File: RTModel_3_parameters.ini

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<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS>

  <NODE name="RTModel">
    <NODE name="1">
      <ITEM name="in" value="input.IdXML" type="string"/>
      <ITEM name="out" value="svm.model" type="string"/>
      <ITEM name="total_gradient_time" value="1" type="float"/>
      <ITEM name="number_of_partitions" value="5" type="int"/>
      <ITEM name="number_of_runs" value="1" type="int"/>
      <ITEM name="border_length" value="22" type="int"/>
      <ITEM name="k_mer_length" value="1" type="int"/>
      <ITEM name="additive_cv" value="false" type="string"/>
      <!-- SVM type can be NU_SVR or EPSILON_SVR. -->
      <ITEM name="svm_type" value="NU_SVR" type="string"/>
      <ITEM name="kernel_type" value="OLIGO" type="string"/>
      <!-- The penalty parameter for generalisation. -->
      <ITEM name="c" value="0.001953125" type="float"/>
      <ITEM name="c_start" value="0.001953125" type="float"/>
      <ITEM name="c_step_size" value="2" type="float"/>
      <ITEM name="c_stop" value="0.001953125" type="float"/>
      <!-- The nu parameter in NU_SVR. -->
      <ITEM name="nu" value="0.5" type="float"/>
      <ITEM name="nu_start" value="0.4" type="float"/>
      <ITEM name="nu_step_size" value="1.2" type="float"/>
      <ITEM name="nu_stop" value="0.4" type="float"/>
      <!-- The sigma parameter for the oligo kernel-->
      <ITEM name="sigma" value="1" type="float"/>
      <ITEM name="sigma_start" value="5" type="float"/>
      <ITEM name="sigma_step_size" value="1.221055" type="float"/>
      <ITEM name="sigma_stop" value="5" type="float"/>
    </NODE>
  </NODE>

</PARAMETERS>