Graph-of-Entity: A Model for Combined Data Representation and Retrieval

Managing large volumes of digital documents along with the information they contain, or are associated with, can be challenging. As systems become more intelligent, it increasingly makes sense to power retrieval through all available data, where every lead makes it easier to reach relevant documents or entities. Modern search is heavily powered by structured knowledge, but users still query using keywords or, at the very best, telegraphic natural language. As search becomes increasingly dependent on the integration of text and knowledge, novel approaches for a unified representation of combined data present the opportunity to unlock new ranking strategies. We tackle entity-oriented search using graph-based approaches for representation and retrieval. In particular, we propose the graph-of-entity, a novel approach for indexing combined data, where terms, entities and their relations are jointly represented. We compare the graph-of-entity with the graph-of-word, a text-only model, verifying that, overall, it does not yet achieve a better performance, despite obtaining a higher precision. Our assessment was based on a small subset of the INEX 2009 Wikipedia Collection, created from a sample of 10 topics and respectively judged documents. The offline evaluation we do here is complementary to its counterpart from TREC 2017 OpenSearch track, where, during our participation, we had assessed graph-of-entity in an online setting, through team-draft interleaving

A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes

Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant–pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species

Network Capacity Bound for Personalized PageRank in Multimodal Networks

In a former paper the concept of Bipartite PageRank was introduced and a theorem on the limit of authority flowing between nodes for personalized PageRank has been generalized. In this paper we want to extend those results to multimodal networks. In particular we introduce a hypergraph type that may be used for describing multimodal network where a hyperlink connects nodes from each of the modalities. We introduce a generalisation of PageRank for such graphs and define the respective random walk model that can be used for computations. we finally state and prove theorems on the limit of outflow of authority for cases where individual modalities have identical and distinct damping factors.Comment: 28 pages. arXiv admin note: text overlap with arXiv:1702.0373

Approximation and relaxation of semantic web path queries

Given the heterogeneity of complex graph data on the web, such as RDF linked data, it is likely that a user wishing to query such data will lack full knowledge of the structure of the data and of its irregularities. Hence, providing flexible querying capabilities that assist users in formulating their information seeking requirements is highly desirable. In this paper we undertake a detailed theoretical investigation of query approximation, query relaxation, and their combination, for this purpose. The query language we adopt comprises conjunctions of regular path queries, thus encompassing recent extensions to SPARQL to allow for querying paths in graphs using regular expressions (SPARQL 1.1). To this language we add standard notions of query approximation based on edit distance, as well as query relaxation based on RDFS inference rules. We show how both of these notions can be integrated into a single theoretical framework and we provide incremental evaluation algorithms that run in polynomial time in the size of the query and the data, returning answers in ranked order of their `distance' from the original query. We also combine for the first time these two disparate notions into a single `flex' operation that simultaneously applies both approximation and relaxation to a query conjunct, providing even greater flexibility for users, but still retaining polynomial time evaluation complexity and the ability to return query answers in ranked order

Applications of flexible querying to graph data

Graph data models provide flexibility and extensibility that makes them well-suited to modelling data that may be irregular, complex, and evolving in structure and content. However, a consequence of this is that users may not be familiar with the full structure of the data, which itself may be changing over time, making it hard for users to formulate queries that precisely match the data graph and meet their information seeking requirements. There is a need therefore for flexible querying systems over graph data that can automatically make changes to the user's query so as to find additional or different answers, and so help the user to retrieve information of relevance to them. This chapter describes recent work in this area, looking at a variety of graph query languages, applications, flexible querying techniques and implementations

InnateDB: facilitating systems-level analyses of the mammalian innate immune response

Although considerable progress has been made in dissecting the signaling pathways involved in the innate immune response, it is now apparent that this response can no longer be productively thought of in terms of simple linear pathways. InnateDB (www.innatedb.ca) has been developed to facilitate systems-level analyses that will provide better insight into the complex networks of pathways and interactions that govern the innate immune response. InnateDB is a publicly available, manually curated, integrative biology database of the human and mouse molecules, experimentally verified interactions and pathways involved in innate immunity, along with centralized annotation on the broader human and mouse interactomes. To date, more than 3500 innate immunity-relevant interactions have been contextually annotated through the review of 1000 plus publications. Integrated into InnateDB are novel bioinformatics resources, including network visualization software, pathway analysis, orthologous interaction network construction and the ability to overlay user-supplied gene expression data in an intuitively displayed molecular interaction network and pathway context, which will enable biologists without a computational background to explore their data in a more systems-oriented manner

Human-machine cooperation in large-scale multimedia retrieval : a survey

Large-Scale Multimedia Retrieval(LSMR) is the task to fast analyze a large amount of multimedia data like images or videos and accurately find the ones relevant to a certain semantic meaning. Although LSMR has been investigated for more than two decades in the fields of multimedia processing and computer vision, a more interdisciplinary approach is necessary to develop an LSMR system that is really meaningful for humans. To this end, this paper aims to stimulate attention to the LSMR problem from diverse research fields. By explaining basic terminologies in LSMR, we first survey several representative methods in chronological order. This reveals that due to prioritizing the generality and scalability for large-scale data, recent methods interpret semantic meanings with a completely different mechanism from humans, though such humanlike mechanisms were used in classical heuristic-based methods. Based on this, we discuss human-machine cooperation, which incorporates knowledge about human interpretation into LSMR without sacrificing the generality and scalability. In particular, we present three approaches to human-machine cooperation (cognitive, ontological, and adaptive), which are attributed to cognitive science, ontology engineering, and metacognition, respectively. We hope that this paper will create a bridge to enable researchers in different fields to communicate about the LSMR problem and lead to a ground-breaking next generation of LSMR systems

Human-Machine Cooperation in Large-Scale Multimedia Retrieval: A Survey

Large-Scale Multimedia Retrieval(LSMR) is the task to fast analyze a large amount of multimedia data like images or videos and accurately find the ones relevant to a certain semantic meaning. Although LSMR has been investigated for more than two decades in the fields of multimedia processing and computer vision, a more interdisciplinary approach is necessary to develop an LSMR system that is really meaningful for humans. To this end, this paper aims to stimulate attention to the LSMR problem from diverse research fields. By explaining basic terminologies in LSMR, we first survey several representative methods in chronological order. This reveals that due to prioritizing the generality and scalability for large-scale data, recent methods interpret semantic meanings with a completely different mechanism from humans, though such humanlike mechanisms were used in classical heuristic-based methods. Based on this, we discuss human-machine cooperation, which incorporates knowledge about human interpretation into LSMR without sacrificing the generality and scalability. In particular, we present three approaches to human-machine cooperation (cognitive, ontological, and adaptive), which are attributed to cognitive science, ontology engineering, and metacognition, respectively. We hope that this paper will create a bridge to enable researchers in different fields to communicate about the LSMR problem and lead to a ground-breaking next generation of LSMR systems