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Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup [article]

Alexander S. Yeh, Lynette Hirschman, Alexander A. Morgan
2003 arXiv   pre-print
RESULTS: We report on a Challenge Evaluation task that we created for the Knowledge Discovery and Data Mining (KDD) Challenge Cup.  ...  We report on the the evaluation results and describe the techniques used by the top performing groups. CONTACT: KEYWORDS: text mining, evaluation, curation, genomics, data management  ...  In addition, many people at FlyBase have contributed to the KDD Cup task, especially William Gelbart, Beverly Matthews, Leyla Bayraktaroglu, David Emmert and Don Gilbert.  ... 
arXiv:cs/0308032v1 fatcat:u5qu25hggbctrk6if4vgdgyhbe

Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup

A. S. Yeh, L. Hirschman, A. A. Morgan
2003 Bioinformatics  
Results: We report on a Challenge Evaluation task that we created for the Knowledge Discovery and Data Mining (KDD) Challenge Cup.  ...  However, as the volume of literature increases, the burden of curation increases. Text mining may provide useful tools to assist in the curation process.  ...  In addition, many people at FlyBase have contributed to the KDD Cup task, especially William Gelbart, Beverly Matthews, Leyla Bayraktaroglu, David Emmert and Don Gilbert.  ... 
doi:10.1093/bioinformatics/btg1046 pmid:12855478 fatcat:bjfhisawmzcwnp2hwb3e23coiy

The BioLink SIG Workshop at ISMB2004

Lynette Hirschman, Christian Blaschke, Alfonso Valencia
2005 Comparative and Functional Genomics  
This paper reports on work done in part at the MITRE Corporation under support from the National Science Foundation (Grant No. EIA-0326404).  ...  Acknowledgements We would like to thank the Program Committee for their careful reviewing: Luc Dehaspe, Robert Gaizauskas, William Hersh, Karin Verspoor and Alexander Yeh.  ...  They include invited and contributed papers, with a focus on developing shared infrastructure (tools, corpora, ontologies) and challenge evaluations, in the style of the KDD Challenge Cups [2] .  ... 
doi:10.1002/cfg.455 pmid:18629301 pmcid:PMC2448605 fatcat:lfl62kerhbdvblziets4jxihqa

Overview of the BioCreative III Workshop

Cecilia N Arighi, Zhiyong Lu, Martin Krallinger, Kevin B Cohen, W Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H Wu
2011 BMC Bioinformatics  
The overall goal of the BioCreative Workshops is to promote the development of text mining and text processing tools which are useful to the communities of researchers and database curators in the biological  ...  Results: The BioCreative III Workshop was held in September of 2010 and continued the tradition of a challenge evaluation on several tasks judged basic to effective text mining in biology, including a  ...  This article has been published as part of BMC Bioinformatics Volume 12 Supplement 8, 2011: The Third BioCreative -Critical Assessment of Information Extraction in Biology Challenge.  ... 
doi:10.1186/1471-2105-12-s8-s1 pmid:22151647 pmcid:PMC3269932 fatcat:lp7c4vnknraqrkganmnqt4hfse

Biological applications of multi-relational data mining

David Page, Mark Craven
2003 SIGKDD Explorations  
Biological databases contain a wide variety of data types, often with rich relational structure. Consequently multirelational data mining techniques frequently are applied to biological data.  ...  This paper presents several applications of multi-relational data mining to biological data, taking care to cover a broad range of multi-relational data mining techniques.  ...  The last two KDD Cup competitions have focused on biological databases and, not coincidentally, have highlighted the need for multi-relational data mining tools [9; 11] .  ... 
doi:10.1145/959242.959250 fatcat:kqnuj6o55zhq3fr2jfyyy6u6tm

Evaluation of BioCreAtIvE assessment of task 2

Christian Blaschke, Eduardo Leon, Martin Krallinger, Alfonso Valencia
2005 BMC Bioinformatics  
In order to make text mining tools useable in real world scenarios, for instance to assist database curators during annotation of protein function, comparisons and evaluations of different approaches on  ...  Information relating to functional descriptions is generally extracted manually from textual data and stored in biological databases to build up annotations for large collections of gene products.  ...  In the domain of biomedical literature, the knowledge discovery and data mining (KDD) challenge cup [7] evaluated how text mining tools could aid in the process of database curation, in this case of  ... 
doi:10.1186/1471-2105-6-s1-s16 pmid:15960828 pmcid:PMC1869008 fatcat:2pbvytvsqjcdbivxu7yia6oyue

Rutabaga by any other name: extracting biological names

Lynette Hirschman, Alexander A. Morgan, Alexander S. Yeh
2002 Journal of Biomedical Informatics  
of terms, frequent introduction of new terms, and a mismatch between evaluation tasks as defined for news and real biological problems.  ...  Multiple factors may be involved, including absence of shared training and test sets for rigorous measures of progress, lack of annotated training data specific to biological tasks, pervasive ambiguity  ...  Database curation aids provide a (semi-automated) mapping from literature to database, as evaluated in the recent Challenge Cup Evaluation for Knowledge Discovery and Data Mining Conference 2002 (see http  ... 
doi:10.1016/s1532-0464(03)00014-5 pmid:12755519 fatcat:4w2eigmhuzecvnpe76dj7uu2u4

Evaluation of biomedical text-mining systems: Lessons learned from information retrieval

