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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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Towards mature use of semantic resources for biomedical analyses

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Journal of Biomedical Semantics 2011年第5期2卷 1-4页

作者： Rebholz-Schuhmann, D Rinaldi, F Pyysalo, S Collier, N Hahn, U European Bioinformatics Institute EMBL Outstation Hinxton Cambridge CB10 1SD United Kingdom University of Zürich Zürich Switzerland University of Tokyo Department of Computer Science Tokyo Japan National Institute of Informatics 2-1-2 Hitotsubashi Tokyo Chiyoda-ku Japan Friedrich-Schiller-Universität Language and Information Engineering (JULIE) Lab Jena Germany

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Biped walking using coronal and sagittal movements based on truncated fourier series

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14th Annual RoboCup International Symposium, 2010

作者： Shafii, Nima Reis, Luís Paulo Lau, Nuno DEI/FEUP – Informatics Engineering Department Faculty of Engineering University of Porto Rua Dr. Roberto Frias s/n Porto4200 465 Portugal LIACC – Artificial Intelligence and Computer Science Lab. Porto Portugal UA – University of Aveiro Campus Universitário de Santiago Aveiro3810 193 Portugal IEETA – Institute of Electronics and Telematics Engineering Aveiro Portugal

ISBN: (纸本)9783642202162

Biped walking by using all joint movements and DOFs in both directions (sagittal plane and coronal plane) is one of the most complicated research topics in robotics. In this paper, angular trajectories of a stable biped walking for a humanoid robot are generated by a Truncated Fourier Series (TFS) approach. The movements of legs and arms in sagittal plane are implemented by an optimized gait generator and a new model is proposed that can also produce the movement of legs in coronal plane based on TFS. Particle Swarm Optimization (PSO) is used to find the best angular trajectories and optimize TFS. Experimental results show that the using joints movements in sagittal and coronal planes to compose the walking skill allowed the biped robot to walk faster than previous methods that only used the joints in sagittal plane. © Springer-Verlag Berlin Heidelberg 2011.

关键词： Anthropomorphic robots

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A web services-based exergaming platform for senior citizens: the Long Lasting Memories project approach to e-health care

A web services-based exergaming platform for senior citizens...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society

作者： Panagiotis D. Bamidis Evdokimos I. Konstantinidis Antonis Billis Christos Frantzidis Magda Tsolaki Walter Hlauschek Efthyvoulos Kyriacou Marios Neofytou Constantinos S. Pattichis Lab of Medical Informatics Medical School Aristotle University of Thessaloniki Medical School Aristotle University of Thessaloniki CEIT RALTEC Institute for Rehabilitation and Assisted Living Technologies University of Cyprus Dept. of Computer Science

ISBN: (纸本)9781424441211

This piece of research describes an innovative e-health service that supports the cognitive and physical training of senior citizens and promotes their active ageing. The approach is adopted by the Long Lasting Memories (LLM) project, elements of which are discussed herein in the light of the functionalities provided to the users and the therapists. The aim of this work is to describe those technical elements that demonstrate the unique and integrative character of the LLM service, which is based on a modular Web service architecture, rendering the system available in different settings like the homes of seniors. The underlying database as well as the remote user interface empower therapists to set personalized training schemes, to view the progress of training sessions, as well as, adding new games and exercises into the system, thereby increasing the services sustainability and marketability.

关键词： aged person senior citizen Health Care Physical Education Homes Memory Web search engines World Wide Web congenital web

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Data recording in primary care field studies: Patient records enhancement project

Data recording in primary care field studies: Patient record...

