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biojava-protein-disorder from group org.biojava (version 7.1.3)

This module is for predicting disordered regions in protein sequences

Group: org.biojava Artifact: biojava-protein-disorder
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Download biojava-protein-disorder.jar (7.1.3)
 

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Artifact biojava-protein-disorder
Group org.biojava
Version 7.1.3
Last update 06. September 2024
Organization not specified
URL Not specified
License GNU LGPL v2
Dependencies amount 6
Dependencies biojava-core, slf4j-api, log4j-slf4j-impl, log4j-api, log4j-core, jaxb-api,
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gridSearch from group nz.ac.waikato.cms.weka (version 1.0.12)

Performs a grid search of parameter pairs for the a classifier (Y-axis, default is LinearRegression with the "Ridge" parameter) and the PLSFilter (X-axis, "# of Components") and chooses the best pair found for the actual predicting. The initial grid is worked on with 2-fold CV to determine the values of the parameter pairs for the selected type of evaluation (e.g., accuracy). The best point in the grid is then taken and a 10-fold CV is performed with the adjacent parameter pairs. If a better pair is found, then this will act as new center and another 10-fold CV will be performed (kind of hill-climbing). This process is repeated until no better pair is found or the best pair is on the border of the grid. In case the best pair is on the border, one can let GridSearch automatically extend the grid and continue the search. Check out the properties 'gridIsExtendable' (option '-extend-grid') and 'maxGridExtensions' (option '-max-grid-extensions <num>'). GridSearch can handle doubles, integers (values are just cast to int) and booleans (0 is false, otherwise true). float, char and long are supported as well. The best filter/classifier setup can be accessed after the buildClassifier call via the getBestFilter/getBestClassifier methods. Note on the implementation: after the data has been passed through the filter, a default NumericCleaner filter is applied to the data in order to avoid numbers that are getting too small and might produce NaNs in other schemes.

Group: nz.ac.waikato.cms.weka Artifact: gridSearch
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Download gridSearch.jar (1.0.12)
 

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Artifact gridSearch
Group nz.ac.waikato.cms.weka
Version 1.0.12
Last update 30. October 2018
Organization University of Waikato, Hamilton, NZ
URL http://weka.sourceforge.net/doc.packages/gridSearch
License GNU General Public License 3
Dependencies amount 2
Dependencies weka-dev, partialLeastSquares,
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