Exploring Topic Variants Through an Hybrid Biclustering Approach

In large text corpora, analytic journalists need to identify facts, verify them by locating corroborating documents and survey all related viewpoints. This requires them to make sense of document relationships at two levels of granularity: high-level topics and low-level topic variants. We propose a visual analytics software allowing analytic journalists to verify and refine hypotheses without having to read all documents. Our system relies on a hybrid biclustering approach. A new Topic Weighted Map visualization conveys all top-level topics reflecting their importance and their relative similarity. Then, coordinated multiple views allow to drill down into topic variants through an interactive term hierarchy visualization. Hence, the analyst can select, compare and filter out the subtle co-occurrences of terms shared by multiple documents to find interesting facts or stories. The usefulness of the tool is shown through a usage scenario and further assessed through a qualitative evaluation by an expert user.Dans des corpus textuels volumineux, les journalistes analytiques cherchent des documents et des récits qui corroborent des faits, en les examinant sous tous les angles. Nous présentons un outil de visualisation analytique leur permettant de vérifier, d’affiner et de générer des hypothèses sans avoir à lire la totalité des contenus. Notre système repose sur une approche hybride de biclustering. Les sujets de haut niveau sont présentés via une carte pondérée de sujets, reflétant à la fois leur importance et leur similarité relative. Pour chaque sujet, une vue hiérarchique et interactive dresse un aperçu de toutes ses variantes, de manière à identifier les documents traités sous un même angle ou partageant des faits communs. Des vues multiples et coordonnées permettent une analyse plus fine, en filtrant, sélectionnant et comparant les variantes de sujet, au regard des motifs de co-occurrence de termes les plus intéressants. L’utilité de l’outil est montrée par un scénario d’usage, puis évaluée qualitativement par un journaliste analytique

The Long COVID experience from a patient's perspective: a clustering analysis of 27,216 Reddit posts

ObjectiveThis work aims to study the profiles of Long COVID from the perspective of the patients spontaneously sharing their experiences and symptoms on Reddit.MethodsWe collected 27,216 posts shared between July 2020 and July 2022 on Long COVID-related Reddit forums. Natural language processing, clustering techniques and a Long COVID symptoms lexicon were used to extract the different symptoms and categories of symptoms and to study the co-occurrences and correlation between them.ResultsMore than 78% of the posts mentioned at least one Long COVID symptom. Fatigue (29.4%), pain (22%), clouded consciousness (19.1%), anxiety (17.7%) and headaches (15.6%) were the most prevalent symptoms. They also highly co-occurred with a variety of other symptoms (e.g., fever, sinonasal congestion). Different categories of symptoms were found: general (45.5%), neurological/ocular (42.9%), mental health/psychological/behavioral (35.2%), body pain/mobility (35.1%) and cardiorespiratory (31.2%). Posts focusing on other concerns of the community such as vaccine, recovery and relapse and, symptom triggers were detected.ConclusionsWe demonstrated the benefits of leveraging large volumes of data from Reddit to characterize the heterogeneity of Long COVID profiles. General symptoms, particularly fatigue, have been reported to be the most prevalent and frequently co-occurred with other symptoms. Other concerns, such as vaccination and relapse following recovery, were also addressed by the Long COVID community

Frequency selective surfaces-based miniaturized wideband high-gain monopole antenna for UWB systems

In the suggested manuscript, an antenna functional over an ultrawide band with a small geometrical configuration and simplified structure is given. The recommended antenna is designed for the Roger 6002, having overall measurements of 40 mm × 30 mm × 1.52 mm. The wideband is obtained after loading stubs and etching slots from the basic antenna design. In order to improve the antenna’s performance further, an FSS sheet is designed. The sheet of FSS is placed behind the antenna to reflect the antenna’s backward radiation and improve antenna gain. In the results, the gain of the antenna improved from 4.5 dBi to 9.5 dBi. The resultant antenna loaded with FSS is capable of operating over UWB ranging from 3.4 to 9.8 GHz with stable gain throughout the functional bandwidth. The hardware model is manufactured and tested to validate the estimated results achieved from HFSS (High Frequency Structure Simulator). Moreover, the recommended work is differentiated in the form of a table with literature. The compact size, wideband, high gain and stable performance of proposed antenna system over-performs the literature work and makes it potential candidate for the UWB system requiring high gain

