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Intrinsic evaluation of text mining tools may not predict performance on realistic tasks

J Gregory Caporaso, Nita Deshpande, J Lynn Fink, Philip E Bourne, K Bretonnel Cohen, Lawrence Hunter
2008 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
We find that high performance on gold standard data (an intrinsic evaluation) does not necessarily translate to high performance for database annotation (an extrinsic evaluation).  ...  In this article we focus on the problem of annotating mutations in Protein Data Bank (PDB) entries, and evaluate the relationship between performance of two automated techniques, a text-mining-based approach  ...  Acknowledgments The authors would like to acknowledge Sue Brozowski for evaluating the MutationFinder normalization of PDB mutation fields, Jeffrey Haemer, Kristina Williams, and William Baumgartner for  ... 
pmid:18229722 pmcid:PMC2517250 fatcat:zoyqgvmibzbyvk3ihocq23eidu

INTRINSIC EVALUATION OF TEXT MINING TOOLS MAY NOT PREDICT PERFORMANCE ON REALISTIC TASKS

J. GREGORY CAPORASO, NITA DESHPANDE, J. LYNN FINK, PHILIP E. BOURNE, K. BRETONNEL COHEN, LAWRENCE HUNTER
2007 Biocomputing 2008  
We find that high performance on gold standard data (an intrinsic evaluation) does not necessarily translate to high performance for database annotation (an extrinsic evaluation).  ...  In this article we focus on the problem of annotating mutations in Protein Data Bank (PDB) entries, and evaluate the relationship between performance of two automated techniques, a text-mining-based approach  ...  Acknowledgments The authors would like to acknowledge Sue Brozowski for evaluating the MutationFinder normalization of PDB mutation fields, Jeffrey Haemer, Kristina Williams, and William Baumgartner for  ... 
doi:10.1142/9789812776136_0061 fatcat:pdiaz5yu2varfe3mdn3zd2hu6a

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges

Ayush Singhal, Robert Leaman, Natalie Catlett, Thomas Lemberger, Johanna McEntyre, Shawn Polson, Ioannis Xenarios, Cecilia Arighi, Zhiyong Lu
2016 Database: The Journal of Biological Databases and Curation  
on the difficulty of applying trained systems to text genres that are not seen previously during development.  ...  In this article, we argue that text-mining technologies have become essential tools in real-world biomedical research.  ...  Acknowledgement We also acknowledge the BioCreative steering committee http:// www.biocreative.org Conflict of interest. None declared.  ... 
doi:10.1093/database/baw161 pmid:28025348 pmcid:PMC5199160 fatcat:q22gw7owfjejznsrom3c4xnlem

A text-mining perspective on the requirements for electronically annotated abstracts

Florian Leitner, Alfonso Valencia
2008 FEBS Letters  
A second generation of systems could then attempt to address the problems of annotating protein interactions and protein/gene functions, a more difficult task for text-mining systems.  ...  The recent introduction of the first meta-server for the annotation of biological text, with the possibility of collecting annotations from available text-mining systems, adds credibility to the technical  ...  This work was supported by the ENFIN NoE (LSHG-CT-2005-518254) and the Spanish National Bioinformatics Institute (www.inab.org), a platform of Genoma España (www.genes.org).  ... 
doi:10.1016/j.febslet.2008.02.072 pmid:18328824 fatcat:umlsoplbdrds5ope6fzexaxmv4

From Public Polls to Tweets: Developing an Algorithm for Classifying Sentiment from Twitter Based on Computing with Words

Saad M. Darwish, Magda M. Madbouly, Mohamed A. Hassan
2016 Journal of Computers  
Uncertainty is an intrinsic part of sentiment analysis, especially when dealing with social media (Twitter data) that known as noisy texts.  ...  CWW can provide a solid basis for the computational theory of perceptions under the environments of imprecision, uncertainty, and partial truth.  ...  Evaluation In this section, we evaluate the whole system and present results for predicting the semantic orientations on Twitter.  ... 
doi:10.17706/jcp.11.3.238-246 fatcat:xxkbkksgufhjvkskyc353p7pwu

A Survey on Educational Data Mining and Research Trends

Rajni Jindal, Malaya Dutta Borah
2013 International Journal of Database Management Systems  
In this survey work focuses on components, research trends (1998 to 2012) of EDM highlighting its related Tools, Techniques and educational Outcomes. It also highlights the Challenges EDM.  ...  It provides intrinsic knowledge of teaching and learning process for effective education planning.  ...  The major outcomes of research during 2005-2008 was an intelligent tutoring system which identifies Meta cognitive skills of students, DSS which evaluates overall academic performance and survey on EDM  ... 
doi:10.5121/ijdms.2013.5304 fatcat:5iqbydoopnbupav73ji2k4hkfa

Mutation extraction tools can be combined for robust recognition of genetic variants in the literature

Antonio Jimeno Yepes, Karin Verspoor
2014 F1000Research  
.: Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Pac Symp Biocomput. 2008; 640-651. PubMed Abstract | Free Full Text 32.  ...  In the intrinsic evaluation on the Variome corpus, the combined performance is above 0.95 in F-measure, while in the extrinsic evaluation the combined recall performance is above 0.71 for COSMIC and above  ...  We would like to thank the developers of SETH and tmVar for making their tools available and for their support using their tools.  ... 
doi:10.12688/f1000research.3-18.v2 pmid:25285203 pmcid:PMC4176422 fatcat:hr2jlid5pjdsjjj3uaivp6oxwy

