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Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

Journal of Biomedical Semantics 2011年第5期2卷 1-12页

作者： Rebholz-Schuhmann, Dietrich Yepes, Antonio Jimeno Li, Chen Kafkas, Senay Lewin, Ian Kang, Ning Corbett, Peter Milward, David Buyko, Ekaterina Beisswanger, Elena Hornbostel, Kerstin Kouznetsov, Alexandre Witte, René Laurila, Jonas B Baker, Christopher JO Kuo, Cheng-Ju Clematide, Simone Rinaldi, Fabio Farkas, Richárd Móra, György Hara, Kazuo Furlong, Laura I Rautschka, Michael Neves, Mariana Lara Pascual-Montano, Alberto Wei, Qi Collier, Nigel Chowdhury, Md Faisal Mahbub Lavelli, Alberto Berlanga, Rafael Morante, Roser Van Asch, Vincent Daelemans, Walter Marina, José Luís van Mulligen, Erik Kors, Jan Hahn, Udo European Bioinformatics Institute EMBL Outstation Hinxton Cambridge CB10 1SD United Kingdom Erasmus University Medical Center Dept. of Medical Informatics Rotterdam Netherlands St. John's Innovation Centre Linguamatics Ltd Cambridge United Kingdom Friedrich-Schiller-Universität Language and Information Engineering (JULIE) Lab Jena Germany University of New Brunswick Dept. of Computer Science and Applied Statistics Canada Concordia University Dept. of Computer Science and Software Engineering Montreal Canada Academia Sinica Institute of Information Science Taipei 115 Taiwan University of Zürich Switzerland Hungarian Academy of Sciences Research Group on Artificial Intelligence Hungary Nara Institute of Science and Technology Nara Japan IMIM (Hospital del Mar Research Institute) Universitat Pompeu Fabra Research Programme on Biomedical Informatics (GRIB) Barcelona Spain National Center for Biotechnology-CSIC Madrid Spain National Institute of Informatics Tokyo Japan Fondazione Bruno Kessler Trento Italy Universitat Jaume I Spain University of Antwerp CLiPS Belgium Complutense University of Madrid Spain

Background: Competitions in text mining have been used to measure the performance of automatic text processing solutions against a manually annotated gold standard corpus (GSC). The preparation of the GSC is time-consuming and costly and the final corpus consists at the most of a few thousand documents annotated with a limited set of semantic groups. To overcome these shortcomings, the CALBC project partners (PPs) have produced a large-scale annotated biomedical corpus with four different semantic groups through the harmonisation of annotations from automatic text mining solutions, the first version of the Silver Standard Corpus (SSC-I). The four semantic groups are chemical entities and drugs (CHED), genes and proteins (PRGE), diseases and disorders (DISO) and species (SPE). This corpus has been used for the First CALBC Challenge asking the participants to annotate the corpus with their text processing solutions. Results: All four PPs from the CALBC project and in addition, 12 challenge participants (CPs) contributed annotated data sets for an evaluation against the SSC-I. CPs could ignore the training data and deliver the annotations from their genuine annotation system, or could train a machine-learning approach on the provided pre-annotated data. In general, the performances of the annotation solutions were lower for entities from the categories CHED and PRGE in comparison to the identification of entities categorized as DISO and SPE. The best performance over all semantic groups were achieved from two annotation solutions that have been trained on the SSC-I. The data sets from participants were used to generate the harmonised Silver Standard Corpus II (SSC-II), if the participant did not make use of the annotated data set from the SSC-I for training purposes. The performances of the participants' solutions were again measured against the SSC-II. The performances of the annotation solutions showed again better results for DISO and SPE in comparison to CHED and P

关键词： Chemical Entity Cosine Similarity Semantic Type Semantic Group Annotate Corpus

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Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

Assessment of NER solutions against the first and second CAL...

