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Adam Woznica

Feature selection with background knowledge (1)

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Sample workflow that exploits background knowledge in the form of links connecting attributes in the different measurement data. The input data is assumed to be labeled and consists of different interconnected biological levels. Additionally a number of files defining links between attributes in the different measurement data are provided. This data was used in the KUP data mining challenge (http://tunedit.org/challenge/ON). Here we focus on two biological levels: protein data measured by ...

Created: 2011-05-25 | Last updated: 2011-05-25

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Adam Woznica

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Input data and background knowledge used in the KUP ...

Created: 2011-05-25 16:39:48

Credits: Adam Woznica

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Compressed RM repository directory containing input data and background knowledge used in the KUP data mining challenge (http://tunedit.org/challenge/ON)

File type: ZIP archive

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Adam Woznica

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Plots fibrosis data (R script)

Created: 2011-05-23 13:02:34 | Last updated: 2011-05-24 20:27:58

Credits: Adam Woznica

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Plots a (modified) heatmap of the fibrosis gene data describing different genes used in various studies on fibrosis. The input dataset is prepared in the "prepare-fibrosis-data" RM workflow. Possible values in the input data are: 1 (a gene is Up regulated), -1 (Down regulated), 0 (Unmodified) and -2 (missing value). It requires the "gplots" R package.

File type: Trident (Package)

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Adam Woznica

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Plots an attribute similarity matrix on gene data (R...

Created: 2011-05-23 13:01:44 | Last updated: 2011-05-25 15:46:10

Credits: Adam Woznica

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Plots an attribute similarity matrix computed from the provided data frame. The input dataset is prepared in the "prepare-gene-correlation" RM workflow and is assumed to contain genes as rows, and gene functions and locations as columns. In the visualized matrix columns correspond to gene locations and rows correspond to gene functions. The supported types of attribute similarities are: the covariance, the Hamming distance, and a modified Hamming distance that focuses on columns wit...

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Adam Woznica

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R library

Created: 2011-05-23 12:50:59 | Last updated: 2011-05-24 20:27:32

Credits: Adam Woznica

License: Creative Commons Attribution-Share Alike 3.0 Unported License

R library used by other R scripts.

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Adam Woznica

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RM repository directory containing data

Created: 2011-05-23 12:49:04 | Last updated: 2011-05-24 20:26:36

Credits: Adam Woznica

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Compressed directory from RM repository containing data used by the different workflows and R scirpts.

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RapidMiner

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Adam Woznica

Frequent Itemset and association rules ana... (1)

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Generates frequent itemsets and association rules from the gene data. Frequent itemsets correspond to different gene characteristics (locations and functions) that frequently occur together across different genes. The quality of a frequent itemset is given by its support which is the fraction of genes for which a given combination of gene characteristics hold; the longer the itemset the lower its support. Based on the frequent itemset this WF also generates association rules which have some...