In this paper, we describe a taxonomy of generic graph related tasks and an evaluation aiming at assessing the readability of two representations of graphs: matrix-based representations and nodelink diagrams. This evaluation bears on seven generic tasks and leads to important recommendations with regard to the representation of graphs according to their size and density. For instance, we show that when graphs are bigger than twenty vertices, the matrix-based visualization performs better than node-link diagrams on most tasks. Only path finding is consistently in favor of nodelink diagrams throughout the evaluation.

In this article, we describe a taxonomy of generic graph related tasks along with a computer-based evaluation designed to assess the readability of two representations of graphs: matrix-based representations and node-link diagrams. This evaluation encompasses seven generic tasks and leads to insightful recommendations for the representation of graphs according to their size and density. Typically, we show that when graphs are bigger than twenty vertices, the matrix-based visualization outperforms node-link diagrams on most tasks. Only path finding is consistently in favor of node-link diagrams throughout the evaluation. Information Visualization (2005) 4, 114-135.

Large financial institutions such as Bank of America handle hundreds of thousands of wire transactions per day. Although most transactions are legitimate, these institutions have legal and financial obligations in discovering those that are suspicious. With the methods of fraudulent activities ever changing, searching on predefined patterns is often insufficient in detecting previously undiscovered methods. In this paper, we present a set of coordinated visualizations based on identifying specific keywords within the wire transactions. The different views used in our system depict relationships among keywords and accounts over time. Furthermore, we introduce a search-by-example technique which extracts accounts that show similar transaction patterns. In collaboration with the Anti-Money Laundering division at Bank of America, we demonstrate that using our tool, investigators are able to detect accounts and transactions that exhibit suspicious behaviors.

Bast fibres are long extraxylary cells which mechanically support the phloem and they are divided into xylan- and gelatinous-type, depending on the composition of their secondary cell walls. The former, typical of jute/kenaf bast fibres, are characterized by the presence of xylan and a high degree of lignification, while the latter, found in tension wood, as well as flax, ramie and hemp bast fibres, have a high abundance of crystalline cellulose. During their differentiation, bast fibres undergo specific developmental stages: the cells initially elongate rapidly by intrusive growth, subsequently they cease elongation and start to thicken. The goal of the present study is to provide a transcriptomic close-up of the key events accompanying bast fibre development in textile hemp (Cannabis sativa L.), a fibre crop of great importance. Bast fibres have been sampled from different stem regions. The developmental stages corresponding to active elongation and cell wall thickening have been studied using RNA-Seq. The results show that the fibres sampled at each stem region are characterized by a specific transcriptomic signature and that the major changes in cell wall-related processes take place at the internode containing the snap point. The data generated also identify several interesting candidates for future functional analysis.

Modelling relationship between entities in real‐world systems with a simple graph is a standard approach. However, reality is better embraced as several interdependent subsystems (or layers). Recently, the concept of a multilayer network model has emerged from the field of complex systems. This model can be applied to a wide range of real‐world data sets. Examples of multilayer networks can be found in the domains of life sciences, sociology, digital humanities and more. Within the domain of graph visualization, there are many systems which visualize data sets having many characteristics of multilayer graphs. This report provides a state of the art and a structured analysis of contemporary multilayer network visualization, not only for researchers in visualization, but also for those who aim to visualize multilayer networks in the domain of complex systems, as well as those developing systems across application domains. We have explored the visualization literature to survey visualization techniques suitable for multilayer graph visualization, as well as tools, tasks and analytic techniques from within application domains. This report also identifies the outstanding challenges for multilayer graph visualization and suggests future research directions for addressing them.

Large financial institutions such as Bank of America handle hundreds of thousands of wire transactions per day. Although most transactions are legitimate, these institutions have legal and financial obligations to discover those that are suspicious. With the methods of fraudulent activities ever changing, searching on predefined patterns is often insufficient in detecting previously undiscovered methods. In this paper, we present a set of coordinated visualizations based on identifying specific keywords within the wire transactions. The different views used in our system depict relationships among keywords and accounts over time. Furthermore, we introduce a search-by-example technique, which extracts accounts that show similar transaction patterns. Our system can be connected to a database to handle millions of transactions and still preserve high interactivity. In collaboration with the Anti-Money Laundering division at Bank of America, we demonstrate that using our tool, investigators are able to detect accounts and transactions that exhibit suspicious behaviors.

BackgroundRecent advances in high-throughput sequencing allow for much deeper exploitation of natural and engineered microbial communities, and to unravel so-called “microbial dark matter” (microbes that until now have evaded cultivation). Metagenomic analyses result in a large number of genomic fragments (contigs) that need to be grouped (binned) in order to reconstruct draft microbial genomes. While several contig binning algorithms have been developed in the past 2 years, they often lack consensus. Furthermore, these software tools typically lack a provision for the visualization of data and bin characteristics.ResultsWe present ICoVeR, the Interactive Contig-bin Verification and Refinement tool, which allows the visualization of genome bins. More specifically, ICoVeR allows curation of bin assignments based on multiple binning algorithms. Its visualization window is composed of two connected and interactive main views, including a parallel coordinates view and a dimensionality reduction plot. To demonstrate ICoVeR’s utility, we used it to refine disparate genome bins automatically generated using MetaBAT, CONCOCT and MyCC for an anaerobic digestion metagenomic (AD microbiome) dataset. Out of 31 refined genome bins, 23 were characterized with higher completeness and lower contamination in comparison to their respective, automatically generated, genome bins. Additionally, to benchmark ICoVeR against a previously validated dataset, we used Sharon’s dataset representing an infant gut metagenome.ConclusionsICoVeR is an open source software package that allows curation of disparate genome bins generated with automatic binning algorithms. It is freely available under the GPLv3 license at https://git.list.lu/eScience/ICoVeR. The data management and analytical functions of ICoVeR are implemented in R, therefore the software can be easily installed on any system for which R is available. Installation and usage guide together with the example files ready to be visualized are also provided via the project wiki. ICoVeR running instance preloaded with AD microbiome and Sharon’s datasets can be accessed via the website.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-017-1653-5) contains supplementary material, which is available to authorized users.

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