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4th International Symposium on Semantic Mining in Biomedicine, SMBM 2010

作者： Rebholz-Schuhmann, Dietrich Yepes, Antonio Jimeno Li, Chen Kafkas, Senay Lewin, Ian Kang, Ning Corbett, Peter Milward, David Buyko, Ekaterina Beisswanger, Elena Hornbostel, Kerstin Kouznetsov, Alexandre Witte, René Laurila, Jonas B. Baker, Christopher J.O. Kuo, Cheng-Ju Clematide, Simone Rinaldi, Fabio Farkas, Richárd Móra, György Hara, Kazuo Furlong, Laura Rautschka, Michael Neves, Mariana Lara Pascual-Montano, Alberto Wei, Qi Collier, Nigel Chowdhury, Md. Faisal Mahbub Lavelli, Alberto Berlanga, Rafael Morante, Roser Van Asch, Vincent Daelemans, Walter Marina, José Luís Van Mulligen, Erik Kors, Jan Hahn, Udo EMBL Outstation European Bioinformatics Institute Hinxton Cambridge CB10 1SD United Kingdom Dept. of Medical Informatics Erasmus University Medical Center Rotterdam NL Netherlands Linguamatics Ltd. St. John's Innovation Centre Cambridge United Kingdom Lab. Friedrich-Schiller-Universität Jena Germany Dept. of Computer Science and Applied Statistics University of New Brunswick Canada Dept. of Computer Science and Software Engineering Concordia University Montreal Canada Institute of Information Science Academia Sinica Taipei 115 Taiwan University of Zürich Switzerland Research Group on Artificial Intelligence Hungarian Academy of Sciences Hungary Institute of Science and Technology Nara Japan IMIM DCEX Universitat Pompeu Fabra Barcelona Spain Madrid Spain National Institute of Informatics Tokyo Japan Fondazione Bruno Kessler Trento Italy Universitat Jaume I Spain CLiPS University of Antwerp Belgium Complutense University of Madrid Spain

Background: Text mining challenges have been organised to measure the performance of automatic text mining solutions against a manually annotated gold standard corpus (GSC). The preparation of the GSC is timeconsuming and costly and the final corpus consists at the most of a few thousand documents annotated with a limited set of semantic groups. To overcome these shortcomings, the CALBC project partners (PPs) have produced a large-scale annotated biomedical corpus with four different semantic groups through the harmonisation of annotations from automatic text mining solutions, the first version of the Silver Standard Corpus (SSC-I). The four semantic groups were chemical entities and drugs (CHED), genes and proteins (PRGE), diseases and disorders (DISO) and species (SPE). This corpus has been used for the First CALBC Challenge asking the participants to annotate the corpus with their annotation solutions.

关键词： Semantics

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Feature-Modeling and Aspect-Oriented Programming: Integration and Automation

Feature-Modeling and Aspect-Oriented Programming: Integratio...

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ACIS International Conference on software engineering, Artificial Intelligence, Networking, and Parallel/Distributed Computing (SNPD)

作者： Kwanwoo Lee Goetz Botterweck Steffen Thiel Department of Information Systems Engineering Hansung University Seoul South Korea Lero – the Irish Software Engineering Research Centre University of Limerick Limerick Ireland Department of Computer Science Furtwangen University of Applied Sciences Furtwangen Germany

Feature modeling is an essential activity for modeling and managing the variability of a software product line. On the other hand, aspect-oriented programming provides effective means for modularizing feature implementation. Although current AOP tools (e.g., AJDT) provide a mechanism for switching aspect modules on and off to configure a product, this becomes infeasible in the context of large-scale product lines with thousands of variations. In this paper, we describe how feature modeling can be integrated with aspect-oriented programming to perform automated product derivation efficiently and effectively in the context of large-scale product lines.

关键词： Automatic programming Automation software engineering Switches Artificial intelligence Intelligent networks Distributed computing Parallel programming Management information systems Systems engineering and theory

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Two-stage offshoring: An investigation of the Irish bridge

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MIS Quarterly: Management Information Systems 2008年第2期32卷 257-279页

作者： Olsson, Helena Holmström Conchúir, Eoin Ó. Ågerfalk, Par J. Fitzgerald, Brian Department of Applied Information Technology IT University of Gothenburg Gothenburg Sweden Lero - The Irish Software Engineering Research Centre University of Limerick Limerick Ireland Department of Information Science Computer and Systems Science Uppsala University Uppsala Sweden Lero - The Irish Software Engineering Research Centre

