Adaptive Semantic Annotation of Entity and Concept Mentions in Text

The recent years have seen an increase in interest for knowledge repositories that are useful across applications, in contrast to the creation of ad hoc or application-specific databases. These knowledge repositories figure as a central provider of unambiguous identifiers and semantic relationships between entities. As such, these shared entity descriptions serve as a common vocabulary to exchange and organize information in different formats and for different purposes. Therefore, there has been remarkable interest in systems that are able to automatically tag textual documents with identifiers from shared knowledge repositories so that the content in those documents is described in a vocabulary that is unambiguously understood across applications. Tagging textual documents according to these knowledge bases is a challenging task. It involves recognizing the entities and concepts that have been mentioned in a particular passage and attempting to resolve eventual ambiguity of language in order to choose one of many possible meanings for a phrase. There has been substantial work on recognizing and disambiguating entities for specialized applications, or constrained to limited entity types and particular types of text. In the context of shared knowledge bases, since each application has potentially very different needs, systems must have unprecedented breadth and flexibility to ensure their usefulness across applications. Documents may exhibit different language and discourse characteristics, discuss very diverse topics, or require the focus on parts of the knowledge repository that are inherently harder to disambiguate. In practice, for developers looking for a system to support their use case, is often unclear if an existing solution is applicable, leading those developers to trial-and-error and ad hoc usage of multiple systems in an attempt to achieve their objective. In this dissertation, I propose a conceptual model that unifies related techniques in this space under a common multi-dimensional framework that enables the elucidation of strengths and limitations of each technique, supporting developers in their search for a suitable tool for their needs. Moreover, the model serves as the basis for the development of flexible systems that have the ability of supporting document tagging for different use cases. I describe such an implementation, DBpedia Spotlight, along with extensions that we performed to the knowledge base DBpedia to support this implementation. I report evaluations of this tool on several well known data sets, and demonstrate applications to diverse use cases for further validation

DBpedia Spotlight: Shedding Light on the Web of Documents

Interlinking text documents with Linked Open Data enables the Web of Data to be used as background knowledge within document-oriented applications such as search and faceted browsing. As a step towards interconnecting the Web of Documents with the Web of Data, we developed DBpedia Spotlight, a system for automatically annotating text documents with DBpedia URIs. DBpedia Spotlight allows users to congure the annotations to their specic needs through the DBpedia Ontology and quality measures such as prominence, topical pertinence, contextual ambiguity and disambiguation condence. We compare our approach with the state of the art in disambiguation, and evaluate our results in light of three baselines and six publicly available annotation systems, demonstrating the competitiveness of our system. DBpedia Spotlight is shared as open source and deployed as a Web Service freely available for public use

Prognostic factor of emergency patients aged 90 years and older

学位記番号：医博甲146

Web

The Web of Linked Data grows rapidly and already contains data originating from hundreds of data sources. The quality of data from those sources is very diverse, as values may be out of date, incomplete or incorrect. Moreover, data sources may provide conflicting values for a single real-world object. In order for Linked Data applications to consume data from this global data space in an integrated fashion, a number of challenges have to be overcome. One of these challenges is to rate and to integrate data based on their quality. However, quality is a very subjective matter, and finding a canonic judgement that is suitable for each and every task is not feasible. To simplify the task of consuming high-quality data, we present Sieve, a framework for flexibly expressing quality assessment methods as well as fusion methods. Sieve is integrated into the Linked Data Integration Framework (LDIF), which handles Data Access, Schema Mapping and Identity Resolution, all crucial preliminaries for quality assessment and fusion. We demonstrate Sieve in a data integration scenario importing data from the English and Portuguese versions of DBpedia, and discuss how we increase completeness, conciseness and consistency through the use of our framework

TcruziKB: Enabling Complex Queries for Genomic Data Exploration

We developed a novel analytical environment to aid in the examination of the extensive amount of interconnected data available for genome projects. Our focus is to enable flexibility and abstraction from implementation details, while retaining the expressivity required for post-genomic research. To achieve this goal, we associated genomics data to ontologies and implemented a query formulation and execution environment with added visualization capabilities. We use ontology schemas to guide the user through the process of building complex queries in a flexible Web interface. Queries are serialized in SPARQL and sent to servers via Ajax. A component for visualization of the results allows researchers to explore result sets in multiple perspectives to suit different analytical needs. We show a use case of semantic computing with real world data. We demonstrate facilitated access to information through expressive queries in a flexible and friendly user interface. Our system scores 90.54% in a user satisfaction evaluation with 30 subjects. In comparison with traditional genome databases, preliminary evaluation indicates a reduction of the amount of user interaction required to answer the provided sample queries

Using Provenance for Quality Assessment and Repair in Linked Open Data

As the number of data sources publishing their data on the Web of Data is growing, we are experiencing an immense growth of the Linked Open Data cloud. The lack of control on the published sources, which could be untrustworthy or unreliable, along with their dynamic nature that often invalidates links and causes conflicts or other discrepancies, could lead to poor quality data. In order to judge data quality, a number of quality indicators have been proposed, coupled with quality metrics that quantify the “quality level” of a dataset. In addition to the above, some approaches address how to improve the quality of the datasets through a repair process that focuses on how to correct invalidities caused by constraint violations by either removing or adding triples. In this paper we argue that provenance is a critical factor that should be taken into account during repairs to ensure that the most reliable data is kept. Based on this idea, we propose quality metrics that take into account provenance and evaluate their applicability as repair guidelines in a particular data fusion setting

