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A framework and baseline results for the CLEF medical automatic annotation task

Mark O. Güld, Christian Thies, Benedikt Fischer, Thomas M. Deserno
2008 Pattern Recognition Letters  
This paper provides baseline results for the medical automatic annotation task of CLEF 2007.  ...  Therefore, the algorithms initially used for the corresponding tasks in 2005 and 2006 are applied, using the same parameterization.  ...  Introduction This paper provides baseline results for the medical automatic annotation challenge of CLEF 2007.  ... 
doi:10.1016/j.patrec.2008.05.020 fatcat:aebyflqzpra3tafh2fotustsyu

Baseline Results for the ImageCLEF 2006 Medical Automatic Annotation Task [chapter]

Mark O Güld, Christian Thies, Benedikt Fischer, Thomas M Deserno
2007 Lecture Notes in Computer Science  
This work reports baseline results for the CLEF 2008 Medical Automatic Annotation Task (MAAT) by applying a classifier with a fixed parameter set to all tasks 2005 -2008.  ...  In 2008, the baseline classifier yields error scores of 170.34 and 182.77 for k=1 and k=5 when the full code is reported, which corresponds to error rates of 51.3% and 52.8% for 1-NN and 5-NN, respectively  ...  Introduction In 2008, the Medical Automatic Annotation Task (MAAT) is held for the fourth time as part of the annual challenge issued by the Cross-Language Evaluation Forum (CLEF).  ... 
doi:10.1007/978-3-540-74999-8_84 fatcat:yr6jutpelneenky7oofzlqgcf4

Overview of the CLEF 2009 Medical Image Annotation Track [chapter]

Tatiana Tommasi, Barbara Caputo, Petra Welter, Mark Oliver Güld, Thomas M. Deserno
2010 Lecture Notes in Computer Science  
This paper describe the last round of the medical image annotation task in ImageCLEF 2009. After four years, we defined the task as a survey of all the past experience.  ...  They were asked to train their algorithms on 12,677 images, labeled according to four different settings representing the yearly annotation tasks, and to classify 1,733 images in the four annotation frameworks  ...  Acknowledgements We would like to thank the CLEF campaign for supporting the ImageCLEF initiative.  ... 
doi:10.1007/978-3-642-15751-6_9 fatcat:iewz5mraxbdahmgaropmenr2hi

The ImageCLEFmed Medical Image Retrieval Task Test Collection

William Hersh, Henning Müller, Jayashree Kalpathy-Cramer
2008 Journal of digital imaging  
The goal of the ImageCLEF medical image retrieval task (Image-CLEFmed) is to improve understanding and system capability in search for medical images.  ...  We also provide baseline results with the new collection and describe them in the context of past research with portions of the collection.  ...  Instructions for obtaining the data described in this paper can be obtained from the ImageCLEFmed Website (http://ir.ohsu. edu/image/).  ... 
doi:10.1007/s10278-008-9154-8 pmid:18769965 pmcid:PMC3043731 fatcat:msdjjtocxffopbydj7bbwdgwja

Automatic Annotation of X-Ray Images: A Study on Attribute Selection [chapter]

Devrim Unay, Octavian Soldea, Ahmet Ekin, Mujdat Cetin, Aytul Ercil
2010 Lecture Notes in Computer Science  
As a result, medical image classification and retrieval has recently gained high interest in the scientific community.  ...  Advances in the medical imaging technology has lead to an exponential growth in the number of digital images that need to be acquired, analyzed, classified, stored and retrieved in medical centers.  ...  The ImageCLEF Medical Image Annotation task, run as part of the Cross-Language Evaluation Forum (CLEF) campaign, is a yearly held medical image annotation challenge for automatic classification of an X-Ray  ... 
doi:10.1007/978-3-642-11769-5_10 fatcat:6ncybzfquvehfojyy3ea7qzgm4

Reducing Workload of Systematic Review Searching and Screening Processes

Harrisen Scells
2017 BCS-IRSG Symposium on Future Directions in Information Access  
This research explores automatic methodologies to reduce the workload relating to the searching and screening processes.  ...  Systematic reviews, in particular medical systematic reviews, are time consuming and costly to produce.  ...  The keywords in the boolean query of the search strategies are annotated with relevant PICO elements manually. Studies are also annotated automatically to extract the PICO elements.  ... 
doi:10.14236/ewic/fdia2017.2 dblp:conf/fdia/Scells17 fatcat:3hbng4ebivgpfkrimv5f5rhc24

Automatic medical image annotation in ImageCLEF 2007: Overview, results, and discussion

Thomas Deselaers, Thomas M. Deserno, Henning Müller
2008 Pattern Recognition Letters  
In this paper, the automatic medical annotation task of the 2007 CLEF cross-language image retrieval campaign (ImageCLEF) is described.  ...  Since 2005, the medical automatic image annotation task exists in ImageCLEF with increasing complexity to evaluate the performance of state-of-the-art methods for completely automatic annotation of medical  ...  Medical Automatic Image Annotation Tasks 2005 and 2006.  ... 
doi:10.1016/j.patrec.2008.03.001 fatcat:zr6dsbf2rnf3bp32phfe7wwreu

