Bioinformatics Supplement

Bioinformatics Supplement

Paper:
Topon Kumar Paul and Hitoshi Iba(2005). Extraction of Informatics Genes from Microarray Data. In the Proceedings of the Genetic and Evolutionary Computation Conference 2005 (GECCO2005), Washington DC, USA, pages 453-460. ACM Press.

Experimental Setup:

Population Size=100, Offspring Size=100
Total Run=20 (except single gene case)
Maximum number of generation=100
Weight of accuracy=0.75
Alpha=0.1 (for PBIL, alpha=0.45)
Replacement strategy: CHC
SVM Parameters: C=32, gamma=0.0078125
Termination: No improvement in the fitness of the best individual in 10 consecutive generations or maximum number of generations has passed.

Data Sets Description:

Data Set	#Genes Left after preprocessing	#Classes	#Training Samples	#Test Samples	#Total Samples
Lung Carcinoma	3312	5	50% of total samples	50% of total samples	203
Brain Cancer	4434	2	21(given)	29(given)	50
Prostate Cancer	5966	2	50% of total samples	50% of total samples	102

Preprocessing Method:

Example: Brain cancer data set. For Lung Carcinoma and Prostate Cancer data sets, please read the paper.

Experimental Results:

Detailed experimental results by our method (RPMBGA) and PBIL.

Data Set Name Single Gene
Training and Test Accuracy
Overall accuracy

RPMBGA PBIL

Lung Carcinoma SingleGeneLung TrainTestRPMBGALung TrainTestPBILLung OverallLung

Brain Cancer SingleGeneBrain TrainTestRPMBGABrain TrainTestPBILBrain OverallBrain

Prostate Cancer SingleGeneProstate TrainTestRPMBGAProstate TrainTestPBILProstate OverallProstate

(We suggest the researchers to save a result file as a text file and to open it with Microsoft Excel to manipulate it.)

This webpage has been created by Topon Kumar Paul. If you have any question regarding this paper or results, contact topon@ibalab, iba@ibalab (ibalab=iba.k.u-tokyo.ac.jp) .

Data Set Name	Single Gene	Training and Test Accuracy		Overall accuracy
Data Set Name	Single Gene	RPMBGA	PBIL	Overall accuracy
Lung Carcinoma	SingleGeneLung	TrainTestRPMBGALung	TrainTestPBILLung	OverallLung
Brain Cancer	SingleGeneBrain	TrainTestRPMBGABrain	TrainTestPBILBrain	OverallBrain
Prostate Cancer	SingleGeneProstate	TrainTestRPMBGAProstate	TrainTestPBILProstate	OverallProstate