Riazanskaia, David S. Arnold, Sara Johansson Fernstad, Adrian M. Smith, Liam M. Heaney, James C. Reynolds, C. L. Paul Thomas, Mark Harker
2014 FEMS Microbiology Ecology  
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

Jessica L. Mark Welch, Yuko Hasegawa, Nathan P. McNulty, Jeffrey I. Gordon, Gary G. Borisy
2017 Proceedings of the National Academy of Sciences of the United States of America  
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

A P Baptista, B J Olivier, G Goverse, M Greuter, M Knippenberg, K Kusser, R G Domingues, H Veiga-Fernandes, A D Luster, A Lugering, T D Randall, T Cupedo (+1 others)
2012 Mucosal Immunology  
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

S. Gon, Kushi-Nidhi Kumar, Klaus Nüsslein, Maria M. Santore
2012 Macromolecules  
"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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