Mining clinical relationships from patient narratives

Angus Roberts, Robert Gaizauskas, Mark Hepple, Yikun Guo
2008 BMC Bioinformatics  
The Clinical E-Science Framework (CLEF) project has built a system to extract clinically significant information from the textual component of medical records in order to support clinical research, evidence-based  ...  extraction tasks, this result has significance for clinical text mining more generally, though further work to confirm our encouraging results should be carried out on a larger sample of narratives and  ...  CLEF is funded by the UK Medical Research Council, grant reference GO300607.  ... 
doi:10.1186/1471-2105-9-s11-s3 pmid:19025689 pmcid:PMC2586752 fatcat:3xrbc3ueg5esfm4evwk334r7wm

Conceptual language models for domain-specific retrieval

Edgar Meij, Dolf Trieschnigg, Maarten de Rijke, Wessel Kraaij
2010 Information Processing & Management  
Second, we propose a method for updating a textual query model using the concepts in conceptual representation.  ...  Overall, conceptual language models have the added advantage of offering query and browsing suggestions in the form of conceptual annotations.  ...  Acknowledgments We thank the anonymous reviewers for their helpful comments and remarks. We also thank Wouter Weerkamp for his insightful suggestions.  ... 
doi:10.1016/j.ipm.2009.09.005 fatcat:x3dlcuwvxjby3cacqos4nkfbke

Concept Extraction to Identify Adverse Drug Reactions in Medical Forums: A Comparison of Algorithms [article]

Alejandro Metke-Jimenez, Sarvnaz Karimi
2015 arXiv   pre-print
We compare different approaches to automatically identify and normalise medical concepts in consumer reviews in medical forums.  ...  Most of the existing studies use dictionary-based methods which are not evaluated independently from the overall signal detection task.  ...  Acknowledgements AskaPatient kindly provided the data used in this study for research purposes only.  ... 
arXiv:1504.06936v1 fatcat:wneokxxv4na3hmqx5kzpppu4f4

MIRACLE-GSI at ImageCLEFphoto 2008: Different Strategies for Automatic Topic Expansion [chapter]

Julio Villena-Román, Sara Lana-Serrano, José Carlos González-Cristóbal
2009 Lecture Notes in Computer Science  
This paper describes the participation of MIRACLE-GSI research consortium at the ImageCLEFphoto task of ImageCLEF 2008.  ...  Last, the result list is reranked using an implementation of k-Medoids clustering algorithm with the target number of clusters set to 20. 14 fully-automatic runs were finally submitted.  ...  -67407-C03-03 and by Madrid R+D Regional Plan, by means of the project MAVIR (Enhancing the Access and the Visibility of Networked Multilingual Information for the Community of Madrid), S-0505/TIC/000267  ... 
doi:10.1007/978-3-642-04447-2_70 fatcat:linbpu6q4reinnteybnifgod6q

MIRACLE at ImageCLEFmed 2008: Semantic vs. Statistical Strategies for Topic Expansion [chapter]

Sara Lana-Serrano, Julio Villena-Román, José Carlos González-Cristóbal
2009 Lecture Notes in Computer Science  
The main purpose of our experiments was to determine if any improvement of the linguistic expansion modules that were developed for the previous CLEF campaign, in terms of precision and recall, was possible  ...  This paper describes the participation of MIRACLE research consortium at the ImageCLEFmed task of ImageCLEF 2009.  ...  -67407-C03-03 and by Madrid R+D Regional Plan, by means of the project MAVIR (Enhancing the Access and the Visibility of Networked Multilingual Information for the Community of Madrid), S-0505/TIC/000267  ... 
doi:10.1007/978-3-642-04447-2_91 fatcat:2ekrffsasvhb3ixnsrftvo7cam

Leveraging coreference to identify arms in medical abstracts: An experimental study

Elisa Ferracane, Iain Marshall, Byron C. Wallace, Katrin Erk
2016 Proceedings of the Seventh International Workshop on Health Text Mining and Information Analysis  
We examine how coreference resolution can aid in identifying the arms of a study, an often overlooked piece of information needed to synthesize the results in a systematic review.  ...  A classification model 1 that performs better with the coreference features supports the intuition that coreference is able to capture the discourse salience of arms.  ...  Rodney Summerscales for providing us with the annotated corpus, and the anonymous reviewers for their helpful feedback.  ... 
doi:10.18653/v1/w16-6112 dblp:conf/acl-louhi/FerracaneMWE16 fatcat:shh2yuho2ffbdojyym5n2ovrbm

Relation Extraction for Open and Closed Domain Question Answering [chapter]

Gosse Bouma, Ismail Fahmi, Jori Mur
2011 Interactive Multi-modal Question-Answering  
We show that dependency patterns enriched with semantic concept labels give accurate results for relations that are relevant for a medical question answering system.  ...  In a second experiment, we concentrate on medical relation extraction for the question answering module of the IMIX system.  ...  We also used Joost to participate in the CLEF QA evaluation tasks, and achieved the best results for Dutch (Bouma et al, 2006) .  ... 
doi:10.1007/978-3-642-17525-1_8 dblp:series/tanlp/BoumaFM11 fatcat:jkoly4jsljaxfgfky3xs547j3i

Automated Component–Level Evaluation: Present and Future [chapter]

Allan Hanbury, Henning Müller
2010 Lecture Notes in Computer Science  
The advantages of such an approach are considered, as well as the requirements for implementing it.  ...  Based on these systems, propositions are made for a comprehensive framework for web service-based component-level IR system evaluation.  ...  Acknowledgements This work was partially supported by the European Commission FP7 Network of Excellence PROMISE (258191). We thank the referees who provided a number of excellent suggestions.  ... 
doi:10.1007/978-3-642-15998-5_14 fatcat:bhydfwpcwjf5dmhp6zfeu7nclu
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