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BioWeka
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Martin Szugat
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Introduction and overview for the BioWeka project
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BioWeka
1.
BioWeka Extending the
Weka framework for Bioinformatics Martin Szugat ( [email_address] ) http:// www.bioweka.org
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3.
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Knowledge Discovery Process
Data Selection and Preparation Transformation and Reduction Data Mining Evaluation and Visualization
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Knowledge Discovery Experiment
Data Selection and Preparation Transformation and Reduction Data Mining Evaluation and Visualization
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Intermediate data format
Format A Tool X Tool Y Tool Z Format C Format B Mediator
10.
Unified interfaces Loader
Data Classifier Filter 1 … Filter n FastaLoader CSVLoader … SymbolCounter SymbolAnalyzer … Alignment SVM … Extendable and Customizable Execution Pipeline
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Weka Explorer
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Weka Experimenter
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Implementation Patterns
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Training Eclat Sequences
Codon frequencies Norm- alization SVM Frames Factors 1 Model 1 Codon frequencies Norm- alization SVM Factors 2 Model 2
27.
Evaluating Eclat Sequence
Frames Norm- alization SVM Factors 2 Model 2 Codon frequencies Norm- alization SVM Factors 1 Model 1 Correct Frame
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EclatClassifier/Filter Filtered Classifier
SMO Random Forest Naive Bayes JRip J4.8 Multiple Filter Translate Terminator Symbol Counter Sum Normalizer Remove/ Copy Normalize MinMax Normalizer newMin = -1.0 newMax = 1.0 pseudoCount = 1.0 alphabet = DNA symbolWidth = 3.0
29.
Classifier Comparison 1)
LibSVM vs. SMO 10 x Sampling with Stratification (2:1) 10 x 3-fold CV 0.7 1.1 0.7 0.7 0.2 Deviation 81.5 (1.3) 84.8 (1.1) 87.1 (1.0) 88.2 (1.0) 93.1 (0.7) BioWeka 82.2 (1.6) 85.9 (1.8) 87.8 (0.9) 88.9 (1.0) 92.9 (0.6) Eclat J4.8 JRip Naïve Bayes Random Forest SVM 1 Accuracy [%] (SD)
30.
EclatFrameFinder/Classifier EclatFrame Classifier
EclatFrame Finder EclatFrame Shifter Frame Shifter Eclat Classifier
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32.
Eclat Eclat EclatFrame
Finder Eclat Classifier
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