A Distributed Multilevel Force-directed Algorithm

The wide availability of powerful and inexpensive cloud computing services naturally motivates the study of distributed graph layout algorithms, able to scale to very large graphs. Nowadays, to process Big Data, companies are increasingly relying on PaaS infrastructures rather than buying and maintaining complex and expensive hardware. So far, only a few examples of basic force-directed algorithms that work in a distributed environment have been described. Instead, the design of a distributed multilevel force-directed algorithm is a much more challenging task, not yet addressed. We present the first multilevel force-directed algorithm based on a distributed vertex-centric paradigm, and its implementation on Giraph, a popular platform for distributed graph algorithms. Experiments show the effectiveness and the scalability of the approach. Using an inexpensive cloud computing service of Amazon, we draw graphs with ten million edges in about 60 minutes.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Hydrogenated fat intake during pregnancy and lactation caused increase in TRAF-6 and reduced AdipoR1 in white adipose tissue, but not in muscle of 21 days old offspring rats

<p>Abstract</p> <p>Background</p> <p>Although lipids transfer through placenta is very limited, modification in dietary fatty acids can lead to implications in fetal and postnatal development. <it>Trans </it>fatty acid (TFA) intake during gestation and lactation have been reported to promote dyslipidemia and increase in pro- inflammatory adipokines in offspring. The aim of this study was to evaluate whether the alterations on pro-inflammatory cytokines and dyslipidemia observed previously in 21-d-old offspring of rats fed a diet containing hydrogenated vegetable fat during gestation and lactation were related to alterations in TLR-4, TRAF-6 and adipo-R1 receptor in white adipose tissue and muscle. On the first day of gestation, rats were randomly divided into two groups: (C) received a control diet, and (T) received a diet enriched with hydrogenated vegetable fat, rich in <it>trans </it>fatty acids. The diets were maintained throughout gestation and lactation. Each mother was given eight male pups. On the 21st day of life the offspring were killed. Blood, soleus and extensor digital longus (EDL) muscles, and retroperitoneal (RET) white adipose tissue were collected.</p> <p>Results</p> <p>21-d-old of T rats had higher serum triacylglycerols, cholesterol, and insulin. The Adipo R1 protein expression was lower in RET and higher in EDL of T group than C. TLR-4 protein content in all studied tissues were similar between groups, the same was verified in TRAF-6 protein expression in soleus and EDL. However, TRAF-6 protein expression in RET was higher in T than C.</p> <p>Conclusion</p> <p>These results demonstrated that maternal ingestion of hydrogenated vegetable fat rich in TFAs during gestation and lactation decrease in Adipo R1 protein expression and increase in TRAF-6 protein expression in retroperitoneal adipose tissue, but not in skeletal muscle, which could contributed for hyperinsulinemia and dyslipidemia observed in their 21-d-old offspring.</p

A Sparse Stress Model

Force-directed layout methods constitute the most common approach to draw general graphs. Among them, stress minimization produces layouts of comparatively high quality but also imposes comparatively high computational demands. We propose a speed-up method based on the aggregation of terms in the objective function. It is akin to aggregate repulsion from far-away nodes during spring embedding but transfers the idea from the layout space into a preprocessing phase. An initial experimental study informs a method to select representatives, and subsequent more extensive experiments indicate that our method yields better approximations of minimum-stress layouts in less time than related methods.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Modularity clustering is force-directed layout

Two natural and widely used representations for the community structure of networks are clusterings, which partition the vertex set into disjoint subsets, and layouts, which assign the vertices to positions in a metric space. This paper unifies prominent characterizations of layout quality and clustering quality, by showing that energy models of pairwise attraction and repulsion subsume Newman and Girvan's modularity measure. Layouts with optimal energy are relaxations of, and are thus consistent with, clusterings with optimal modularity, which is of practical relevance because both representations are complementary and often used together.Comment: 9 pages, 7 figures, see http://code.google.com/p/linloglayout/ for downloading the graph clustering and layout softwar

Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps

Background For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. Results We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor) algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. Conclusions Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html

The relationship between mood and sleep in different female reproductive states

Peer reviewe

TULIP 5

International audienceTulip is an information visualization framework dedicated to the analysis and visualization of relational data. Based on more than 16 years of research and development, Tulip is built on a suite of tools and techniques, that can be used to address a large variety of domain-specific problems. With \tulip, we aim to provide Python and/or C++ developers a complete library, supporting the design of interactive information visualization applications for relational data, that can be customized to address a wide range of visualization problems. In its current iteration, \tulip enables the development of algorithms, visual encodings, interaction techniques, data models, and domain-specific visualizations. This development pipeline makes the framework efficient for creating research prototypes as well as developing end-user applications. The recent addition of a complete Python programming layer wraps up Tulip as an ideal tool for fast prototyping and treatment automation, allowing to focus on problem solving, and as a great system for teaching purposes at all education levels