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OVA_Breast

OVA_Breast

active ARFF Publicly available Visibility: public Uploaded 07-10-2014 by Joaquin Vanschoren
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Author: Source: Unknown - Date unknown Please cite: GEMLeR provides a collection of gene expression datasets that can be used for benchmarking gene expression oriented machine learning algorithms. They can be used for estimation of different quality metrics (e.g. accuracy, precision, area under ROC curve, etc.) for classification, feature selection or clustering algorithms. This repository was inspired by an increasing need in machine learning / bioinformatics communities for a collection of microarray classification problems that could be used by different researches. This way many different classification or feature selection techniques can finally be compared to eachother on the same set of problems. Origin of data Each gene expression sample in GEMLeR repository comes from a large publicly available expO (Expression Project For Oncology) repository by International Genomics Consortium. The goal of expO and its consortium supporters is to procure tissue samples under standard conditions and perform gene expression analyses on a clinically annotated set of deidentified tumor samples. The tumor data is updated with clinical outcomes and is released into the public domain without intellectual property restriction. The availability of this information translates into direct benefits for patients, researchers and pharma alike. Source: expO website Although there are various other sources of gene expression data available, a decision to use data from expO repository was made because of: - consistency of tissue samples processing procedure - same microarray platform used for all samples - availability of additional information for combined genotype-phenotype studies - availability of a large number of samples for different tumor types In case of publishing material based on GEMLeR datasets, then, please note the assistance you received by using this repository. This will help others to obtain the same datasets and replicate your experiments. Please cite as follows when referring to this repository: Stiglic, G., & Kokol, P. (2010). Stability of Ranked Gene Lists in Large Microarray Analysis Studies. Journal of biomedicine biotechnology, 2010, 616358. You are also welcome to acknowledge the contribution of expO (Expression Project For Oncology) and International Genomics Consortium for providing their gene expression samples to the public.

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0 missing
208794_s_atnumeric1521 unique values
0 missing
209182_s_atnumeric1419 unique values
0 missing
209687_atnumeric1520 unique values
0 missing
210605_s_atnumeric1482 unique values
0 missing
211720_x_atnumeric1542 unique values
0 missing
212232_atnumeric1494 unique values
0 missing
212737_atnumeric1508 unique values
0 missing
213366_x_atnumeric1536 unique values
0 missing
214118_x_atnumeric1482 unique values
0 missing
215416_s_atnumeric1490 unique values
0 missing
217703_x_atnumeric1492 unique values
0 missing
218096_atnumeric1510 unique values
0 missing
218668_s_atnumeric1469 unique values
0 missing
219622_atnumeric1487 unique values
0 missing
221502_atnumeric1507 unique values
0 missing
222433_atnumeric1530 unique values
0 missing
223162_s_atnumeric1494 unique values
0 missing
224415_s_atnumeric1492 unique values
0 missing
224917_atnumeric1540 unique values
0 missing
225364_atnumeric1471 unique values
0 missing
225953_atnumeric1498 unique values
0 missing
226617_atnumeric1472 unique values
0 missing
227449_atnumeric1399 unique values
0 missing
228662_atnumeric1438 unique values
0 missing
230416_atnumeric1480 unique values
0 missing
233899_x_atnumeric1431 unique values
0 missing
238625_atnumeric1314 unique values
0 missing
33322_i_atnumeric1537 unique values
0 missing
1552619_a_atnumeric1448 unique values
0 missing
1564796_atnumeric1381 unique values
0 missing
200727_s_atnumeric1466 unique values
0 missing
201017_atnumeric1499 unique values
0 missing
201346_atnumeric1473 unique values
0 missing
201669_s_atnumeric1535 unique values
0 missing
202053_s_atnumeric1504 unique values
0 missing
202501_atnumeric1493 unique values
0 missing
202939_atnumeric1499 unique values
0 missing
203513_atnumeric1501 unique values
0 missing
Show first 100 features

