_PROBLEM CoEPrA-2006_Classification_004

_GROUP_NAME Reiji Teramoto

_GROUP_MEMBERS
Reiji Teramoto

_ADDRESS
Fundamental and Environmental Research Laboratories
NEC Corporatopn

_MODELING_PROCEDURE
  We used marginalized count kernels for amino acid
sequences to generate
  new descriptors and suppor vector machines as
classifier.[1,2].
  To select descriptors and calibrate model, we performed
10-fold 
  cross-validation via tuning types of marginalized count
kernel,  
  gaussian kernel parameter g and coefficient of slack
variables C using 
  the calibration dataset with setting class +1 to weight 5.
  We examined 6 types of marginalized count kernel as
follows:
  1. 1st-order maginalized count kernel with hidden markov
models that hidden states is 3(abbreviation MCK1(h=3)).
  2. 2nd-order maginalized count kernel with hidden markov
models that hidden states is 3(abbreviation MCK2(h=3)).
  3. 1st-order maginalized count kernel with hidden markov
models that hidden states is 3(abbreviation MCK1(h=4)).
  4. 2nd-order maginalized count kernel with hidden markov
models that hidden states is 4(abbreviation MCK2(h=4)).
  5. 1st-order maginalized count kernel with hidden markov
models that hidden states is 5(abbreviation MCK1(h=5)).
  6. 2nd-order maginalized count kernel with hidden markov
models that hidden states is 5(abbreviation MCK2(h=5)).

  We examined gaussian kernel parameter g defined as
follows:
  K(u,v) = exp(-g*|u-v|^2)

  We determined the final model based on the performance
of 10-fold cross-validation as follows:
 MCK1(h=5): c=32.0, g=8.0, accuracy=73.8739%.

1. Tsuda K, Kin T, Asai K., Marginalized kernels for
biological sequences, Bioinformatics. 2002;18 Suppl
1:S268-75. 
2. Vapnik V, The Nature of Statistical Learning Theory,
Springer, 1999.

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