Species abundance information improves sequence taxonomy classification accuracy.

Popular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linearly with the degree to which that assumption is violated, and in practice it is always violated. By incorporating environment-specific taxonomic abundance information, we demonstrate a significant increase in the species-level classification accuracy across common sample types. At the species level, overall average error rates decline from 25% to 14%, which is favourably comparable to the error rates that existing classifiers achieve at the genus level (16%). Our findings indicate that for most practical purposes, the assumption that reference species are equally likely to be observed is untenable. q2-clawback provides a straightforward alternative for samples from common environments

Species abundance information improves sequence taxonomy classification accuracy

Popular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linearly with the degree to which that assumption is violated, and in practice it is always violated. By incorporating environment-specific taxonomic abundance information, we demonstrate a significant increase in the species-level classification accuracy across common sample types. At the species level, overall average error rates decline from 25% to 14%, which is favourably comparable to the error rates that existing classifiers achieve at the genus level (16%). Our findings indicate that for most practical purposes, the assumption that reference species are equally likely to be observed is untenable. q2-clawback provides a straightforward alternative for samples from common environments.QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. This work was supported by an NHMRC project grant APP1085372, awarded to G.A.H., J.G.C., and R.K

A 'glocal' approach for real-time emergency event detection in Twitter

Social media like Twitter offer not only an unprecedented amount of user-generated content covering developing emergencies but also act as a collector of news produced by heterogeneous sources, including big and small media companies as well as public authorities. However, this volume, velocity, and variety of data constitute the main value and, at the same time, the key challenge to implement and automatic detection and tracking of independent emergency events from the real-time stream of tweets. Leveraging online clustering and considering both textual and geographical features, we propose, implement, and evaluate an algorithm to automatically detect emergency events applying a ‘glocal’ approach, i.e., offering a global coverage while detecting events at local (municipality level) scale

Viewpoints on emergent semantics

Authors include:Philippe Cudr´e-Mauroux, and Karl Aberer (editors), Alia I. Abdelmoty, Tiziana Catarci, Ernesto Damiani, Arantxa Illaramendi, Robert Meersman, Erich J. Neuhold, Christine Parent, Kai-Uwe Sattler, Monica Scannapieco, Stefano Spaccapietra, Peter Spyns, and Guy De Tr´eWe introduce a novel view on how to deal with the problems of semantic interoperability in distributed systems. This view is based on the concept of emergent semantics, which sees both the representation of semantics and the discovery of the proper interpretation of symbols as the result of a self-organizing process performed by distributed agents exchanging symbols and having utilities dependent on the proper interpretation of the symbols. This is a complex systems perspective on the problem of dealing with semantics. We highlight some of the distinctive features of our vision and point out preliminary examples of its applicatio

Linked Data based Health Information Representation, Visualization and Retrieval System on the Semantic Web

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.To better facilitate health information dissemination, using flexible ways to represent, query and visualize health data becomes increasingly important. Semantic Web technologies, which provide a common framework by allowing data to be shared and reused between applications, can be applied to the management of health data. Linked open data - a new semantic web standard to publish and link heterogonous data- allows not only human, but also machine to brows data in unlimited way. Through a use case of world health organization HIV data of sub Saharan Africa - which is severely affected by HIV epidemic, this thesis built a linked data based health information representation, querying and visualization system. All the data was represented with RDF, by interlinking it with other related datasets, which are already on the cloud. Over all, the system have more than 21,000 triples with a SPARQL endpoint; where users can download and use the data and – a SPARQL query interface where users can put different type of query and retrieve the result. Additionally, It has also a visualization interface where users can visualize the SPARQL result with a tool of their preference. For users who are not familiar with SPARQL queries, they can use the linked data search engine interface to search and browse the data. From this system we can depict that current linked open data technologies have a big potential to represent heterogonous health data in a flexible and reusable manner and they can serve in intelligent queries, which can support decision-making. However, in order to get the best from these technologies, improvements are needed both at the level of triple stores performance and domain-specific ontological vocabularies

An ActOn-based Semantic Information Service for EGEE

We describe a semantic information service that aggregates metadata from a large number of information sources of a large-scale Grid infrastructure. It uses an ontology-based information integration architecture (ActOn) suitable for the highly dynamic distributed information sources available in Grid systems, where information changes frequently and where the information of distributed sources has to be aggregated in order to solve complex queries. These two challenges are addressed by a Metadata Cache that works with an update-on-demand policy and by an information source selection module that selects the most suitable source at a given point in time. We have evaluated the quality of this information service, and compared it with other similar services from the EGEE production testbed, with promising results