This paper investigates two-stage offshoring as experienced by the Irish sites of two large global companies, headquartered in the United States, with significant software development operations. As part of these companies, the Irish sites act as a bridge in their offshoring arrangements: While the U.S. sites offshore work to Ireland, the Irish sites offshore work further to India and, hence, have experience of being both customer and vendor in two-stage offshore sourcing relationships. Using a framework derived from relational exchange theory (RET), we conducted multiple case study research to investigate and develop an initial theoretical model of the implementation of this two-stage offshoring bridge model. Our study shows that while both companies act as bridges in two-stage offshoring arrangements, their approaches differ in relation to (1) team integration, (2) organizational level implementation, and (3) site hierarchy. Although, there are opportunities afforded by the bridge model at present, the extent to which these opportunities will be viable into the future is open to question. As revealed in our study, temporal location seems to favor a bridge location such as Ireland, certainly with United States-Asian partners. However, location alone will not be enough to maintain position in future two-stage offshoring arrangements. Furthermore, our research supports the view that offshoring tends to progress through a staged sequence of progressively lower cost destinations. Such a development suggests that two-stage offshoring, as described in this paper, will eventually become what we would term multistage offshoring.

关键词： software engineering

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ArchMDE approach for the development of embedded real time systems

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12th Ada-Europe International Conference on Reliable software Technologies, Ada-Europe 2007

作者： Elleuch, Nourchène Khalfallah, Adel Ahmed, Samir Ben Department of Software Engineering Higher Institute of Computer Science El Manar 2 Rue Abou Raihan El Bayrouni 2080 Ariana Tunisia National Institute of Applied Sciences and Technology Centre Urbain Nord de Tunis B.P.676 Cedex Tunis- 1080 Tunisia

ISBN: (纸本)9783540732297

The development of Embedded Real Time Systems (ERTS) is generally a complex task that requires high costs and long delays. New development tools should be elaborated in order to improve ERTS developers productivity. Model Driven engineering (MDE) is an emerging paradigm that advances the idea to use models and models transformations to make the development process cost effective. This paper introduces the Architecture-centric Model Driven engineering (ArchMDE) approach that stresses architecture-based development and validation of ERTS. We have defined a set of architectural meta-models and a set of QVT transformation rules to automate the generation of architecture-specific models of ERTS. © Springer-Verlag Berlin Heidelberg 2007.

关键词： Embedded systems

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software Architecture in Model Driven Architecture

Software Architecture in Model Driven Architecture

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International Symposium on Computational Intelligence and Intelligent Informatics, ISCIII

作者： Nourchene Elleuch Adel Khalfallah Samir Ben Ahmed Department of software engineering Higher Institute of Computer Science Ariana Tunisia Centre urbain nord de Tunis National Institute of Applied Science and Technology Tunis Tunisia

The development of software architecture is complex due to the absence of a standard way that would lead the generation of software architecture artifacts. This paper proposes a method that would allow to derive the software architecture of any system based on its analysis model. For that purpose, we introduce a new layer to the model driven architecture (MDA) that takes into account the software architecture. The analysis model is termed the architecture independant model (AIM), which is compliant to the UML 2.0 metamodel. In addition, we consider the software architecture in the architecture specific model (ASM), which complies to the defined architectural metamodel. The mapping of AIM into ASM is conducted by using the both metamodels.

关键词： software architecture computer architecture Model driven engineering software engineering computer science software systems software standards Standards development Unified modeling language Spine

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Integrating probability with time and shared-variable concurrency

Integrating probability with time and shared-variable concur...

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30th Annual NASA/IEEE software engineering Workshop

作者： Zhu, Huibiao Qin, Shengchao He, Jifeng Bowen, Jonathan P. Software Engineering Institute East China Normal University Department of Computer Science University of Durham Centre for Applied Formal Methods London South Bank University

ISBN: (纸本)9780769526249

Complex software systems typically involve-features like time, concurrency and probability, where probabilistic computations play an increasing role. It is challenging to formalize languages comprising all these features. In this paper we integrate probability, time and concurrency in one single model, where the concurrency-feature is modelled using shared-variable based communication. The probability feature is represented by a probabilistic nondeterministic choice, probabilistic guarded choice and a probabilistic version of parallel composition. We formalize an operational semantics for such an integration. Based on this model we define a bisimulation relation, from which an observational equivalence between probabilistic programs is investigated and a collection of algebraic laws are explored. We also implement a prototype of the operational semantics to animate the execution of probabilistic programs.

关键词： Probability

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Minimal-power, delay-balanced smart repeaters for interconnects in the nanometer regime 06

Minimal-power, delay-balanced smart repeaters for interconne...

