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Old 10-08-2014, 02:27 AM   #1
ROSSY THOE
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Location: Bogor

Join Date: Oct 2014
Posts: 1
Default feature selection for metagenomic binning

Dear all. I need some help for doing my research in metagenomic binning. Since Bioinformatics is still new in my country, I take this topic for my research. My topic is "Feature selection with Particle Swarm Optimization for metagenome fragment classification ". I use SVM as classifier.

The main goal of my research is to reduce computation needed for classification using k-mers frequency by selecting only a few feature will be used for classification, as we know that high accuracy will be obtained with longer length k (ex: 20-mers), but the number of features wil be huge, it will be (4 power 20 = 1.099.511.627.776 features extracted ) when we use 20-mers. So I will try to use PSO for feature selection.

But I haven't get idea how to
1. Represent the features of DNA dataset to particle in PSO. As the real atribute value of DNA features are in k-mers form (ex: AAA, AAC, AAT,AAG, GTG,...).
2. How to initialize the number of particles, and to compute and updating the position and velocity.

please give me any idea. thank you very much
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computational biology, feature, metagenomic analysis

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