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2011 5th International Conference on Pervasive Computing Technologies for Healthcare and Workshops, PervasiveHealth 2011

作者： Axelrod, Lesley Henwood, Flis Fitzpatrick, Geraldine Cassell, Jackie Smith, Helen Nicholson, Amanda Rait, Greta Human Centred Technology Lab School of Informatics University of Sussex Falmer Sussex BN1 9QH United Kingdom Social Informatics Research Unit School of Applied Social Science University of Brighton Falmer Brighton Sussex BN1 9PH United Kingdom Human-Computer Interaction Group Technical University of Vienna Karlsplatz 13 1040 Vienna Austria Brighton and Sussex Medical School Mayfield House Falmer Brighton Sussex BN1 9PH United Kingdom Department of Primary Care and Population Health University College London Medical School London NW3 2NF United Kingdom

ISBN: (纸本)9781936968152

This position paper describes the Human-computer Interaction (HCI) field studies component of the multidisciplinary Patient Records Enhancement Project (PREP). PREP seeks to understand variability of data found in primary care electronic records, in particular the balance between coded data and doctor's 'free text' notes. HCI fieldwork will establish variables that affect recording practices. In field studies we observe and record data recording practices in general practice (GP) surgeries, interview staff, video consultations with real patients and video consultations with standardized patients (played by medical actors). By standardizing patients we can compare the impact of other variables: different doctors, in different surgeries, using different e-health systems. Our early findings suggest that variability is due to a complex web of reasons, driven by personal, contextual and organizational processes. Findings from thematic analysis will result in design implications for studies by epidemiologists and public health researchers, design of NHS training and work processes, and design of electronic health record interfaces. © 2011 ICST.

关键词： Human computer interaction

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Group-in-a-Box Layout for Multi-faceted Analysis of Communities

Group-in-a-Box Layout for Multi-faceted Analysis of Communit...

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IEEE International Conference on and IEEE International Confernece on Social Computing (SocialCom) Privacy, Security, Risk and Trust (PASSAT)

作者： Eduarda Mendes Rodrigues Natasa Milic-Frayling Marc Smith Ben Shneiderman Derek Hansen Department of Informatics Engineering Faculty of Engineering University of Porto Portugal Microsoft Research Cambridge UK Connected Action Consulting Group Belmont CA USA Department of Computer Science & Human-Computer Interaction Lab University of Maryland College Park MD USA College of Information Studies & Center of the Advanced Study of Communities and Information University of Maryland College Park MD USA

Communities in social networks emerge from interactions among individuals and can be analyzed through a combination of clustering and graph layout algorithms. These approaches result in 2D or 3D visualizations of clustered graphs, with groups of vertices representing individuals that form a community. However, in many instances the vertices have attributes that divide individuals into distinct categories such as gender, profession, geographic location, and similar. It is often important to investigate what categories of individuals comprise each community and vice-versa, how the community structures associate the individuals from the same category. Currently, there are no effective methods for analyzing both the community structure and the category-based partitions of social graphs. We propose Group-In-a-Box (GIB), a meta-layout for clustered graphs that enables multi-faceted analysis of networks. It uses the tree map space filling technique to display each graph cluster or category group within its own box, sized according to the number of vertices therein. GIB optimizes visualization of the network sub-graphs, providing a semantic substrate for category-based and cluster-based partitions of social graphs. We illustrate the application of GIB to multi-faceted analysis of real social networks and discuss desirable properties of GIB using synthetic datasets.

关键词： Layout Communities Clustering algorithms Visualization Algorithm design and analysis Social network services Image edge detection

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A toolkit to explore lived experience of motivation: When words are not enough

A toolkit to explore lived experience of motivation: When wo...

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2011 5th International Conference on Pervasive Computing Technologies for Healthcare and Workshops, PervasiveHealth 2011

作者： Axelrod, Lesley Balaam, Madeline Burridge, Jane Smith, Penny Probert Fitzpatrick, Geraldine Mawson, Sue Ricketts, Ian Rodden, Tom User Centred Technology Lab Interactive Systems Informatics University of Sussex Falmer Brighton BN1 9QH United Kingdom Culture Lab Newcastle University Newcastle upon Tyne NE1 7RU United Kingdom School of Health Sciences University of Southampton Southampton S017 1BJ United Kingdom Dept Engineering Science University of Oxford Oxford 0X1 3PJ United Kingdom Human Computer Interaction Group Technical University of Vienna Favoritenstrase 9-11 A-1040 Vienna Austria Centre for Health and Social Care Research Sheffield Hallam University Sheffield S10 2BP United Kingdom School of Computing University of Dundee Dundee DD1 4HN United Kingdom Dept. Computer Science University of Nottingham NG8 IBB United Kingdom

