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A Five-Level Design Framework for Bicluster Visualizations

Maoyuan Sun, Chris North, Naren Ramakrishnan
2014 IEEE Transactions on Visualization and Computer Graphics  
However, due to the lack of systematic design guidelines, it is still a challenge to design effective and usable visualizations of biclusters to enhance their perceptibility and interactivity for exploring  ...  Finally, we discuss future research challenges for bicluster visualizations and their incorporation into visual analytics tools.  ...  For example, Jigsaw [35] supports exploratory text analysis, and its List View provides a solution for exploring simple 1:1 relationships from textual datasets based on term co-occurrence.  ... 
doi:10.1109/tvcg.2014.2346665 pmid:26356885 fatcat:hxp73gpigraaphc26pbtmbgj6u

The human is the loop: new directions for visual analytics

Alex Endert, M. Shahriar Hossain, Naren Ramakrishnan, Chris North, Patrick Fiaux, Christopher Andrews
2014 Journal of Intelligent Information Systems  
Visual analytics is the science of marrying interactive visualizations and analytic algorithms to support exploratory knowledge discovery in large datasets.  ...  We survey a range of projects that provide visual analytic support contextually in the sensemaking loop, and outline a research agenda along with future challenges. A. Endert Pacific  ...  Acknowledgements This work is supported in part by the Institute for Critical Technology and Applied Science, Virginia Tech, and the US National Science Foundation through grant CCF-0937133.  ... 
doi:10.1007/s10844-014-0304-9 fatcat:mnq2g4zq6ve77cmuyq42mgb7zm

Network Analysis Reveals Sex- and Antibiotic Resistance-Associated Antivirulence Targets in Clinical Uropathogens

Kaveri S. Parker, James D. Wilson, Jonas Marschall, Peter J. Mucha, Jeffrey P. Henderson
2015 ACS Infectious Diseases  
To identify clinically relevant VF combinations, we applied contemporary network analysis and biclustering algorithms to VF profiles from a large, previously characterized inpatient clinical cohort.  ...  These mathematical approaches identified four stereotypical VF combinations with distinctive relationships to antibiotic resistance and patient sex that are independent of traditional phylogenetic grouping  ...  Foxman and L. Zhang (University of Michigan, Ann Arbor, MI, USA) for dot-blot hybridization analysis. We also thank C. A. Burnham, E.  ... 
doi:10.1021/acsinfecdis.5b00022 pmid:26985454 pmcid:PMC4788272 fatcat:3i5ggtqurjcffbffgalgkn7ngu

SightBi: Exploring Cross-View Data Relationships with Biclusters [article]

Maoyuan Sun, Abdul Rahman Shaikh, Hamed Alhoori, Jian Zhao
2021 IEEE Transactions on Visualization and Computer Graphics   accepted
Multiple-view visualization (MV) has been heavily used in visual analysis tools for sensemaking of data in various domains (e.g., bioinformatics, cybersecurity and text analytics).  ...  One common task of visual analysis with multiple views is to relate data across different views.  ...  ACKNOWLEDGMENTS This research is supported in part by NSF Grants IIS-2002082, SMA-2022443, the NSERC Discovery Grant, and the Research and Artistry Opportunity Grant from Northern Illinois University.  ... 
doi:10.1109/tvcg.2021.3114801 pmid:34591764 arXiv:2108.01044v2 fatcat:ikqheliqbjhobkvwgsmxplvene

The Gibbs-plaid biclustering model

Thierry Chekouo, Alejandro Murua, Wolfgang Raffelsberger
2015 Annals of Applied Statistics  
We propose and develop a Bayesian plaid model for biclustering that accounts for the prior dependency between genes (and/or conditions) through a stochastic relational graph.  ...  This work is motivated by the need for improved understanding of the molecular mechanisms of human diseases for which effective drugs are lacking, and based on the extensive raw data available through  ...  A proof of the convergence of the stochastic algorithm of Section 3 and further details on Lin's similarity (Section 2.2) are also included.  ... 
doi:10.1214/15-aoas854 fatcat:fc36nydctfhe5c7qefkpi7rvna

On Integrating Information Visualization Techniques into Data Mining: A Review [article]

Keqian Li
2015 arXiv   pre-print
More specifically, we study the intersection from a data mining point of view, explore how information visualization can be used to complement and improve different stages of data mining through established  ...  We organize the survey by identifying three main stages of typical process of data mining, the preliminary analysis of data, the model construction, as well as the model evaluation, and study how each  ...  The BETA system [83] used entity In the field of literature analysis it is commonplace to analyze a text or a collection of texts by extracting concordance: an alphabetical index of all the words in  ... 
arXiv:1503.00202v1 fatcat:ucl72q5hwnccxdqeuksly4uu3q

2014 Index IEEE Transactions on Visualization and Computer Graphics Vol. 20

2015 IEEE Transactions on Visualization and Computer Graphics  
., +, TVCG Dec. 2014 1943-1952 Text analysis Exploring the Placement and Design of Word-Scale Visualizations.  ...  Debernardis, Saverio, +, TVCG Jan. 2014 125-139 The Effects of Interactive Latency on Exploratory Visual Analysis.  ... 
doi:10.1109/tvcg.2014.2368193 fatcat:nm3sijdvbza5nmxyina4rqinnu

