Ontology Enrichment by Discovering Multi-Relational Association Rules from Ontological Knowledge Bases

International audienceIn the Semantic Web context, OWL ontologies represent the con-ceptualization of domains of interest while the corresponding as-sertional knowledge is given by the heterogeneous Web resources referring to them. Being strongly decoupled, ontologies and assertion can be out-of-sync. An ontology can be incomplete, noisy and sometimes inconsistent with regard to the actual usage of its conceptual vocabulary in the assertions. Data mining can support the discovery of hidden knowledge patterns in the data, to enrich the ontologies. We present a method for discovering multi-relational association rules, coded in SWRL, from ontological knowledge bases. Unlike state-of-the-art approaches, the method is able to take the intensional knowledge into account. Furthermore, since discovered rules are represented in SWRL, they can be straightforwardly integrated within the ontology, thus (i) enriching its expressive power and (ii) augmenting the assertional knowledge that can be derived. Discovered rules may also suggest new axioms to be added to the ontology. We performed experiments on publicly available ontologies validating the performances of our approach

Towards a representation of uncertain geospatial information in knowledge graphs

International audienceThis paper highlights the challenges of representing uncertain geospatial information in knowledge graphs. We propose to use Real Estate advertisements since professionals use a lot of vernacular and vague places in order to promote a house to their target audience. Then, we suggest to model local place names using fuzzy set theory. Finally, we discuss how to build a knowledge graph that represents extracted geospatial objects and their uncertainty. CCS CONCEPTS • Information systems → Geographic information systems

Interoperable AI: Evolutionary Race Towards Sustainable Knowledge Sharing

Article and Supplementary MaterialInternational audienceThe advancement and deployment of artificial intelligent agents brought numerous benefits in knowledge and data gathering and processing. However, one of the key challenges in deploying such agents in an open environment like the Web is their interoperability as they currently mostly run in silos. In this paper we report on a simulation and evaluation based on evolutionary agent-based modelling to empirically test how sustainable different strategies are for knowledge sharing in open multi-agent systems (MAS). Our results show the importance of translation-based approaches and the need for incentives to support these

Testing OWL Axioms against RDF Facts: A Possibilistic Approach

International audienceAutomatic knowledge base enrichment methods rely criti-cally on candidate axiom scoring. The most popular scoring heuristics proposed in the literature are based on statistical inference. We argue that such a probability-based framework is not always completely satis-factory and propose a novel, alternative scoring heuristics expressed in terms of possibility theory, whereby a candidate axiom receives a bipolar score consisting of a degree of possibility and a degree of necessity. We evaluate our proposal by applying it to the problem of testing SubClassOf axioms against the DBpedia RDF dataset

Dynamically Time-Capped Possibilistic Testing of SubClassOf Axioms Against RDF Data to Enrich Schemas

International audienceAxiom scoring is a critical task both for the automatic en-richment/learning and for the automatic validation of knowledge bases and ontologies. We designed and developed an axiom scoring heuristic based on possibility theory, which aims at overcoming some limitations of scoring heuristics based on statistical inference and taking into account the open-world assumption of the linked data on the Web. Since computing the possibilistic score can be computationally quite heavy for some candidate axioms, we propose a method based on time capping to alleviate the computation of the heuristic without giving up the precision of the scores. We evaluate our proposal by applying it to the problem of testing SubClassOf axioms against the DBpedia RDF dataset

Answering N-Relation Natural Language Questions in the Commercial Domain

International audienceThis paper presents SynchroBot, a Natural Language Question Answering system in the Commercial Domain.It relies on an RDF dataset and an RDFS ontology that we have developed for the commercial domain of the mobile phone industry. We propose an approach to understand and interpret natural language questions, based on the use of regular expressions to identify both the properties connecting entities, and their values. These regex are automatically learned from a subset of our dataset with a genetic algorithm

Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies

The unpalatable and warning-patterned butterflies _Heliconius erato_ and _Heliconius melpomene_ provide the best studied example of mutualistic Müllerian mimicry, thought – but rarely demonstrated – to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and this was initially hailed as the most striking known case of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence) that argued against codivergence. We present the first explicit cophylogenetic test of codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and re-examine the timing of these radiations. We find statistically significant topological congruence between multilocus coalescent population phylogenies of _H. erato_ and _H. melpomene_, supporting repeated codivergence of mimetic populations. Divergence time estimates, based on a Bayesian coalescent model, suggest that the evolutionary radiations of _H. erato_ and _H. melpomene_ occurred over the same time period, and are compatible with a series of temporally congruent codivergence events. This evidence supports a history of reciprocal coevolution between Müllerian co-mimics characterised by phylogenetic codivergence and parallel phenotypic change

