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CollaborationViz: Interactive Visual Exploration of Biomedical Research Collaboration Networks

Jiang Bian, Mengjun Xie, Teresa J. Hudson, Hari Eswaran, Mathias Brochhausen, Josh Hanna, William R. Hogan, Zhong-Ke Gao
2014 PLoS ONE  
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

Christopher Ochs, Yehoshua Perl, James Geller, Melissa Haendel, Matthew Brush, Sivaram Arabandi, Samson Tu
2015 Journal of Biomedical Informatics  
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

Christopher Ochs, James Geller, Yehoshua Perl, Mark A. Musen
2016 Journal of Biomedical Informatics  
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

Hannah Spitzer, Katrin Amunts, Stefan Harmeling, Timo Dickscheid
2017 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017)  
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

Qian Wang, Yang Yu, Keqin Pan, Jing Liu
2014 IEEE Transactions on Biomedical Engineering  
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

Suresh Subramani, Raja Kalpana, Pankaj Moses Monickaraj, Jeyakumar Natarajan
2015 Journal of Biomedical Informatics  
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

Bo Hu, Ye Tang, Eric I-Chao Chang, Yubo Fan, Maode Lai, Yan Xu
2018 IEEE journal of biomedical and health informatics  
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

Mohammad Sultan Mahmud, David W. Cadotte, Barry Vuong, Carry Sun, Timothy W. H. Luk, Adrian Mariampillai, Victor X. D. Yang
2013 Journal of Biomedical Optics  
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

Barbara Mirel, Felix Eichinger, Benjamin Keller, Matthias Kretzler
2011 Journal of Biomedical Discovery and Collaboration  
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

Ryunosuke Kodera, Shigehito Tanahashi, Atsuhiko Iijima, Yoshinobu Maeda
2017 Advanced Biomedical Engineering  
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]

Yeseul Jeon and Dongjun Chung and Jina Park and Ick Hoon Jin
2021 arXiv   pre-print
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

Ya-Yuan Fu, Chih-Hsuan Lu, Chi-Wen Lin, Jyuhn-Huarng Juang, Grigori Enikolopov, Eric Sibley, Ann-Shyn Chiang, Shiue-Cheng Tang
2010 Journal of Biomedical Optics  
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

D. Bento, A. I. Pereira, J. Lima, J. M. Miranda, R. Lima
2017 Computer Methods in Biomechanics and Biomedical Engineering Imaging & Visualization  
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

Mingchen Gao, Ulas Bagci, Le Lu, Aaron Wu, Mario Buty, Hoo-Chang Shin, Holger Roth, Georgios Z. Papadakis, Adrien Depeursinge, Ronald M. Summers, Ziyue Xu, Daniel J. Mollura
2016 Computer Methods in Biomechanics and Biomedical Engineering Imaging & Visualization  
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

Duc-Hau Le, Alper Uzun
2020 PLoS ONE  
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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