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Annotating Answer-Set Programs in LANA? [article]

Marina De Vos, Doğa Gizem Kıza, Johannes Oetsch, Jörg Pührer, Hans Tompits
2012 arXiv   pre-print
In particular, we propose to augment answer-set programs with additional meta-information formulated in a dedicated annotation language, called LANA.  ...  While past research in answer-set programming (ASP) mainly focused on theory, ASP solver technology, and applications, the present work situates itself in the context of a quite recent research trend:  ...  To this end, we devised a dedicated annotation language, LANA, standing for "Language for ANnotating Answer-set programs", that specifies specially formatted program comments.  ... 
arXiv:1210.2195v1 fatcat:3scweyzegfagzk33wwxogludpq

Annotating answer-set programs in Lana

MARINA DE VOS, DOĞA GIZEM KISA, JOHANNES OETSCH, JÖRG PÜHRER, HANS TOMPITS
2012 Theory and Practice of Logic Programming  
In particular, we propose to augment answer-set programs with additional meta-information formulated in a dedicated annotation language, calledLana.  ...  AbstractWhile past research in answer-set programming (ASP) mainly focused on theory, ASP solver technology, and applications, the present work situates itself in the context of a quite recent research  ...  To this end, we devised a dedicated annotation language, LANA, standing for "Language for ANnotating Answer-set programs", that specifies specially formatted program comments.  ... 
doi:10.1017/s147106841200021x fatcat:r6ls6zd2jbealdyz5m3whso4ja

SingleCite: Towards an improved Single Citation Search in PubMed

Lana Yeganova, Donald C Comeau, Won Kim, W John Wilbur, Zhiyong Lu
2018 Proceedings of the BioNLP 2018 workshop  
A search that is targeted at finding a specific document in databases is called a Single Citation search.  ...  In this work we describe SingleCite, a single citation matching system designed to facilitate user's search for a specific document.  ...  Acknowledgments This research was supported by the Intramural Research Program of the NIH, National Library of Medicine.  ... 
doi:10.18653/v1/w18-2318 dblp:conf/bionlp/YeganovaCKWL18 fatcat:kidxegplc5ggllnkb5dsiyzmni

Machine learning with naturally labeled data for identifying abbreviation definitions

Lana Yeganova, Donald C Comeau, W Wilbur
2011 BMC Bioinformatics  
The machine learner is trained to distinguish between these two sets of examples. Then, the learned feature weights are used to identify the abbreviation full form.  ...  Methods: In this work, we develop a machine learning algorithm for abbreviation definition identification in text which makes use of what we term naturally labeled data.  ...  To answer the second question, we applied feature weights to identify correct definitions in PSF-PLF pairs.  ... 
doi:10.1186/1471-2105-12-s3-s6 pmid:21658293 pmcid:PMC3111592 fatcat:6of76rvkg5czjosa4fvqyasua4

PubMed Phrases, an open set of coherent phrases for searching biomedical literature

Sun Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2018 Scientific Data  
Acknowledgements This research was supported by the Intramural Research Program of the NIH, National Library of Medicine.  ...  Using phrases as atomic search units has also been shown to improve the retrieval performance in a question answering task 34 .  ...  The annotation task was performed in two rounds and conducted by two annotators with backgrounds in biomedical informatics research and experience in annotating biomedical corpora.  ... 
doi:10.1038/sdata.2018.104 pmid:29893755 pmcid:PMC5996850 fatcat:rbs53zhjnveqfadl7uaak3w2ha

New Perspectives on the Use of Online Learning for Congestion Level Prediction over Traffic Data [article]

Eric L. Manibardo, Ibai Laña, Jesus L. Lobo, Javier Del Ser
2020 arXiv   pre-print
In this manuscript we elaborate on the suitability of online learning methods to predict the road congestion level based on traffic speed time series data.  ...  As opposed to what is done in most literature, we provide evidence of the importance of assessing the distribution of classes over time before designing and tuning the learning model.  ...  Manibardo receives funding support from the Basque Government through its BIKAINTEK PhD support program (grant no. 48AFW22019-00002).  ... 
arXiv:2003.14304v1 fatcat:dglnjjwhqnemha77a5ksy7uqcq

PubTermVariants: biomedical term variants and their use for PubMed search

Lana Yeganova, Won Kim, Sun Kim, Rezarta Islamaj Doğan, Wanli Liu, Donald C Comeau, Zhiyong Lu, W John Wilbur
2016 Proceedings of the 15th Workshop on Biomedical Natural Language Processing  
Term normalization is frequently used in information retrieval task to reduce variant word forms to a common form.  ...  The most general term normalization technique used in practice is stemming, however it has been found to not be completely reliable.  ...  Acknowledgements The authors thank Grigory Balasanov for his help in preparing the web-based tool for the manual annotation task.  ... 
doi:10.18653/v1/w16-2919 dblp:conf/bionlp/YeganovaKKDLCLW16 fatcat:3c3zh3uomjhwxpcpobhadzxcxi

Identifying Abbreviation Definitions Machine Learning with Naturally Labeled Data

Lana Yeganova, Donald C. Comeau, W. John Wilbur
2010 2010 Ninth International Conference on Machine Learning and Applications  
In this work, we develop a machine learning algorithm for abbreviation definition identification in text.  ...  The machine learner is trained to distinguish between these two sets of examples. Then, the learned feature weights are used to identify the abbreviation full form.  ...  ACKNOWLEDGEMENT This research was supported by the Intramural Research Program of the NIH, National Library of Medicine.  ... 
doi:10.1109/icmla.2010.166 dblp:conf/icmla/YeganovaCW10 fatcat:by5z2q3vnvbgnpn5opprkjkvsq