Evolution of infectious bronchitis virus in the field after homologous vaccination introduction

International audienceAbstractDespite the fact that vaccine resistance has been typically considered a rare phenomenon, some episodes of vaccine failure have been reported with increasing frequency in intensively-raised livestock. Infectious bronchitis virus (IBV) is a widespread avian coronavirus, whose control relies mainly on extensive vaccine administration. Unfortunately, the continuous emergence of new vaccine-immunity escaping variants prompts the development of new vaccines. In the present work, a molecular epidemiology study was performed to evaluate the potential role of homologous vaccination in driving IBV evolution. This was undertaken by assessing IBV viral RNA sequences from the ORF encoding the S1 portion of viral surface glycoprotein (S) before and after the introduction of a new live vaccine on broiler farms in northern-Italy. The results of several biostatistics analyses consistently demonstrate the presence of a higher pressure in the post-vaccination period. Natural selection was detected essentially on sites located on the protein surface, within or nearby domains involved in viral attachment or related functions. This evidence strongly supports the action of vaccine-induced immunity in conditioning viral evolution, potentially leading to the emergence of new vaccine-escape variants. The great plasticity of rapidly-evolving RNA-viruses in response to human intervention, which extends beyond the poultry industry, is demonstrated, claiming further attention due to their relevance for animal and especially human health

Ecological conditions determine extinction risk in co-evolving bacteria-phage populations.

BACKGROUND: Antagonistic coevolution between bacteria and their viral parasites, phage, drives continual evolution of resistance and infectivity traits through recurrent cycles of adaptation and counter-adaptation. Both partners are vulnerable to extinction through failure of adaptation. Environmental conditions may impose unequal abiotic selection pressures on each partner, destabilising the coevolutionary relationship and increasing the extinction risk of one partner. In this study we explore how the degree of population mixing and resource supply affect coevolution-induced extinction risk by coevolving replicate populations of Pseudomonas fluorescens SBW25 with its associated lytic phage SBW25Ф2 under four treatment regimens incorporating low and high resource availability with mixed or static growth conditions. RESULTS: We observed an increased risk of phage extinction under population mixing, and in low resource conditions. High levels of evolved bacterial resistance promoted phage extinction at low resources under both mixed and static conditions, whereas phage populations could survive when phage susceptible bacterial genotypes rose to high frequency. CONCLUSIONS: These findings demonstrate that phage extinction risk is influenced by multiple abiotic conditions, which together act to destabilise the bacteria-phage coevolutionary relationship. The risk of coevolution-induced extinction is therefore dependent on the ecological context

Quorum Sensing Inhibition Selects for Virulence and Cooperation in Pseudomonas aeruginosa

With the rising development of bacterial resistance the search for new medical treatments beyond conventional antimicrobials has become a key aim of public health research. Possible innovative strategies include the inhibition of bacterial virulence. However, consideration must be given to the evolutionary and environmental consequences of such new interventions. Virulence and cooperative social behaviour of the bacterium Pseudomonas aeruginosa rely on the quorum-sensing (QS) controlled production of extracellular products (public goods). Hence QS is an attractive target for anti-virulence interventions. During colonization, non-cooperating (and hence less virulent) P. aeruginosa QS-mutants, benefiting from public goods provided by wild type isolates, naturally increase in frequency providing a relative protection from invasive infection. We hypothesized that inhibition of QS-mediated gene expression removes this growth advantage and selection of less virulent QS-mutants, and maintains the predominance of more virulent QS-wild type bacteria. We addressed this possibility in a placebo-controlled trial investigating the anti-QS properties of azithromycin, a macrolide antibiotic devoid of bactericidal activity on P. aeruginosa, but interfering with QS, in intubated patients colonized by P. aeruginosa. In the absence of azithromycin, non-cooperating (and hence less virulent) lasR (QS)-mutants increased in frequency over time. Azithromycin significantly reduced QS-gene expression measured directly in tracheal aspirates. Concomitantly the advantage of lasR-mutants was lost and virulent wild-type isolates predominated during azithromycin treatment. We confirmed these results in vitro with fitness and invasion experiments. Azithromycin reduced growth rate of the wild-type, but not of the lasR-mutant. Furthermore, the lasR-mutant efficiently invaded wild-type populations in the absence, but not in the presence of azithromycin. These in vivo and in vitro results demonstrate that anti-virulence interventions based on QS-blockade diminish natural selection towards reduced virulence and therefore may increase the prevalence of more virulent genotypes in the Hospital environment. More generally, the impact of intervention on the evolution of virulence of pathogenic bacteria should be assessed