A text-mining system for extracting metabolic reactions from full-text articles

Jan Czarnecki, Irene Nobeli, Adrian M Smith, Adrian J Shepherd
2012 BMC Bioinformatics  
Results: When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our method performs surprisingly well.  ...  Increasingly biological text mining research is focusing on the extraction of complex relationships relevant to the construction and curation of biological networks and pathways.  ...  This perception may explain why relatively little attention has been paid to the task of extracting metabolic reactions from free text.  ... 
doi:10.1186/1471-2105-13-172 pmid:22823282 pmcid:PMC3475109 fatcat:leqjw2phkbe6veikxy5pcjbhkq

Overview of the PAN/CLEF 2015 Evaluation Lab [chapter]

Efstathios Stamatatos, Martin Potthast, Francisco Rangel, Paolo Rosso, Benno Stein
2015 Lecture Notes in Computer Science  
During the last decade, PAN has been established as the main forum of text mining research focusing on the identification of personal traits of authors left behind in texts unintentionally.  ...  A new corpus was built for this challenging, yet realistic, task covering four languages.  ...  Acknowledgements We thank the organizing committees of PAN's shared tasks Fabio Celli, Walter Daelemans, Ben Verhoeven, Patrick Juola, and Aurelio López-López.  ... 
doi:10.1007/978-3-319-24027-5_49 fatcat:fcpf2p7nujet5ez4zswoiscatq

A Survey on Recognizing Textual Entailment as an NLP Evaluation [article]

Adam Poliak
2020 arXiv   pre-print
In this survey paper, we provide an overview of different approaches for evaluating and understanding the reasoning capabilities of NLP systems.  ...  We then focus our discussion on RTE by highlighting prominent RTE datasets as well as advances in RTE dataset that focus on specific linguistic phenomena that can be used to evaluate NLP systems on a fine-grained  ...  this draft, and Yonatan Belinkov and Sasha Rush for the encouragement to write a survey on RTE.  ... 
arXiv:2010.03061v1 fatcat:jfmgkh4ginalzauawlqdbkb6pq

A Framework for Employee Appraisals Based on Inductive Logic Programming and Data Mining Methods [chapter]

Darah Aqel, Sunil Vadera
2013 Lecture Notes in Computer Science  
Moreover, 86% of the cases that are considered "realistic" are actually predicted as "realistic", and 100% of the cases that are considered not "realistic" are actually detected as not "realistic".  ...  The tools supported by the WEKA workbench are based on statistical evaluations of the models (algorithms).  ...  Appendix A A1 The Grammar Rules Learned by ALEPH from the First Corpus The following presents the grammar rules for SMART objectives learned by ALEPH from the corpus of objectives related to the sales  ... 
doi:10.1007/978-3-642-38824-8_49 fatcat:3bcsstk5tnhobijhl2gmpdi2jy

Mutation extraction tools can be combined for robust recognition of genetic variants in the literature

Antonio Jimeno Yepes, Karin Verspoor
2014 F1000Research  
.: Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Pac Symp Biocomput. 2008; 640-651. PubMed Abstract | Free Full Text 32.  ...  In the intrinsic evaluation on the Variome corpus, the combined performance is above 0.95 in F-measure, while in the extrinsic evaluation the combined recall performance is above 0.71 for COSMIC and above  ...  We would like to thank the developers of SETH and tmVar for making their tools available and for their support using their tools.  ... 
doi:10.12688/f1000research.3-18.v1 pmid:25285203 pmcid:PMC4176422 fatcat:pfy5365bfrfsxau46xdebmpbqy

Biomedical Language Processing: What's Beyond PubMed?

Lawrence Hunter, K. Bretonnel Cohen
2006 Molecular Cell  
Computational tools that classify documents, extract factual information, generate summaries, and generally process human language are providing powerful new tools for staying on top of the torrent of  ...  , and the number of new entries in MEDLINE each year has grown at a compounded annual growth rate of ~3.1% (see Figure 1 ).  ...  Acknowledgements The authors thank Hao Chen, Hans-Michael Müller, and Parantu Shah for usage data; Lynne Fox for information on PubMed; MITRE's Biomedical Information Processing group for data on Drosophila  ... 
doi:10.1016/j.molcel.2006.02.012 pmid:16507357 pmcid:PMC1702322 fatcat:yqvaab5kvjcl5norxcrh7fbvdm

Interpretation of the Consequences of Mutations in Protein Kinases: Combined Use of Bioinformatics and Text Mining

Jose M. G. Izarzugaza, Martin Krallinger, Alfonso Valencia
2012 Frontiers in Physiology  
Finally, we will discuss how text mining approaches constitute a powerful tool for the interpretation of the consequences of mutations in the context of disease genome analysis with particular focus on  ...  of text mining implementations for mutation extraction.  ...  In a later phase, blind tests are conducted to evaluate the performance simulating a more realistic scenario.  ... 
doi:10.3389/fphys.2012.00323 pmid:23055974 pmcid:PMC3449330 fatcat:i2qqkuh4nfde3pxeknjbvgpfpe

A novel deterministic approach for aspect-based opinion mining in tourism products reviews

Edison Marrese-Taylor, Juan D. Velásquez, Felipe Bravo-Marquez
2014 Expert systems with applications  
Since Liu's approach is focused on physical product reviews, it could not be directly applied to the tourism domain, which presents features that are not considered by the model.  ...  However, on average, the algorithms were only capable of extracting 35% of the explicit aspect expressions, using a non-extended approach for this task.  ...  Acknowledgements This work was supported partially by the FONDEF project D10I-1198, entitled WHALE: Web Hypermedia Analysis Latent Environment and the Millennium Institute on Complex Engineering Systems  ... 
doi:10.1016/j.eswa.2014.05.045 fatcat:44l7i4apozbstlwzazulf6anfu
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