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CollaborationViz: Interactive Visual Exploration of Biomedical Research Collaboration Networks
2014
PLoS ONE
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We applied our visualization techniques to explore the biomedical RCNs at the University of Arkansas for Medical Sciences -a CTSA institution. ...
The basis of our design is multidimensional, visual aggregation of network dynamics. ...
The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
Author Contributions ...
doi:10.1371/journal.pone.0111928
pmid:25405477
pmcid:PMC4236011
fatcat:kxjogcqw7fgitisbegfkmmxbni
Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network
2015
Journal of Biomedical Informatics
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In this paper, we introduce Diff Abstraction Networks ("Diff AbNs"), compact networks that summarize and visualize global structural changes due to ontology editing operations that result in a new ontology ...
When editing a biomedical ontology, small local updates may affect large portions of the ontology, leading to unintended and potentially erroneous changes. ...
The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. ...
doi:10.1016/j.jbi.2015.05.018
pmid:26048076
pmcid:PMC4532611
fatcat:v6ewyvfolndojldseseyg3aluq
A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies
2016
Journal of Biomedical Informatics
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Abstraction networks summarize the structure and content of ontologies. ...
Software tools play a critical role in the development and maintenance of biomedical ontologies. One important task that is difficult without software tools is ontology quality assurance. ...
The content is solely the responsibility of the authors and does not necessarily represent the views of the National Institutes of Health. ...
doi:10.1016/j.jbi.2016.06.008
pmid:27345947
pmcid:PMC4987206
fatcat:aetz22yux5aftoxywhu4x44gzi
Parcellation of visual cortex on high-resolution histological brain sections using convolutional neural networks
2017
2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017)
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2017 pre-print arXiv:1705.10545v1 fatcat:sakx7pbznrcipisxnjnvwyjo44
Its high resolution allows the study of laminar and columnar patterns of cell distributions, which build an important basis for the simulation of cortical areas and networks. ...
The model is applied to visual areas and trained on a sparse set of partial annotations. We show how predictions are transferable to new brains and spatially consistent across sections. ...
Fig. 1 shows details of our network architecture. ...
doi:10.1109/isbi.2017.7950666
dblp:conf/isbi/SpitzerAHD17
fatcat:itnsozjhtvb5pf3wuxzktullqa
Liquid Metal Angiography for Mega Contrast X-Ray Visualization of Vascular Network in Reconstructing In-Vitro Organ Anatomy
2014
IEEE Transactions on Biomedical Engineering
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2013 pre-print arXiv:1311.6717v1 fatcat:bk4aspiydvdc3jneb3ol6truru
Visualizing the anatomical vessel networks plays a vital role in physiological or pathological investigations. ...
It was disclosed that the usually invisible capillary networks now become distinctively clear in the gallium angiograms. ...
Overall, the liquid metal angiography has demonstrated significant values in the
field of vascular network visualization. ...
doi:10.1109/tbme.2014.2317554
pmid:24759980
fatcat:f223n6g6ajevffggl5akd3z2v4
HPIminer: A text mining system for building and visualizing human protein interaction networks and pathways
2015
Journal of Biomedical Informatics
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Because much of that information is buried in biomedical literature, an automated text mining system for visualizing human PPI and pathways is highly desirable. ...
HPIminer extracts human PPI information and PPI pairs from biomedical literature, and visualize their associated interactions, networks and pathways using two curated databases HPRD and KEGG. ...
Acknowledgments The research has received funding from the Department of Biotechnology (DBT), Government of India, Grant No. BT/ PR15378/BID/07/361/2011. ...
doi:10.1016/j.jbi.2015.01.006
pmid:25659452
fatcat:crlnnsuoqzhwnfwxrfwikvbsba
Unsupervised Learning For Cell-level Visual Representation with Generative Adversarial Networks
2018
IEEE journal of biomedical and health informatics
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2018 pre-print arXiv:1711.11317v3 fatcat:hfmtkwmy5faq3ac2e6tl7qtecmOther Versions
In this paper, we propose a unified generative adversarial networks architecture with a new formulation of loss to perform robust cell-level visual representation learning in an unsupervised setting. ...
The visual attributes of cells, such as the nuclear morphology and chromatin openness, are critical for histopathology image analysis. ...
The authors would like to thank the First Affiliated Hospital of Zhejiang University for providing data and help. ...
doi:10.1109/jbhi.2018.2852639
pmid:29994411
fatcat:ba6uehoubvf6jkaqqzo4lrtf34
Review of speckle and phase variance optical coherence tomography to visualize microvascular networks
2013
Journal of Biomedical Optics
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In addition, we highlight ongoing work in the development of variance-based techniques to further refine the characterization of microvascular networks. © The Authors. ...
Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI. ...
Acknowledgments The authors thank the Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Council, and Ryerson Bio-photonics and Bioengineering Laboratory for funding contributions ...
doi:10.1117/1.jbo.18.5.050901
pmid:23616094
fatcat:3cjcsnbdnnbczo26ocxpx62p3q
A cognitive task analysis of a visual analytic workflow: Exploring molecular interaction networks in systems biology
2011
Journal of Biomedical Discovery and Collaboration
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We created representations at levels of detail Journal of Biomedical Discovery and Collaboration 2011: 6, 1-33; doi:10.5210/disco.v6i0.3410 2 that could strategically guide visualization development, and ...
Bioinformatics visualization tools are often not robust enough to support biomedical specialists' complex exploratory analyses. ...
We are grateful to Terry Weymouth for developing the visualization prototype from the findings of our cognitive task analysis. ...
doi:10.5210/disco.v6i0.3410
pmid:21455901
pmcid:PMC3090070
fatcat:mn72wsk52fb7pmm57rgkbchfhi
Measurement of Eye Movement in Visual Search for a Target Symbol and Simulation to Construct a Small-World Network
2017
Advanced Biomedical Engineering
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The constructed network has the features of a small-world network. ...
We suggest, therefore, that there is a physiological mechanism in visual search, which reduces the size of the physically wide search area. ...
Disclosing Con ict of Interest We have no con ict of interest with any company or commercial organization. ...
doi:10.14326/abe.6.129
fatcat:qz3hcffbhfbbridtpvpegde3s4
Network-based Trajectory Analysis of Topic Interaction Map for Text Mining of COVID-19 Biomedical Literature
[article]
2021
arXiv
pre-print
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Based on this assumption, after summarizing topics with their topic-word distributions using the biterm topic model, we mapped these latent topics on networks to visualize relationships among the topics ...
In order to address these challenges, we propose a novel analytical framework for estimating topic interactions and effective visualization for topic interpretation. ...
However, in this approach, the network information needs to be given to construct and visualize the topic network, which is not a trivial task in practice. ...
arXiv:2106.07374v3
fatcat:oj7myhp7w5ewxmrqmokhooqqb4
Three-dimensional optical method for integrated visualization of mouse islet microstructure and vascular network with subcellular-level resolution
2010
Journal of Biomedical Optics
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Microscopic visualization of islets of Langerhans under normal and diabetic conditions is essential for understanding the pathophysiology of the disease. ...
Because the standard microtome-based, 2-D tissue analysis confines visualization of the islet architecture at a specific cut plane, 3-D representation of image data is preferable for islet assessment. ...
This approach led to a clear visualization of the vascular network, including the capillaries in the islet. Fig. 4͑e͒ , large blood vessels can be seen using transmitted light imaging. ...
doi:10.1117/1.3470241
pmid:20799820
pmcid:PMC3188637
fatcat:qf3q4erkjnfvtcpubmluezjbvu
Cell-free layer measurements of in vitro blood flow in a microfluidic network: an automatic and manual approach
2017
Computer Methods in Biomechanics and Biomedical Engineering Imaging & Visualization
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It was also clear that, for the full length of the network, the CFL thickness tends to decrease with the increase of the concentration of cells. ...
Overall, the results have shown that the concentration of cells and the geometrical configuration of the network have a major impact on the CFL thickness. ...
models of blood flowing through microvascular networks. ...
doi:10.1080/21681163.2017.1329029
fatcat:othcbj7oirckjiapjbpz3x557i
Holistic classification of CT attenuation patterns for interstitial lung diseases via deep convolutional neural networks
2016
Computer Methods in Biomechanics and Biomedical Engineering Imaging & Visualization
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Accurate classification of these patterns plays a significant role in precise clinical decision making of the extent and nature of the diseases. ...
Conventionally, this task relies on experts' manual identification of regions of interest (ROIs) as a prerequisite to diagnose potential diseases. ...
CNN Architecture The architecture of our CNN is similar to the convolutional neural network proposed by Krizhevsky, et al. [7] . ...
doi:10.1080/21681163.2015.1124249
pmid:29623248
pmcid:PMC5881940
fatcat:fmqhxhd2unb73cqwne3wqgedai
UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization
2020
PLoS ONE
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Based on the similarity calculation, UFO can calculate the similarity between two sets of entities and weigh imported entity networks as well as generate functional similarity networks. ...
Note that the methods can be applied to all types of biomedical ontologies. ...
Furthermore, by exploiting visualization functions of Cytoscape, UFO can visualize the relationships between ontology terms and annotated biomedical entities. ...
doi:10.1371/journal.pone.0235670
pmid:32645039
fatcat:mlusphcmovc4ddnkdvkjm3byye
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