Methods and Trends in Information Retrieval in Big Data Genomic Research

This paper described information retrieval (IR) and the common methods of finding, extracting, and mining information in genomic research through text mining, and natural language processing (NLP).  ...  There was a surge of genomic information from the different literature and the production of genome datasets that catapulted the development of several tools for analyzing and presenting new found knowledge  ...  The paper also described the importance components of cancer gene discovery through the cancer genome analysis and unbiased genetic screening.  ... 
doi:10.35940/ijitee.i1109.0789s219 fatcat:j2uramagd5a75jusrcor75w7ue

2018 Index IEEE Transactions on Visualization and Computer Graphics Vol. 24

2019 IEEE Transactions on Visualization and Computer Graphics  
June 2018 2023-2036 Summarization and Stage Analysis of Event Sequence Data; TVCG Jan. 2018 56-65 Guo, Y., see Liu, L., TVCG June 2018 1956-1968  ...  ., and Dai, Q., Errata to "Robust Non-Rigid Motion Tracking and Surface Reconstruction Using L 0 Regularization"; TVCG July 2018 2268 Guo, K., Xu, F., Wang, Y., Liu, Y., and Dai, Q., Robust Non-Rigid  ...  ., þ, TVCG Jan. 2018 457-467 The Interactive Visualization Gap in Initial Exploratory Data Analysis.  ... 
doi:10.1109/tvcg.2018.2885445 fatcat:xtccdnalwfhudp3qdxofz4kqpi

New challenges in gene expression data analysis and the extended GEPAS

J. Herrero, J. M. Vaquerizas, F. Al-Shahrour, L. Conde, A. Mateos, J. S. R. Diaz-Uriarte, J. Dopazo
2004 Nucleic Acids Research  
Since the first papers published in the late nineties, including, for the first time, a comprehensive analysis of microarray data, the number of questions that have been addressed through this technique  ...  In addition to this, the availability of accurate genomic data and the recent implementation of CGH arrays has made mapping expression and genomic data on the chromosomes possible.  ...  ACKNOWLEDGEMENTS Our special thanks to Amanda Wren for revising the English of the manuscript.  ... 
doi:10.1093/nar/gkh421 pmid:15215434 pmcid:PMC441559 fatcat:2qtkxfhrgfdcrf2jz3o43xvuq4

Seriation and matrix reordering methods: An historical overview

Innar Liiv
2010 Statistical analysis and data mining  
Seriation is an exploratory combinatorial data analysis technique to reorder objects into a sequence along a one-dimensional continuum so that it best reveals regularity and patterning among the whole  ...  ; cartography, graphics, and information visualization; sociology and sociometry; psychology and psychometry; ecology; biology and bioinformatics; cellular manufacturing; and operations research.  ...  analysis and proposed a node-deletion algorithm to search for biclusters.  ... 
doi:10.1002/sam.10071 fatcat:6rzbdp6gvvg6rpm4b2mwxvfdbu

Big-Data-Augmented Approach to Emerging Technologies Identification: Case of Agriculture and Food Sector

Leonid Gokhberg, Ilya F. Kuzminov, Pavel Bakhtin, Elena Tochilina, Alexander Chulok, Anton Timofeev, Alina Lavrynenko
2017 Social Science Research Network  
The paper discloses a new approach to emerging technologies identification, which strongly relies on capacity of big data analysis, namely text mining augmented by syntactic analysis techniques.  ...  It discusses the wide context of the task of identifying emerging technologies in a systemic and timely manner, including its place in the methodology of foresight and future-oriented technology analysis  ...  So, this is not the issue of text mining, but of future oriented technology analysis in general.  ... 
doi:10.2139/ssrn.3078499 fatcat:o6ver5pxordcnmyoehokv5vuqa

Clustering of high throughput gene expression data

Harun Pirim, Burak Ekşioğlu, Andy D. Perkins, Çetin Yüceer
2012 Computers & Operations Research  
Clustering is one of the methods used to gain insight into biological processes, particularly at the genomics level. Clearly, clustering can be used in many areas of biological data analysis.  ...  High throughput biological data need to be processed, analyzed, and interpreted to address problems in life sciences.  ...  There are visualization and exploratory tools for gene clusters to be interpreted more easily.  ... 
doi:10.1016/j.cor.2012.03.008 pmid:23144527 pmcid:PMC3491664 fatcat:zfc3l22vmvfvlphpqmoox5ka54

ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization

Enrico Glaab, Jonathan M Garibaldi, Natalio Krasnogor
2009 BMC Bioinformatics  
By interlinking different analysis tools in a modular fashion, new exploratory routes become available, e.g. ensemble sample classification using features obtained from a gene set analysis and data from  ...  To take advantage of the multitude of available data sets and analysis methods, it is desirable to combine both different algorithms and data from different studies.  ...  Biotechnology and Biological Sciences Research Council (BB/F01855X/1).  ... 
doi:10.1186/1471-2105-10-358 pmid:19863798 pmcid:PMC2776026 fatcat:gv7le26ylzb6rft2bqgg2z2i4m

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

Georgios A. Pavlopoulos, Dimitris Malliarakis, Nikolas Papanikolaou, Theodosis Theodosiou, Anton J. Enright, Ioannis Iliopoulos
2015 GigaScience  
Here we discuss the past, present and future of genomic and systems biology visualization. We briefly comment on many visualization and analysis tools and the purposes that they serve.  ...  This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of information.  ...  D3's functional style allows code reuse through a diverse collection of components and plugins. It is extensively documented and code examples can be found at [135] .  ... 
doi:10.1186/s13742-015-0077-2 pmid:26309733 pmcid:PMC4548842 fatcat:w7hxgunagfcbxctnio7kwnucsy
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