GiViP: A Visual Profiler for Distributed Graph Processing Systems

Analyzing large-scale graphs provides valuable insights in different application scenarios. While many graph processing systems working on top of distributed infrastructures have been proposed to deal with big graphs, the tasks of profiling and debugging their massive computations remain time consuming and error-prone. This paper presents GiViP, a visual profiler for distributed graph processing systems based on a Pregel-like computation model. GiViP captures the huge amount of messages exchanged throughout a computation and provides an interactive user interface for the visual analysis of the collected data. We show how to take advantage of GiViP to detect anomalies related to the computation and to the infrastructure, such as slow computing units and anomalous message patterns.Comment: Appears in the Proceedings of the 25th International Symposium on Graph Drawing and Network Visualization (GD 2017

Pesan Moral Islami Dalam Film Le Grand Voyage Karya Ismael Ferroukhi: Sebuah Tinjauan Struktural

Kata kunci : Film, sastra, struktural, pesan moral, Islam.Film merupakan produk budaya yang tidak hanya menjadi hiburan di masyarakat, tetapi juga sebagai sarana penyampaian pesan moral yang mengarifkan. Salah satufilm Perancis yang dianggap menginspirasi adalah film berjudul Le grand voyageyang ditulis dan disutradarai oleh Ismaël Ferroukhi. Film ini bercerita tentang perjalanan seorang muslim keturunan Maroko dan anaknya yang bernama Reda.Mereka menempuh jarak ribuan mil dari Perancis menuju ke kota Makah untukmelaksanakan haji hanya dengan mengendarai sebuah mobil tua. Penelitian inibertujuan untuk mengetahui pesan moral islami apa saja yang terkandung dalamfilm Le grand voyage dan bagaimana pesan tersebut dimunculkan dalam film.Penelitian ini menggunakan teori Struktural untuk menjawab rumusan masalah.Penelitian ini merupakan penelitian kualitatif dengan menggunakan teknik studipustaka serta dokumentasi sebagai metode pengumpulan data, dan teknikdeskriptif dalam proses analisis data.Berdasarkan hasil penelitian ini, terdapat 13 pesan moral islami yang terkandungdalam film Le grand voyage. Semua pesan moral tersebut mengacu pada sebuahproses perbaikan moral dan spiritual antara manusia dengan manusia dan alam,serta antara manusia dengan TuhanPenulis menyarankan pada penelitian selanjutnya untuk meneliti film Le grandvoyage menggunakan pendekatan sosiologi sastra yang nantinya dapat mengupashal apa saja yang melatarbelakangi pembuatan film ini dan tujuan sebenarnyayang ingin dicapai oleh pembuat film Le grand voyage

A unified data representation theory for network visualization, ordering and coarse-graining

Representation of large data sets became a key question of many scientific disciplines in the last decade. Several approaches for network visualization, data ordering and coarse-graining accomplished this goal. However, there was no underlying theoretical framework linking these problems. Here we show an elegant, information theoretic data representation approach as a unified solution of network visualization, data ordering and coarse-graining. The optimal representation is the hardest to distinguish from the original data matrix, measured by the relative entropy. The representation of network nodes as probability distributions provides an efficient visualization method and, in one dimension, an ordering of network nodes and edges. Coarse-grained representations of the input network enable both efficient data compression and hierarchical visualization to achieve high quality representations of larger data sets. Our unified data representation theory will help the analysis of extensive data sets, by revealing the large-scale structure of complex networks in a comprehensible form.Comment: 13 pages, 5 figure

Impact of amendments on the physical properties of soil under tropical long-term no till conditions