Sense-making strategies in explorative intelligence analysis of network evolutions

Visualising how social networks evolve is important in intelligence analysis in order to detect and monitor issues, such as emerging crime patterns or rapidly growing groups of offenders. It remains an open research question how this type of information should be presented for visual exploration. To get a sense of how users work with different types of visualisations, we evaluate a matrix and a node-link diagram in a controlled thinking aloud study. We describe the sense-making strategies that users adopted during explorative and realistic tasks. Thereby, we focus on the user behaviour in switching between the two visualisations and propose a set of nine strategies. Based on a qualitative and quantitative content analysis we show which visualisation supports which strategy better. We find that the two visualisations clearly support intelligence tasks and that for some tasks the combined use is more advantageous than the use of an individual visualisation

ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins.

BACKGROUND: Recent 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. RESULTS: We 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. CONCLUSIONS: ICoVeR 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

The Global Landscape of Pediatric Bacterial Meningitis Data Reported to the World Health Organization-Coordinated Invasive Bacterial Vaccine-Preventable Disease Surveillance Network, 2014-2019.

BACKGROUND: The World Health Organization (WHO) coordinates the Global Invasive Bacterial Vaccine-Preventable Diseases (IB-VPD) Surveillance Network to support vaccine introduction decisions and use. The network was established to strengthen surveillance and laboratory confirmation of meningitis caused by Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis. METHODS: Sentinel hospitals report cases of children 137 000 suspected meningitis cases were reported by 58 participating countries, with 44.6% (n = 61 386) reported from countries in the WHO African Region. More than half (56.6%, n = 77 873) were among children <1 year of age, and 4.0% (n = 4010) died among those with reported disease outcome. Among suspected meningitis cases, 8.6% (n = 11 798) were classified as probable bacterial meningitis. One of 3 bacterial pathogens was identified in 30.3% (n = 3576) of these cases, namely S. pneumoniae (n = 2177 [60.9%]), H. influenzae (n = 633 [17.7%]), and N. meningitidis (n = 766 [21.4%]). Among confirmed bacterial meningitis cases with outcome reported, 11.0% died; case fatality ratio varied by pathogen (S. pneumoniae, 12.2%; H. influenzae, 6.1%; N. meningitidis, 11.0%). Among the 277 children who died with confirmed bacterial meningitis, 189 (68.2%) had confirmed S. pneumoniae. The proportion of pneumococcal cases with pneumococcal conjugate vaccine (PCV) serotypes decreased as the number of countries implementing PCV increased, from 77.8% (n = 273) to 47.5% (n = 248). Of 397 H. influenzae specimens serotyped, 49.1% (n = 195) were type b. Predominant N. meningitidis serogroups varied by region. CONCLUSIONS: This multitier, global surveillance network has supported countries in detecting and serotyping the 3 principal invasive bacterial pathogens that cause pediatric meningitis. Streptococcus pneumoniae was the most common bacterial pathogen detected globally despite the growing number of countries that have nationally introduced PCV. The large proportions of deaths due to S. pneumoniae reflect the high proportion of meningitis cases caused by this pathogen. This global network demonstrated a strong correlation between PCV introduction status and reduction in the proportion of pneumococcal meningitis infections caused by vaccine serotypes. Maintaining case-based, active surveillance with laboratory confirmation for prioritized vaccine-preventable diseases remains a critical component of the global agenda in public health.The World Health Organization (WHO)-coordinated Invasive Bacterial Vaccine-Preventable Disease (IB-VPD) Surveillance Network reported data from 2014 to 2019, contributing to the estimates of the disease burden and serotypes of pediatric meningitis caused by Streptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis

Outils de visualisation et d'aide à la mise au point de programmes avec contraintes