A Field Sensor: computing the composition and intent of PubMed queries

Lana Yeganova, Won Kim, Donald C Comeau, W John Wilbur, Zhiyong Lu
2018 Database: The Journal of Biological Databases and Curation  
We evaluate the accuracy of our algorithm on a human-annotated corpus of 10 000 PubMed queries, as well as a new machineannotated set of 103 000 PubMed queries.  ...  Given a query, the Field Sensor infers a field for each token or sequence of tokens in a query in multi-step process that includes syntactic chunking, rule-based tagging and probabilistic field prediction  ...  Acknowledgements This research was supported by the Intramural Research Program of the NIH, National Library of Medicine. Conflict of interest. None declared.  ... 
doi:10.1093/database/bay052 pmid:30010750 pmcid:PMC6044290 fatcat:3z3teiexjfclfjlvhppa7wgy7a

The SeaLion has Landed: An IDE for Answer-Set Programming—Preliminary Report [chapter]

Johannes Oetsch, Jörg Pührer, Hans Tompits
2013 Lecture Notes in Computer Science  
In this respect, SeaLion benefits from the research results of a project on methods and methodologies for answer-set program development in whose context SeaLion is realised.  ...  A main goal of SeaLion is to provide a user-friendly environment for supporting a developer to write, evaluate, debug, and test answer-set programs.  ...  SeaLion integrates the documentation generator ASPDoc for ASP that is based on Lana (Language for ANnotating Answer-set programs), an annotation language for structuring, documenting, and testing answer-set  ... 
doi:10.1007/978-3-642-41524-1_19 fatcat:yv65ddhv3rdj7aqoncjdwdl2ze

Transcriptome architecture across tissues in the pig

André LJ Ferraz, Ana Ojeda, Manel López-Béjar, Lana T Fernandes, Anna Castelló, Josep M Folch, Miguel Pérez-Enciso
2008 BMC Genomics  
Artificial selection has resulted in animal breeds with extreme phenotypes.  ...  The interaction in gene × tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.  ...  from Vall d'Hebron Hospital (Barcelona) and in the farm. We are also grateful to J. Reixach and Batallé (Girona, Spain) and to A. Fernández (INIA, Madrid) for sharing unpublished information.  ... 
doi:10.1186/1471-2164-9-173 pmid:18416811 pmcid:PMC2335121 fatcat:nb5z2vawynhmfjdkobqtawnwy4

SeaLion: An eclipse-based IDE for answer-set programming with advanced debugging support

PAULA-ANDRA BUSONIU, JOHANNES OETSCH, JÖRG PÜHRER, PETER SKOČOVSKÝ, HANS TOMPITS
2013 Theory and Practice of Logic Programming  
In this respect,SeaLionis the first IDE for ASP that provides debugging features that work for real-world answer-set programs and supports the rich languages of modern answer-set solvers.  ...  The tool has been realised in the context of a research project whose goal is the development of techniques to support the practical coding process of answer-set programs.  ...  The source editors of SeaLion allow for augmenting answer-set programs with annotations written in Lana (Language for ANnotating Answer-set programs), an annotation language for structuring, documenting  ... 
doi:10.1017/s1471068413000410 fatcat:yvqsto7vlzfqrjzmrb5lqoke3i

On the Design of Graph Embeddings for the Sensorless Estimation of Road Traffic Profiles [article]

Eric L. Manibardo, Ibai Laña, Esther Villar, Javier Del Ser
2022 arXiv   pre-print
Several generation approaches are analyzed in terms of the precision of the synthesized samples.  ...  Manibardo receives funding support from the Basque Government through its BIKAINTEK PhD support program (grant no. 48AFW22019-00002).  ...  ACKNOWLEDGMENTS The authors would like to thank the Basque Government for its funding support through the EMAITEK and ELKARTEK programs (3KIA project, KK-2020/00049). Eric L.  ... 
arXiv:2201.04968v1 fatcat:pkwm5w75qza37mbj3ncaxhnk2e

Health Information Literacy and Competencies of Information Age Students: Results From the Interactive Online Research Readiness Self-Assessment (RRSA)

Lana Ivanitskaya, Irene O'Boyle, Anne Marie Casey
2006 Journal of Medical Internet Research  
Upon answering all questions, students received a results page that summarized their numerical results and displayed individually tailored feedback composed by an experienced librarian.  ...  In an era of easy access to information, university students who will soon enter health professions need to develop their information competencies.  ...  Leonard for providing programming support for our research project.  ... 
doi:10.2196/jmir.8.2.e6 pmid:16867969 pmcid:PMC1550696 fatcat:ppwlg7vstzafrllvn7w3gg35fm

mirMark: a site-level and UTR-level classifier for miRNA target prediction

Mark Menor, Travers Ching, Xun Zhu, David Garmire, Lana X Garmire
2014 Genome Biology  
This method uses experimentally verified miRNA targets from miRecords and mirTarBase as training sets and considers over 700 features.  ...  MiRNAs play important roles in many diseases including cancers. However computational prediction of miRNA target genes is challenging and the accuracies of existing methods remain poor.  ...  Compared to the other programs discussed in this paper, mirMark is algorithmically more similar to SVMicrO.  ... 
doi:10.1186/s13059-014-0500-5 pmid:25344330 pmcid:PMC4243195 fatcat:l52cmsfe5zfu7kvg633cu2gytq
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