ISBN: (纸本)9781936968152

Designing to support motivation is an increasingly important issue, especially as pervasive technologies are used to facilitate various healthy behaviour changes. There are many motivation theories but these do not map specifically to inform design. In 'Motivating Mobility' we explore the lived experiences of motivation of people with stroke, in order to design rehabilitation technologies. Motivation varies between people, between contexts and over time and can be 'difficult to express', particularly for those with communication problems. We describe development of a theoretically based toolkit, principled in both content and form, and using multiple modes of communication, aimed at gathering motivational requirements in order to inspire design. We show use of the toolkit, discuss the rich data collected and reflect on how well the approach works and ties requirements, via their elicitation tool, back to theory. This toolkit has potential to inform design for motivational effect in similar pervasive health applications. © 2011 ICST.

关键词： Motivation

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Modulation spectral features for objective voice quality assessment

Modulation spectral features for objective voice quality ass...

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4th International Symposium on Communications, Control, and Signal Processing, ISCCSP-2010

作者： Markaki, Maria Stylianou, Yannis Multimedia Informatics Lab. Computer Science Dept. University of Crete Greece Institute of Computer Science FORTH Crete Greece

ISBN: (纸本)9781424462858

In this paper, we employ normalized modulation spectral features for objective voice quality assessment regarding grade (hoarseness). Modulation spectra usually produce a high-dimensionality space. For classification purposes, the size of the original space is reduced using Higher Order Singular Value Decomposition (SVD). Further, we select most relevant features based on the mutual information between subjective voice quality (the degree of hoarseness) and the computed features, which leads to an adaptive to the classification task modulation spectral representation. The adaptive modulation spectral features are used as input to a Naive Bayes (NB) classifier. By combining two NB classifiers based on different feature sets a global classification rate of 73.93% for hoarseness was achieved. ©2010 IEEE.

关键词： Modulation

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University of lugano at TREC 2010

University of lugano at TREC 2010

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19th Text REtrieval Conference, TREC 2010

作者： Keikha, Mostafa Mahdabi, Parvaz Gerani, Shima Inches, Giacomo Parapary, Javier Carman, Mark Crestani, Fabio Department of Informatics University of Lugano Lugano Switzerland Dept. of Computer Science Information Retrieval Lab University of A Coruna Spain

We report on the University of Lugano's participation in the Blog and Session tracks of TREC 2010. In particular we describe our system for performing blog distillation, faceted search, top stories identification ... 详细信息

关键词： Distillation

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Adaptive referring expression generation in spoken dialogue systems: Evaluation with real users

Adaptive referring expression generation in spoken dialogue ...

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11th Annual Meeting of the Special Interest Group on Discourse and Dialogue, SIGDIAL 2010

作者： Janarthanam, Srinivasan Lemon, Oliver School of Informatics University of Edinburgh United Kingdom Interaction Lab. Mathematics and Computer Science Heriot-Watt University United Kingdom

ISBN: (纸本)9781932432855

We present new results from a real-user evaluation of a data-driven approach to learning user-adaptive referring expression generation (REG) policies for spoken dialogue systems. Referring expressions can be difficult to understand in technical domains where users may not know the technical 'jargon' names of the domain entities. In such cases, dialogue systems must be able to model the user's (lexical) domain knowledge and use appropriate referring expressions. We present a reinforcement learning (RL) framework in which the system learns REG policies which can adapt to unknown users online. For real users of such a system, we show that in comparison to an adaptive hand-coded baseline policy, the learned policy performs significantly better, with a 20.8% average increase in adaptation accuracy, 12.6% decrease in time taken, and a 15.1% increase in task completion rate. The learned policy also has a significantly better subjective rating from users. This is because the learned policies adapt online to changing evidence about the user's domain expertise. We also discuss the issue of evaluation in simulation versus evaluation with real users. © 2010 Association for Computational Linguistics.

关键词： Reinforcement learning

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