Semantic web approach for italian graduates' surveys: the AlmaLaurea ontology proposal

Il crescente sviluppo e la promozione della trasparenza dei dati nell’ambito della pubblica amministrazione copre molteplici aspetti, fra cui l’educazione universitaria. Attualmente sono difatti numerosi i dataset rilasciati in formato Linked Open Data disponibili a livello nazionale ed internazionale. Fra le informazioni pubblicamente disponibili spiccano concetti riguardo l’occupazione e la numerosità dei laureati. Nonostante il progresso riscontrato, la mancanza di una metodologia standard per la descrizione di informazioni statistiche sui laureati rende difficoltoso un confronto di determinati fatti a partire da differenti sorgenti di dati. Sul piano nazionale, le indagini AlmaLaurea colmano il gap informativo dell’eterogeneità delle fonti proponendo statistiche centralizzate su profilo dei laureati e relativa condizione occupazionale, aggiornate annualmente. Scopo del progetto di tesi è la realizzazione di un’ontologia di dominio che descriva diverse peculiarità dei laureati, promuovendo allo stesso tempo la definizione strutturata dei dati AlmaLaurea e la successiva pubblicazione nel contesto Linked Open Data. Il progetto, realizzato con l’ausilio delle tecnologie del Web Semantico, propone infine la creazione di un endpoint SPARQL e di una interfaccia web per l'interrogazione e la visualizzazione dei dati strutturati

Trade-off among timeliness, messages and accuracy for large-Ssale information management