Tropical regions have been considered the world's primary agricultural frontier; however, some physico-chemical deficiencies, such as low soil organic matter content, poor soil structure, high erodibility, soil acidity, and aluminum toxicity, have affected their productive capacity. Lime and gypsum are commonly used to improve soil chemical fertility, but no information exists about the long-term effects of these products on the physical attributes and C protection mechanisms of highly weathered Oxisols. A field trial was conducted in a sandy clay loam (kaolinitic, thermic Typic Haplorthox) under a no-tillage system for 12 years. The trial consisted of four treatments: a control with no soil amendment application, the application of 2.1 Mg ha-1 phosphogypsum, the application of 2.0 Mg ha-1 lime, and the application of lime + phosphogypsum (2.0 + 2.1 Mg ha-1, respectively). Since the experiment was established in 2002, the rates have been applied three times (2002, 2004, and 2010). Surface liming effectively increased water-stable aggregates > 2.0 mm at a depth of up to 0.2 m; however, the association with phosphogypsum was considered a good strategy to improve the macroaggregate stability in subsoil layers (0.20 to 0.40 m). Consequently, both soil amendments applied together increased the mean weight diameter (MWD) and geometric mean diameter (GMD) in all soil layers, with increases of up to 118 and 89%, respectively, according to the soil layer. The formation and stabilization of larger aggregates contributed to a higher accumulation of total organic carbon (TOC) on these structures. In addition to TOC, the MWD and aggregate stability index were positively correlated with Ca2+ and Mg2+ levels and base saturation. Consequently, the increase observed in the aggregate size class resulted in a better organization of soil particles, increasing the macroporosity and reducing the soil bulk density and penetration resistance. Therefore, adequate soil chemical management plays a fundamental role in improving the soil's physical attributes in tropical areas under conservative management and highly affected by compaction caused by intensive farming

Does the world need a scientific society for research on how to improve healthcare?

In this editorial, we reflect on the arguments for starting a scientific society focused on research on how to improve healthcare. This society would take an inclusive approach to what constitutes healthcare. For instance, it should include mental health healthcare, treatment for substance abuse, the work of allied health professions, and preventive healthcare. The society would be open to researchers from all traditions. Thus, we take an inclusive approach to what constitutes scientific research, as long as it uses rigorous methods, is focused on improving healthcare, and aims at knowledge that can be transferred across settings. The society would primarily target scientific researchers but would invite others with an interest in this area of research, regardless of their discipline, position, field of application, or group affiliation (e.g., improvement science, behavioral medicine, knowledge translation). A society would need fruitful collaboration with related societies and organizations, which may include having combined meetings. Special links may be developed with one or more journals. A website to provide information on relevant resources, events, and training opportunities is another key activity. It would also provide a voice for the field at funding agencies, political arenas, and similar institutions. An organizational structure and financial resources are required to develop and run these activities. Our aim is to start an international debate, to discover if we can establish a shared vision across academics and stakeholders engaged with creating scientific knowledge on how to improve healthcare. We invite readers to express their views in the online questionnaire accessed by following the URL link provided at the end of the editorial

Screening synteny blocks in pairwise genome comparisons through integer programming

<p>Abstract</p> <p>Background</p> <p>It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple "subgenomes" derived from genome duplications, we need to relax the traditional requirements of "one-to-one" syntenic matchings of genomic regions in order to reflect "one-to-many" or more generally "many-to-many" matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we need to eliminate weak, low scoring alignments from pairwise genome comparisons. Our goal is to objectively select subset of synteny blocks whose total scores are maximized while respecting the duplication history of the genomes in comparison. We call this "quota-based" screening of synteny blocks in order to appropriately fill a quota of syntenic relationships within one genome or between two genomes having WGD events.</p> <p>Results</p> <p>We have formulated the synteny block screening as an optimization problem known as "Binary Integer Programming" (BIP), which is solved using existing linear programming solvers. The computer program QUOTA-ALIGN performs this task by creating a clear objective function that maximizes the compatible set of synteny blocks under given constraints on overlaps and depths (corresponding to the duplication history in respective genomes). Such a procedure is useful for any pairwise synteny alignments, but is most useful in lineages affected by multiple WGDs, like plants or fish lineages. For example, there should be a 1:2 ploidy relationship between genome A and B if genome B had an independent WGD subsequent to the divergence of the two genomes. We show through simulations and real examples using plant genomes in the rosid superorder that the quota-based screening can eliminate ambiguous synteny blocks and focus on specific genomic evolutionary events, like the divergence of lineages (in cross-species comparisons) and the most recent WGD (in self comparisons).</p> <p>Conclusions</p> <p>The QUOTA-ALIGN algorithm screens a set of synteny blocks to retain only those compatible with a user specified ploidy relationship between two genomes. These blocks, in turn, may be used for additional downstream analyses such as identifying true orthologous regions in interspecific comparisons. There are two major contributions of QUOTA-ALIGN: 1) reducing the block screening task to a BIP problem, which is novel; 2) providing an efficient software pipeline starting from all-against-all BLAST to the screened synteny blocks with dot plot visualizations. Python codes and full documentations are publicly available <url>http://github.com/tanghaibao/quota-alignment</url>. QUOTA-ALIGN program is also integrated as a major component in SynMap <url>http://genomevolution.com/CoGe/SynMap.pl</url>, offering easier access to thousands of genomes for non-programmers.</p