Robust spin crossover platforms with synchronized spin switch and polymer phase transition

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License.The idea of developing magnetic molecular materials into real functional electronic devices with low-cost and scalable techniques appeared with the emergence of the field several years ago. Today, even though great advances have been done with this aim, the promise of a functional device working at the micro-/nanoscale and at room temperature has unfortunately not completely materialized yet, as their use still strongly depends on the fabrication methodology of a robust device that can be handled and integrated without compromising their functionality. Here we propose the use of polymeric matrices as a platform for the development of such robust switchable structures exhibiting reproducible results independently of the dimension-from macro to micro-/nanoscale-and morphology-from thin-films to nanoparticles and nanoimprinted motives-while allowing to induce an irreversible hysteresis, reminiscent of a non-volatile memory, by synchronization with the polymer phase transition.This work was supported by project MAT2012-38318-C03-02. F.N. thanks the MICINN for a JdC fellowship. N.V. thanks the Spanish government for her Ph.D. Fellowship support.Peer Reviewe

QAPgrid: A Two Level QAP-Based Approach for Large-Scale Data Analysis and Visualization

Background: The visualization of large volumes of data is a computationally challenging task that often promises rewarding new insights. There is great potential in the application of new algorithms and models from combinatorial optimisation. Datasets often contain “hidden regularities” and a combined identification and visualization method should reveal these structures and present them in a way that helps analysis. While several methodologies exist, including those that use non-linear optimization algorithms, severe limitations exist even when working with only a few hundred objects. Methodology/Principal Findings: We present a new data visualization approach (QAPgrid) that reveals patterns of similarities and differences in large datasets of objects for which a similarity measure can be computed. Objects are assigned to positions on an underlying square grid in a two-dimensional space. We use the Quadratic Assignment Problem (QAP) as a mathematical model to provide an objective function for assignment of objects to positions on the grid. We employ a Memetic Algorithm (a powerful metaheuristic) to tackle the large instances of this NP-hard combinatorial optimization problem, and we show its performance on the visualization of real data sets. Conclusions/Significance: Overall, the results show that QAPgrid algorithm is able to produce a layout that represents the relationships between objects in the data set. Furthermore, it also represents the relationships between clusters that are feed into the algorithm. We apply the QAPgrid on the 84 Indo-European languages instance, producing a near-optimal layout. Next, we produce a layout of 470 world universities with an observed high degree of correlation with the score used by the Academic Ranking of World Universities compiled in the The Shanghai Jiao Tong University Academic Ranking of World Universities without the need of an ad hoc weighting of attributes. Finally, our Gene Ontology-based study on Saccharomyces cerevisiae fully demonstrates the scalability and precision of our method as a novel alternative tool for functional genomics

Multivariate Protein Signatures of Pre-Clinical Alzheimer's Disease in the Alzheimer's Disease Neuroimaging Initiative (ADNI) Plasma Proteome Dataset

Background: Recent Alzheimer's disease (AD) research has focused on finding biomarkers to identify disease at the pre-clinical stage of mild cognitive impairment (MCI), allowing treatment to be initiated before irreversible damage occurs. Many studies have examined brain imaging or cerebrospinal fluid but there is also growing interest in blood biomarkers. The Alzheimer's Disease Neuroimaging Initiative (ADNI) has generated data on 190 plasma analytes in 566 individuals with MCI, AD or normal cognition. We conducted independent analyses of this dataset to identify plasma protein signatures predicting pre-clinical AD. Methods and Findings: We focused on identifying signatures that discriminate cognitively normal controls (n = 54) from individuals with MCI who subsequently progress to AD (n = 163). Based on p value, apolipoprotein E (APOE) showed the strongest difference between these groups (p = 2.3×10−13). We applied a multivariate approach based on combinatorial optimization ((α,β)-k Feature Set Selection), which retains information about individual participants and maintains the context of interrelationships between different analytes, to identify the optimal set of analytes (signature) to discriminate these two groups. We identified 11-analyte signatures achieving values of sensitivity and specificity between 65% and 86% for both MCI and AD groups, depending on whether APOE was included and other factors. Classification accuracy was improved by considering “meta-features,” representing the difference in relative abundance of two analytes, with an 8-meta-feature signature consistently achieving sensitivity and specificity both over 85%. Generating signatures based on longitudinal rather than cross-sectional data further improved classification accuracy, returning sensitivities and specificities of approximately 90%. Conclusions: Applying these novel analysis approaches to the powerful and well-characterized ADNI dataset has identified sets of plasma biomarkers for pre-clinical AD. While studies of independent test sets are required to validate the signatures, these analyses provide a starting point for developing a cost-effective and minimally invasive test capable of diagnosing AD in its pre-clinical stages