W. Hersh
2005 Briefings in Bioinformatics  
The developers of text-mining systems need to improve both test collections for system-oriented evaluation and undertake user-oriented evaluations to determine the most effective use of their systems for  ...  Biomedical text-mining systems have great promise for improving the efficiency and productivity of biomedical researchers. However, such systems are still not in routine use.  ...  Acknowledgments This work was supported by grant ITR-0325160 from the National Science Foundation and earlier grants from the National Library of Medicine.  ... 
doi:10.1093/bib/6.4.344 pmid:16420733 fatcat:n7p6o2yhnnbezgf5lrgloljsim

Adversarial Examples in Constrained Domains [article]

Ryan Sheatsley, Nicolas Papernot, Michael Weisman, Gunjan Verma, Patrick McDaniel
2020 arXiv   pre-print
We create an algorithm for generating adversarial sketches: targeted universal perturbation vectors which encode feature saliency within the envelope of domain constraints.  ...  Under the default threat model, the adversary exploits the unconstrained nature of images; each feature (pixel) is fully under control of the adversary.  ...  The MNIST database contains 10 classes, with numerical digits from 0 through 9. It contains 60,000 samples for training and 10,000 samples for testing.  ... 
arXiv:2011.01183v1 fatcat:tdxthy4vfrcqniimnpuvthsmpa

Algorithmic Fairness Datasets: the Story so Far [article]

Alessandro Fabris, Stefano Messina, Gianmaria Silvello, Gian Antonio Susto
2022 arXiv   pre-print
Finally, we analyze these datasets from the perspective of five important data curation topics: anonymization, consent, inclusivity, sensitive attributes, and transparency.  ...  We discuss different approaches and levels of attention to these topics, making them tangible, and distill them into a set of best practices for the curation of novel resources.  ...  Acknowledgements The authors would like to thank the following researchers and dataset creators for the useful feedback on the data briefs: Alain Barrat, Luc Behaghel, Asia Biega, Marko Bohanec, Chris  ... 
arXiv:2202.01711v2 fatcat:5hf4a42pubc5vnt7tw3al4m5bq

Enhancing access to the Bibliome: the TREC 2004 Genomics Track

William R Hersh, Ravi Teja Bhupatiraju, Laura Ross, Phoebe Roberts, Aaron M Cohen, Dale F Kraemer
2006 Journal of Biomedical Discovery and Collaboration  
This paper describes the Genomics Track of the Text Retrieval Conference (TREC) 2004, a forum for evaluation of IR research systems, where retrieval in the genomics domain has recently begun to be assessed  ...  The most effective runs, as measured by the primary evaluation measure of mean average precision (MAP), used a combination of domain-specific and general techniques.  ...  We gratefully acknowledge the help of Ellen Voorhees and NIST in running TREC and the following individuals who interviewed biologists to obtain topics for the ad hoc searching task: Shannon Bradshaw,  ... 
doi:10.1186/1747-5333-1-3 pmid:16722581 pmcid:PMC1440302 fatcat:47rfw3fwafa3nm2huaaxu57de4

Promoting Insight-Based Evaluation of Visualizations: From Contest to Benchmark Repository

C. Plaisant, J.-D. Fekete, G. Grinstein
2008 IEEE Transactions on Visualization and Computer Graphics  
We give a summary of the state of the art of evaluation in information visualization, describe the three contests, summarize their results, discuss outcomes and lessons learned, and conjecture the future  ...  gained while exploring data.  ...  and finally but not least Paolo Buono from the University of Bari, Italy, for participating in the review process.  ... 
doi:10.1109/tvcg.2007.70412 pmid:17993707 fatcat:saiz6tzturakxeufufwjhnhdjm

Leveraging Computational Intelligence Techniques for Defensive Deception: A Review, Recent Advances, Open Problems and Future Directions

Pilla Vaishno Mohan, Shriniket Dixit, Amogh Gyaneshwar, Utkarsh Chadha, Kathiravan Srinivasan, Jung Taek Seo
2022 Sensors  
This survey focuses on Defensive Deception tactics deployed using the help of deep learning and machine learning algorithms.  ...  Defensive Deception tactics are beneficial at introducing uncertainty for adversaries, increasing their learning costs, and, as a result, lowering the likelihood of successful attacks.  ...  The "KDD CUP 1999" dataset revealed that this technique outperforms classic PNN, PCA-PNN, and original DBN-PNN without simplification [1] .  ... 
doi:10.3390/s22062194 pmid:35336373 pmcid:PMC8952217 fatcat:hgtvnjuzxfgudpa76fke433qhy

Evaluation in artificial intelligence: from task-oriented to ability-oriented measurement

José Hernández-Orallo
2016 Artificial Intelligence Review  
The evaluation of artificial intelligence systems and components is crucial for the progress of the discipline.  ...  We analyse some evaluation tests from AI that are better positioned for an ability-oriented evaluation and discuss how their problems and limitations can possibly be addressed with some of the tools and  ...  Acknowledgements I thank the organisers of the AEPIA Summer School On Artificial Intelligence, held in September 2014, for giving me the opportunity to give a lecture on 'AI Evaluation'.  ... 
doi:10.1007/s10462-016-9505-7 fatcat:7ikuoyrubrd2naidtnymj6hxqe

NIH-NSF visualization research challenges report summary

T. Munzner, C. Johnson, R. Moorhead, H. Pfister, P. Rheingans, T.S. Yoo
2006 IEEE Computer Graphics and Applications  
Acknowledgments: We would like to thank all of the panelists for their significant input to this report.  ...  Special thanks to Nathan Galli for the report design and Katharine Coles for her editing assistance.  ...  The rapid and seemingly boundless growth of Google alone is testament to the importance of data mining tools for the public.  ... 
doi:10.1109/mcg.2006.44 pmid:16548457 fatcat:aouq5f5d2rdkvejmewe253sqha
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