La programmation par contraintes est une discipline informatique aux multiples applications dans l'industrie et la recherche. Elle s'attaque \'e0 des probl\'e8mes difficiles\par n\'e9cessitant souvent la mise au point d'algorithmes sophistiqu\'e9s. Or, jusqu'\'e0 pr\'e9sent, les praticiens de l'art de la programmation par contraintes sont d\'e9pourvus d'outils efficaces pour mener \'e0 bien cette entreprise. Dans le pr\'e9sent travail, diverses techniques de visualisation d'information sont mobilis\'e9es pour la surveillance et la mise au point de programmes avec contraintes. Nous commen\'e7ons par d\'e9crire les probl\'e9matiques li\'e9es au d\'e9bogage et \'e0 la mise au point de programmes avec contraintes et les structures de donn\'e9es principales manipul\'e9es par les solveurs de contraintes, \'e0 savoir des files, des arbres et des graphes. Ensuite, nous dressons l'\'e9tat de l'art des techniques de visualisation\par d'information les plus connues et mettons en oeuvre certaines d'entre elles de\par mani\'e8re cibl\'e9e sur les structures de donn\'e9es issues de la programmation par contraintes. Nous nous int\'e9ressons tout particuli\'e8rement \'e0 la visualisation des graphes de taille et de densit\'e9 importante et proposons de les visualiser sous forme de matrices d'adjacence. Gr\'e2ce \'e0 une exp\'e9rience contr\'f4l\'e9e que nous avons mise en place, nous d\'e9montrons que la repr\'e9sentation matricielle des graphes est plus lisible que la repr\'e9sentation traditionnelle sous forme de diagrammes noeuds-liens pour de nombreuses t\'e2ches. Nous d\'e9crivons \'e9galement l'utilisation e\'1bective de cette technique sur divers cas d'\'e9tude issus de la programmation par contraintes et mettons en lumi\'e8re l'utilit\'e9 de cette repr\'e9sentation pour conduire des raisonnements et adapter des strat\'e9gies de r\'e9solution con\'e7ues par des programmeurs en contraintes. Enfin, nous discutons des perspectives ouvertes par ce travail au plan de la programmation par contraintes, au plan du g\'e9nie logiciel, et enfin, de mani\'e8re plus g\'e9n\'e9rale, en termes de visualisation d'information.Constraint-oriented programming finds numerous applications in the industrial and\par academic worlds. It often tackles hard problems that require sophisticated resolution\par algorithms. However, constraint-oriented programmers have so far been left without efficient debugging tools to help them in this endeavour. In the present work, we tackle one of those few problems where two computer science disciplines meet, namely information visualization and constraint-oriented programming. To begin with, we describe the problems related to the debugging and tuning of constraint-oriented programs, as well as the main data structures handled by constraint programs solvers. Then, we report the state of the art in the field of information visualisation and implement some of its most famous techniques suited for the problem at hand. We focus in particular on the visualization of large and dense graphs. For those, we propose a matrix-based visualization. By the means of a user controlled experiment, the matrix-based visualization proves to be more readable than traditional node-link diagrams on numerous tasks. We also describe the actual use of this visualization technique on various cases of study and outline how it can enhance reasoning and help constraint systems programmers adapt the strategies they design. Lastly, we discuss a few perspectives following the present work with regard to constraint programming, as well as software engineering, and more\par generally in terms of information visualization.NANTES-BU Sciences (441092104) / SudocSudocFranceF

A branch-and-price algorithm for a vehicle routing with demand allocation problem

International audienceWe investigate the vehicle routing with demand allocation problem where the decision-maker jointly optimizes the location of delivery sites, the assignment of customers to (preferably convenient) delivery sites, and the routing of vehicles operated from a central depot to serve customers at their designated sites. We propose an effective branch-and-price (B&P) algorithm that is demonstrated to greatly outperform the use of commercial branch-and-bound/cut solvers such as CPLEX. Central to the efficacy of the proposed B&P algorithm is the development of a specialized dynamic programming procedure that extends works on elementary shortest path problems with resource constraints in order to solve the more complex column generation pricing subproblem. Our computational study demonstrates the efficacy of the proposed approach using a set of 60 problem instances. Moreover, the proposed methodology has the merit of providing optimal solutions in run times that are significantly shorter than those reported for decomposition-based heuristics in the literature