Potential Impact of Antiretroviral Therapy and Screening on Cervical Cancer Mortality in HIV-Positive Women in Sub-Saharan Africa: A Simulation

Despite having high cervical cancer incidence and mortality rates, screening for cervical precancerous lesions remains infrequent in sub-Saharan Africa. The need to screen HIV-positive women because of the higher prevalence and faster progression of cervical precancerous lesions may be heightened by the increased access to highly-active antiretroviral therapy (HAART). Policymakers need quantitative data on the effect of HAART and screening to better allocate limited resources. Our aim was to quantify the potential effect of these interventions on cervical cancer mortality.We constructed a Markov state-transition model of a cohort of HIV-positive women in Cameroon. Published data on the prevalence, progression and regression of lesions as well as mortality rates from HIV, cervical cancer and other causes were incorporated into the model. We examined the potential impact, on cumulative cervical cancer mortality, of four possible scenarios: no HAART and no screening (NHNS), HAART and no screening (HNS), HAART and screening once on HAART initiation (HSHI), and HAART and screening once at age 35 (HS35). Our model projected that, compared to NHNS, lifetime cumulative cervical cancer mortality approximately doubled with HNS. It will require 262 women being screened at HAART initiation to prevent one cervical cancer death amongst women on HAART. The magnitudes of these effects were most sensitive to the rate of progression of precancerous lesions.Screening, even when done once, has the potential of reducing cervical cancer mortality among HIV-positive women in Africa. The most feasible and cost-effective screening strategy needs to be determined in each setting

A generic algorithm for layout of biological networks

BackgroundBiological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of knowledge in the life sciences. To aid understanding of biological networks several algorithms for laying out and graphically representing networks and network analysis results have been developed. However, current algorithms are specialized to particular layout styles and therefore different algorithms are required for each kind of network and/or style of layout. This increases implementation effort and means that new algorithms must be developed for new layout styles. Furthermore, additional effort is necessary to compose different layout conventions in the same diagram. Also the user cannot usually customize the placement of nodes to tailor the layout to their particular need or task and there is little support for interactive network exploration.ResultsWe present a novel algorithm to visualize different biological networks and network analysis results in meaningful ways depending on network types and analysis outcome. Our method is based on constrained graph layout and we demonstrate how it can handle the drawing conventions used in biological networks.ConclusionThe presented algorithm offers the ability to produce many of the fundamental popular drawing styles while allowing the exibility of constraints to further tailor these layouts.publishe

The Mind’s Eye on Personal Profiles: A Cognitive Perspective on Profile Elements that Inform Initial Trustworthiness Assessments in Virtual Project Teams

Rusman, E., Van Bruggen, J., Sloep, P., Valcke, M., & Koper, R. (2013). The Mind’s Eye on Personal Profiles: A Cognitive Perspective on Profile Elements that Inform Initial Trustworthiness Assessments and Social Awareness in Virtual Project Teams. Computer Supported Cooperative Work (CSCW), 22(2-3), 159-179.Collaboration in virtual project teams heavily relies on interpersonal trust, for which perceived trustworthiness is an important determinant. This study provides insight in the information that trustors value to assess a trustee’s professional trustworthiness in the initial phase of a virtual project team. We expect trustors in virtual teams to value those particular information elements that provide them with relevant cues of trust warranting properties of a trustee. We identified a list of commonly highly valued information elements to inform trustworthiness assessments (n=226). We then analysed explanations for preferences with the help of a theory-grounded coding scheme. Results show that respondents value those particular information elements that provide them with multiple cues to assess the trustworthiness of a trustee. This enables them to become aware of and assess the trustworthiness of another. Information elements that provide unique cues could not be identified. Insight in these information preferences can inform the design of artefacts, such as personal profile templates, to support acquaintanceships in the initial phase of a virtual project team