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Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup
[article]
2003
arXiv
pre-print
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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: asy@mitre.org 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
2003
Bioinformatics
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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
2005
Comparative and Functional Genomics
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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
2011
BMC Bioinformatics
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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
2003
SIGKDD Explorations
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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
2005
BMC Bioinformatics
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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
2002
Journal of Biomedical Informatics
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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
2005
Briefings in Bioinformatics
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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]
2020
arXiv
pre-print
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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]
2022
arXiv
pre-print
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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
2006
Journal of Biomedical Discovery and Collaboration
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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
2008
IEEE Transactions on Visualization and Computer Graphics
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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
2022
Sensors
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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
2016
Artificial Intelligence Review
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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
2006
IEEE Computer Graphics and Applications
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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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