107 properties

NumberOfInstances
1545
Number of instances (rows) of the dataset.
NumberOfFeatures
10936
Number of attributes (columns) of the dataset.
NumberOfClasses
2
Number of distinct values of the target attribute (if it is nominal).
NumberOfMissingValues
0
Number of missing values in the dataset.
NumberOfInstancesWithMissingValues
0
Number of instances with at least one value missing.
NumberOfNumericFeatures
10935
Number of numeric attributes.
NumberOfSymbolicFeatures
1
Number of nominal attributes.
REPTreeDepth3Kappa
0.81
Kappa coefficient achieved by the landmarker weka.classifiers.trees.REPTree -L 3
DecisionStumpKappa
0.74
Kappa coefficient achieved by the landmarker weka.classifiers.trees.DecisionStump
MaxMeansOfNumericAtts
117603.64
Maximum of means among attributes of the numeric type.
MinMutualInformation
Minimal mutual information between the nominal attributes and the target attribute.
Quartile2SkewnessOfNumericAtts
2.58
Second quartile (Median) of skewness among attributes of the numeric type.
RandomTreeDepth1AUC
0.8
Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.RandomTree -depth 1
Dimensionality
7.08
Number of attributes divided by the number of instances.
MaxMutualInformation
Maximum mutual information between the nominal attributes and the target attribute.
MinNominalAttDistinctValues
2
The minimal number of distinct values among attributes of the nominal type.
PercentageOfBinaryFeatures
0.01
Percentage of binary attributes.
Quartile2StdDevOfNumericAtts
989.49
Second quartile (Median) of standard deviation of attributes of the numeric type.
RandomTreeDepth1ErrRate
0.13
Error rate achieved by the landmarker weka.classifiers.trees.RandomTree -depth 1
EquivalentNumberOfAtts
Number of attributes needed to optimally describe the class (under the assumption of independence among attributes). Equals ClassEntropy divided by MeanMutualInformation.
MaxNominalAttDistinctValues
2
The maximum number of distinct values among attributes of the nominal type.
MinSkewnessOfNumericAtts
-0
Minimum skewness among attributes of the numeric type.
PercentageOfInstancesWithMissingValues
0
Percentage of instances having missing values.
Quartile3AttributeEntropy
Third quartile of entropy among attributes.
RandomTreeDepth1Kappa
0.61
Kappa coefficient achieved by the landmarker weka.classifiers.trees.RandomTree -depth 1
J48.00001.AUC
0.91
Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.J48 -C .00001
MaxSkewnessOfNumericAtts
39.19
Maximum skewness among attributes of the numeric type.
MinStdDevOfNumericAtts
479.93
Minimum standard deviation of attributes of the numeric type.
PercentageOfMissingValues
0
Percentage of missing values.
Quartile3KurtosisOfNumericAtts
38.1
Third quartile of kurtosis among attributes of the numeric type.
AutoCorrelation
0.99
Average class difference between consecutive instances.
RandomTreeDepth2AUC
0.8
Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.RandomTree -depth 2
J48.00001.ErrRate
0.07
Error rate achieved by the landmarker weka.classifiers.trees.J48 -C .00001
MaxStdDevOfNumericAtts
148018.69
Maximum standard deviation of attributes of the numeric type.
MinorityClassPercentage
22.27
Percentage of instances belonging to the least frequent class.
PercentageOfNumericFeatures
99.99
Percentage of numeric attributes.
Quartile3MeansOfNumericAtts
2783.67
Third quartile of means among attributes of the numeric type.
CfsSubsetEval_DecisionStumpAUC
0.86
Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.DecisionStump -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W
RandomTreeDepth2ErrRate
0.13
Error rate achieved by the landmarker weka.classifiers.trees.RandomTree -depth 2
J48.00001.Kappa
0.81
Kappa coefficient achieved by the landmarker weka.classifiers.trees.J48 -C .00001
MeanAttributeEntropy
Average entropy of the attributes.
MinorityClassSize
344
Number of instances belonging to the least frequent class.
PercentageOfSymbolicFeatures
0.01
Percentage of nominal attributes.
Quartile3MutualInformation
Third quartile of mutual information between the nominal attributes and the target attribute.
CfsSubsetEval_DecisionStumpErrRate
0.07
Error rate achieved by the landmarker weka.classifiers.trees.DecisionStump -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W
RandomTreeDepth2Kappa
0.61
Kappa coefficient achieved by the landmarker weka.classifiers.trees.RandomTree -depth 2
J48.0001.AUC
0.91
Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.J48 -C .0001
MeanKurtosisOfNumericAtts
53.91
Mean kurtosis among attributes of the numeric type.
NaiveBayesAUC
0.95
Area Under the ROC Curve achieved by the landmarker weka.classifiers.bayes.NaiveBayes
Quartile1AttributeEntropy
First quartile of entropy among attributes.
Quartile3SkewnessOfNumericAtts
4.67
Third quartile of skewness among attributes of the numeric type.
CfsSubsetEval_DecisionStumpKappa
0.79
Kappa coefficient achieved by the landmarker weka.classifiers.trees.DecisionStump -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W
RandomTreeDepth3AUC
0.8
Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.RandomTree -depth 3
J48.0001.ErrRate
0.07
Error rate achieved by the landmarker weka.classifiers.trees.J48 -C .0001
MeanMeansOfNumericAtts
3374.67
Mean of means among attributes of the numeric type.
NaiveBayesErrRate
0.03
Error rate achieved by the landmarker weka.classifiers.bayes.NaiveBayes
Quartile1KurtosisOfNumericAtts