The increasing amount of data and the number of nodes in large-scale environments require new techniques for information management. Examples of such environments are the decentralized infrastructures of Computational Grid and Computational Cloud applications. These large-scale applications need different kinds of aggregated information such as resource monitoring, resource discovery or economic information. The challenge of providing timely and accurate information in large scale environments arise from the distribution of the information. Reasons for delays in distributed information system are a long information transmission time due to the distribution, churn and failures. A problem of large applications such as peer-to-peer (P2P) systems is the increasing retrieval time of the information due to the decentralization of the data and the failure proneness. However, many applications need a timely information provision. Another problem is an increasing network consumption when the application scales to millions of users and data. Using approximation techniques allows reducing the retrieval time and the network consumption. However, the usage of approximation techniques decreases the accuracy of the results. Thus, the remaining problem is to offer a trade-off in order to solve the conflicting requirements of fast information retrieval, accurate results and low messaging cost. Our goal is to reach a self-adaptive decision mechanism to offer a trade-off among the retrieval time, the network consumption and the accuracy of the result. Self-adaption enables distributed software to modify its behavior based on changes in the operating environment. In large-scale information systems that use hierarchical data aggregation, we apply self-adaptation to control the approximation used for the information retrieval and reduces the network consumption and the retrieval time. The hypothesis of the thesis is that approximation techniquescan reduce the retrieval time and the network consumption while guaranteeing an accuracy of the results, while considering user’s defined priorities. First, this presented research addresses the problem of a trade-off among a timely information retrieval, accurate results and low messaging cost by proposing a summarization algorithm for resource discovery in P2P-content networks. After identifying how summarization can improve the discovery process, we propose an algorithm which uses a precision-recall metric to compare the accuracy and to offer a user-driven trade-off. Second, we propose an algorithm that applies a self-adaptive decision making on each node. The decision is about the pruning of the query and returning the result instead of continuing the query. The pruning reduces the retrieval time and the network consumption at the cost of a lower accuracy in contrast to continuing the query. The algorithm uses an analytic hierarchy process to assess the user’s priorities and to propose a trade-off in order to satisfy the accuracy requirements with a low message cost and a short delay. A quantitative analysis evaluates our presented algorithms with a simulator, which is fed with real data of a network topology and the nodes’ attributes. The usage of a simulator instead of the prototype allows the evaluation in a large scale of several thousands of nodes. The algorithm for content summarization is evaluated with half a million of resources and with different query types. The selfadaptive algorithm is evaluated with a simulator of several thousands of nodes that are created from real data. A qualitative analysis addresses the integration of the simulator’s components in existing market frameworks for Computational Grid and Cloud applications. The proposed content summarization algorithm reduces the information retrieval time from a logarithmic increase to a constant factor. Furthermore, the message size is reduced significantly by applying the summarization technique. For the user, a precision-recall metric allows defining the relation between the retrieval time and the accuracy. The self-adaptive algorithm reduces the number of messages needed from an exponential increase to a constant factor. At the same time, the retrieval time is reduced to a constant factor under an increasing number of nodes. Finally, the algorithm delivers the data with the required accuracy adjusting the depth of the query according to the network conditions.La gestió de la informació exigeix noves tècniques que tractin amb la creixent quantitat de dades i nodes en entorns a gran escala. Alguns exemples d’aquests entorns són les infraestructures descentralitzades de Computacional Grid i Cloud. Les aplicacions a gran escala necessiten diferents classes d’informació agregada com monitorització de recursos i informació econòmica. El desafiament de proporcionar una provisió ràpida i acurada d’informació en ambients de grans escala sorgeix de la distribució de la informació. Una raó és que el sistema d’informació ha de tractar amb l’adaptabilitat i fracassos d’aquests ambients. Un problema amb aplicacions molt grans com en sistemes peer-to-peer (P2P) és el creixent temps de recuperació de l’informació a causa de la descentralització de les dades i la facilitat al fracàs. No obstant això, moltes aplicacions necessiten una provisió d’informació puntual. A més, alguns usuaris i aplicacions accepten inexactituds dels resultats si la informació es reparteix a temps. A més i més, el consum de xarxa creixent fa que sorgeixi un altre problema per l’escalabilitat del sistema. La utilització de tècniques d’aproximació permet reduir el temps de recuperació i el consum de xarxa. No obstant això, l’ús de tècniques d’aproximació disminueix la precisió dels resultats. Així, el problema restant és oferir un compromís per resoldre els requisits en conflicte d’extracció de la informació ràpida, resultats acurats i cost d’enviament baix. El nostre objectiu és obtenir un mecanisme de decisió completament autoadaptatiu per tal d’oferir el compromís entre temps de recuperació, consum de xarxa i precisió del resultat. Autoadaptacío permet al programari distribuït modificar el seu comportament en funció dels canvis a l’entorn d’operació. En sistemes d’informació de gran escala que utilitzen agregació de dades jeràrquica, l’auto-adaptació permet controlar l’aproximació utilitzada per a l’extracció de la informació i redueixen el consum de xarxa i el temps de recuperació. La hipòtesi principal d’aquesta tesi és que els tècniques d’aproximació permeten reduir el temps de recuperació i el consum de xarxa mentre es garanteix una precisió adequada definida per l’usari. La recerca que es presenta, introdueix un algoritme de sumarització de continguts per a la descoberta de recursos a xarxes de contingut P2P. Després d’identificar com sumarització pot millorar el procés de descoberta, proposem una mètrica que s’utilitza per comparar la precisió i oferir un compromís definit per l’usuari. Després, introduïm un algoritme nou que aplica l’auto-adaptació a un ordre per satisfer els requisits de precisió amb un cost de missatge baix i un retard curt. Basat en les prioritats d’usuari, l’algoritme troba automàticament un compromís. L’anàlisi quantitativa avalua els algoritmes presentats amb un simulador per permetre l’evacuació d’uns quants milers de nodes. El simulador s’alimenta amb dades d’una topologia de xarxa i uns atributs dels nodes reals. L’algoritme de sumarització de contingut s’avalua amb mig milió de recursos i amb diferents tipus de sol·licituds. L’anàlisi qualitativa avalua la integració del components del simulador en estructures de mercat existents per a aplicacions de Computacional Grid i Cloud. Així, la funcionalitat implementada del simulador (com el procés d’agregació i la query language) és comprovada per la integració de prototips. L’algoritme de sumarització de contingut proposat redueix el temps d’extracció de l’informació d’un augment logarítmic a un factor constant. A més, també permet que la mida del missatge es redueix significativament. Per a l’usuari, una precision-recall mètric permet definir la relació entre el nivell de precisió i el temps d’extracció de la informació. Alhora, el temps de recuperació es redueix a un factor constant sota un nombre creixent de nodes. Finalment, l’algoritme reparteix les dades amb la precisió exigida i ajusta la profunditat de la sol·licitud segons les condicions de xarxa. Els algoritmes introduïts són prometedors per ser utilitzats per l’agregació d’informació en nous sistemes de gestió de la informació de gran escala en el futur.Postprint (published version