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SLIP'06 - 2006 International Workshop on System Level Interconnect Prediction

作者： Weerasekera, Roshan Pamunuwa, Dinesh Zheng, Li-Rong Tenhunen, Hannu Department of Electronic Computer and Software Systems KTH Information and Communication Technology ELECTRUM 229 164 40 Kista Sweden Centre for Microsystems Engineering Faculty of Applied Sciences Lancaster University Lancaster LA1 4YR United Kingdom

ISBN: (纸本)1595932550

In this paper we propose a smart repeater that consumes less energy and is suitable for driving global interconnections in nanometre technologies. When there is coupling between interconnects, the effective capacitance of a given wire is a function not only of the physical geometry, but also the relative switching pattern described by the bits on the wire in question (the victim) and the adjacent wires (aggressors). The drive strength of a traditional repeater is static, resulting in a spread of the propagation delay, with the repeater strength being essentially too much for every bit pattern other than the worst-case pattern. In the proposed SMART repeater, the drive strength is dynamically altered depending on the relative bit pattern, by partitioning it into a Main Driver and Assistant Driver. For a higher effective load capacitance both drivers switch, while for a lower effective capacitance the assistant driver is quiet. By disconnecting part of the repeater when it is not needed, the total load capacitance to the previous stage is reduced, resulting in reduced energy consumption for those instances. It is shown that the potential average saving in energy can be as much 15% with a 18% jitter reduction over a traditional repeater for typical global wire lengths in nanometre technologies. Copyright 2006 ACM.

关键词： Telecommunication repeaters

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Integrating Probability with Time and Shared-Variable Concurrency

Integrating Probability with Time and Shared-Variable Concur...

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Annual IEEE/ NASA Goddard Workshop on software engineering

作者： Huibiao Zhu Shengchao Qin Jifeng He Jonathan P. Bowen Software Engineering Institute East China Jiao Tong University China Department of Computer Science University of Durham UK Centre for Applied Formal Methods London South Bank University UK

Complex software systems typically involve features like time, concurrency and probability, where probabilistic computations play an increasing role. It is challenging to formalize languages comprising all these features. In this paper, we integrate probability, time and concurrency in one single model, where the concurrency feature is modelled using shared-variable based communication. The probability feature is represented by a probabilistic nondeterministic choice, probabilistic guarded choice and a probabilistic version of parallel composition. We formalize an operational semantics for such an integration. Based on this model we define a bisimulation relation, from which an observational equivalence between probabilistic programs is investigated and a collection of algebraic laws are explored. We also implement a prototype of the operational semantics to animate the execution of probabilistic programs

关键词： Concurrent computing software engineering software systems Helium Prototypes Animation Hardware design languages Command languages computer science Time sharing computer systems

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Automation of MDE processes by using ontologies: The OntMDE roadmap

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WSEAS Transactions on computers 2006年第10期5卷 2263-2269页

作者： Elleuch, Nourchène Khalfallah, Adel Ahmed, Samir Ben Department of Software Engineering Higher Institute of Computer Science 2 Rue Abou Raihan El Bayrouni 2080 Ariana Tunisia National Institute of Applied Sciences and Technology Centre Urbain Nord de Tunis B.P. 676 Cedex Tunis- 1080 Tunisia

The Model Driven Approach (MDA)as supported by the Object Management Group (OMG) seems to be one of the most promising approaches for designing and developing software applications. MDA describes the structural requirements of an engineering discipline where models, instead of source code, comprise the primary artifact. Model Driven engineering (MDE), as outlined by Stuart Kent, brings forth the dynamic aspects of engineering, where models design and transformation are equally important. This paper is a first investigation of the model-driven paradigm enactment using established architecture-centric concepts. It introduces the orchestration of models inside the OntMDE design process. In the depicted process, a distinction is made between two major levels, one is the architecture level of transformation and the other is the implementation level of transformation. We believe that the architecture of model is independent from any platform implementation. Therefore, the architectural considerations that are independent of platforms' considerations must be dealt with at Platform Independent Model (PIM) level. For that, PIM will be decomposed into two models: an Architecture Independent Model (AIM) and an Architecture Dependent Model (ADM). Secondly, domain ontology is used as marking technique to label the AIM and the architectural ontology description is provided to generate an ADM. We think that the use of an ontology representing domain design knowledge can be a way to bridge the gap between abstract and concrete models and to automate the model transformation process.

关键词： computer aided software engineering

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