5.2
First quartile of kurtosis among attributes of the numeric type.
Quartile3StdDevOfNumericAtts
1854.98
Third quartile of standard deviation of attributes of the numeric type.
CfsSubsetEval_NaiveBayesAUC
0.86
Area Under the ROC Curve achieved by the landmarker weka.classifiers.bayes.NaiveBayes -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W
RandomTreeDepth3ErrRate
0.13
Error rate achieved by the landmarker weka.classifiers.trees.RandomTree -depth 3
J48.0001.Kappa
0.81
Kappa coefficient achieved by the landmarker weka.classifiers.trees.J48 -C .0001
MeanMutualInformation
Average mutual information between the nominal attributes and the target attribute.
NaiveBayesKappa
0.91
Kappa coefficient achieved by the landmarker weka.classifiers.bayes.NaiveBayes
Quartile1MeansOfNumericAtts
911.97
First quartile of means among attributes of the numeric type.
REPTreeDepth1AUC
0.92
Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.REPTree -L 1
CfsSubsetEval_NaiveBayesErrRate
0.07
Error rate achieved by the landmarker weka.classifiers.bayes.NaiveBayes -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W
RandomTreeDepth3Kappa
0.61
Kappa coefficient achieved by the landmarker weka.classifiers.trees.RandomTree -depth 3
J48.001.AUC
0.91
Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.J48 -C .001
MeanNoiseToSignalRatio
An estimate of the amount of irrelevant information in the attributes regarding the class. Equals (MeanAttributeEntropy - MeanMutualInformation) divided by MeanMutualInformation.
NumberOfBinaryFeatures
1
Number of binary attributes.
Quartile1MutualInformation
First quartile of mutual information between the nominal attributes and the target attribute.
REPTreeDepth1ErrRate
0.07
Error rate achieved by the landmarker weka.classifiers.trees.REPTree -L 1
CfsSubsetEval_NaiveBayesKappa
0.79
Kappa coefficient achieved by the landmarker weka.classifiers.bayes.NaiveBayes -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W
CfsSubsetEval_kNN1NAUC
0.86
Area Under the ROC Curve achieved by the landmarker weka.classifiers.lazy.IBk -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W
StdvNominalAttDistinctValues
0
Standard deviation of the number of distinct values among attributes of the nominal type.
J48.001.ErrRate
0.07
Error rate achieved by the landmarker weka.classifiers.trees.J48 -C .001
MeanNominalAttDistinctValues
2
Average number of distinct values among the attributes of the nominal type.
Quartile1SkewnessOfNumericAtts
1.63
First quartile of skewness among attributes of the numeric type.
REPTreeDepth1Kappa
0.81
Kappa coefficient achieved by the landmarker weka.classifiers.trees.REPTree -L 1
CfsSubsetEval_kNN1NErrRate
0.07
Error rate achieved by the landmarker weka.classifiers.lazy.IBk -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W
kNN1NAUC
0.89
Area Under the ROC Curve achieved by the landmarker weka.classifiers.lazy.IBk
J48.001.Kappa
0.81
Kappa coefficient achieved by the landmarker weka.classifiers.trees.J48 -C .001
MeanSkewnessOfNumericAtts
4.12
Mean skewness among attributes of the numeric type.
Quartile1StdDevOfNumericAtts
658.37
First quartile of standard deviation of attributes of the numeric type.
REPTreeDepth2AUC
0.92
Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.REPTree -L 2
CfsSubsetEval_kNN1NKappa
0.79
Kappa coefficient achieved by the landmarker weka.classifiers.lazy.IBk -E "weka.attributeSelection.CfsSubsetEval -P 1 -E 1" -S "weka.attributeSelection.BestFirst -D 1 -N 5" -W
kNN1NErrRate
0.08
Error rate achieved by the landmarker weka.classifiers.lazy.IBk
MajorityClassPercentage
77.73
Percentage of instances belonging to the most frequent class.
MeanStdDevOfNumericAtts
2053.18
Mean standard deviation of attributes of the numeric type.
Quartile2AttributeEntropy
Second quartile (Median) of entropy among attributes.
REPTreeDepth2ErrRate
0.07
Error rate achieved by the landmarker weka.classifiers.trees.REPTree -L 2
ClassEntropy
0.76
Entropy of the target attribute values.
kNN1NKappa
0.77
Kappa coefficient achieved by the landmarker weka.classifiers.lazy.IBk
MajorityClassSize
1201
Number of instances belonging to the most frequent class.
MinAttributeEntropy
Minimal entropy among attributes.
Quartile2KurtosisOfNumericAtts
12.58
Second quartile (Median) of kurtosis among attributes of the numeric type.
REPTreeDepth2Kappa
0.81
Kappa coefficient achieved by the landmarker weka.classifiers.trees.REPTree -L 2
REPTreeDepth3AUC
0.92
Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.REPTree -L 3
DecisionStumpAUC
0.89
Area Under the ROC Curve achieved by the landmarker weka.classifiers.trees.DecisionStump
MaxAttributeEntropy
Maximum entropy among attributes.
MinKurtosisOfNumericAtts
-0.85
Minimum kurtosis among attributes of the numeric type.
Quartile2MeansOfNumericAtts
1554.49
Second quartile (Median) of means among attributes of the numeric type.
REPTreeDepth3ErrRate
0.07
Error rate achieved by the landmarker weka.classifiers.trees.REPTree -L 3
DecisionStumpErrRate
0.1
Error rate achieved by the landmarker weka.classifiers.trees.DecisionStump
MaxKurtosisOfNumericAtts
1539
Maximum kurtosis among attributes of the numeric type.
MinMeansOfNumericAtts
42.3
Minimum of means among attributes of the numeric type.
Quartile2MutualInformation
Second quartile (Median) of mutual information between the nominal attributes and the target attribute.
Show all 107 properties

24 tasks

Supervised Classification on OVA_Breast
198 runs - estimation_procedure: 10-fold Crossvalidation - evaluation_measure: predictive_accuracy - target_feature: Tissue
Supervised Classification on OVA_Breast
1 runs - estimation_procedure: 10 times 10-fold Crossvalidation - evaluation_measure: predictive_accuracy - target_feature: Tissue
Supervised Classification on OVA_Breast
0 runs - estimation_procedure: 33% Holdout set - evaluation_measure: predictive_accuracy - target_feature: Tissue
Learning Curve on OVA_Breast
41 runs - estimation_procedure: 10-fold Learning Curve - target_feature: Tissue
Supervised Data Stream Classification on OVA_Breast
0 runs - estimation_procedure: Interleaved Test then Train - target_feature: Tissue
Clustering on OVA_Breast
0 runs - estimation_procedure: 50 times Clustering
Clustering on OVA_Breast
0 runs - estimation_procedure: 50 times Clustering
Clustering on OVA_Breast
0 runs - estimation_procedure: 50 times Clustering
Clustering on OVA_Breast
0 runs - estimation_procedure: 50 times Clustering
Clustering on OVA_Breast
0 runs - estimation_procedure: 50 times Clustering
Clustering on OVA_Breast
0 runs
Clustering on OVA_Breast
0 runs - estimation_procedure: 50 times Clustering
Clustering on OVA_Breast
0 runs - estimation_procedure: 50 times Clustering
Clustering on OVA_Breast
0 runs - estimation_procedure: 50 times Clustering
Clustering on OVA_Breast
0 runs - estimation_procedure: 50 times Clustering
Clustering on OVA_Breast
0 runs - estimation_procedure: 50 times Clustering
Subgroup Discovery on OVA_Breast
1314 runs - target_feature: Tissue
Subgroup Discovery on OVA_Breast
1311 runs - target_feature: Tissue
Subgroup Discovery on OVA_Breast
0 runs - target_feature: Tissue
Subgroup Discovery on OVA_Breast
0 runs - target_feature: Tissue
Subgroup Discovery on OVA_Breast
0 runs - target_feature: Tissue
Subgroup Discovery on OVA_Breast
0 runs - target_feature: Tissue
Subgroup Discovery on OVA_Breast
0 runs - target_feature: Tissue
Subgroup Discovery on OVA_Breast
0 runs - target_feature: Tissue
Define a new task