bootstrapping_validation and W-PLSClassifier

sinae

Hi

There were problems in the development of the model.
process faild : matrix is singular
help.....

<operator activated="true" class="process" compatibility="5.2.008" expanded="true" name="Process">
    <process expanded="true" height="650" width="1090">
      <operator activated="true" class="retrieve" compatibility="5.2.008" expanded="true" height="60" name="Retrieve (3)" width="90" x="45" y="30">
        <parameter key="repository_entry" value="MSN2AR/filter_BasicTSAR_MSN2AR_descriptor"/>
      </operator>
      <operator activated="true" class="parallel:optimize_selection_parallel" compatibility="5.1.000" expanded="true" height="94" name="Optimize Selection (2)" width="90" x="246" y="30">
        <parameter key="generations_without_improval" value="2"/>
        <parameter key="limit_number_of_generations" value="true"/>
        <parameter key="keep_best" value="2"/>
        <parameter key="maximum_number_of_generations" value="5"/>
        <parameter key="user_result_individual_selection" value="true"/>
        <parameter key="number_of_threads" value="8"/>
        <process expanded="true" height="650" width="858">
          <operator activated="true" class="bootstrapping_validation" compatibility="5.2.008" expanded="true" height="112" name="Validation (2)" width="90" x="313" y="165">
            <parameter key="use_local_random_seed" value="true"/>
            <process expanded="true" height="668" width="404">
              <operator activated="true" class="weka:W-PLSClassifier" compatibility="5.1.001" expanded="true" height="76" name="W-PLSClassifier (2)" width="90" x="179" y="30">
                <parameter key="filter" value="weka.filters.supervised.attribute.PLSFilter  -C 8  -A PLS1 -P standardize"/>
                <parameter key="D" value="true"/>
              </operator>
              <connect from_port="training" to_op="W-PLSClassifier (2)" to_port="training set"/>
              <connect from_op="W-PLSClassifier (2)" from_port="model" to_port="model"/>
              <connect from_op="W-PLSClassifier (2)" from_port="exampleSet" to_port="through 1"/>
              <portSpacing port="source_training" spacing="0"/>
              <portSpacing port="sink_model" spacing="0"/>
              <portSpacing port="sink_through 1" spacing="0"/>
              <portSpacing port="sink_through 2" spacing="0"/>
            </process>
            <process expanded="true" height="668" width="404">
              <operator activated="true" class="apply_model" compatibility="5.2.008" expanded="true" height="76" name="Apply Model (2)" width="90" x="45" y="30">
                <list key="application_parameters"/>
              </operator>
              <operator activated="true" class="performance_regression" compatibility="5.2.008" expanded="true" height="76" name="Performance (2)" width="90" x="224" y="30">
                <parameter key="main_criterion" value="root_mean_squared_error"/>
                <parameter key="absolute_error" value="true"/>
                <parameter key="squared_correlation" value="true"/>
              </operator>
              <connect from_port="model" to_op="Apply Model (2)" to_port="model"/>
              <connect from_port="test set" to_op="Apply Model (2)" to_port="unlabelled data"/>
              <connect from_op="Apply Model (2)" from_port="labelled data" to_op="Performance (2)" to_port="labelled data"/>
              <connect from_op="Performance (2)" from_port="performance" to_port="averagable 1"/>
              <portSpacing port="source_model" spacing="0"/>
              <portSpacing port="source_test set" spacing="0"/>
              <portSpacing port="source_through 1" spacing="0"/>
              <portSpacing port="source_through 2" spacing="0"/>
              <portSpacing port="sink_averagable 1" spacing="0"/>
              <portSpacing port="sink_averagable 2" spacing="0"/>
            </process>
          </operator>
          <connect from_port="example set" to_op="Validation (2)" to_port="training"/>
          <connect from_op="Validation (2)" from_port="averagable 1" to_port="performance"/>
          <portSpacing port="source_example set" spacing="0"/>
          <portSpacing port="source_through 1" spacing="0"/>
          <portSpacing port="sink_performance" spacing="0"/>
        </process>
      </operator>
      <operator activated="true" class="weka:W-PLSClassifier" compatibility="5.1.001" expanded="true" height="76" name="W-PLSClassifier" width="90" x="447" y="30">
        <parameter key="filter" value="weka.filters.supervised.attribute.PLSFilter  -C 8  -A PLS 1 -P standardize"/>
        <parameter key="D" value="true"/>
      </operator>
      <operator activated="true" class="apply_model" compatibility="5.2.008" expanded="true" height="76" name="Apply Model" width="90" x="581" y="30">
        <list key="application_parameters"/>
      </operator>
      <operator activated="true" class="performance_regression" compatibility="5.2.008" expanded="true" height="76" name="Performance" width="90" x="715" y="30">
        <parameter key="main_criterion" value="root_mean_squared_error"/>
        <parameter key="absolute_error" value="true"/>
        <parameter key="squared_correlation" value="true"/>
      </operator>
      <connect from_op="Retrieve (3)" from_port="output" to_op="Optimize Selection (2)" to_port="example set in"/>
      <connect from_op="Optimize Selection (2)" from_port="example set out" to_op="W-PLSClassifier" to_port="training set"/>
      <connect from_op="W-PLSClassifier" from_port="model" to_op="Apply Model" to_port="model"/>
      <connect from_op="W-PLSClassifier" from_port="exampleSet" to_op="Apply Model" to_port="unlabelled data"/>
      <connect from_op="Apply Model" from_port="labelled data" to_op="Performance" to_port="labelled data"/>
      <connect from_op="Performance" from_port="performance" to_port="result 1"/>
      <portSpacing port="source_input 1" spacing="0"/>
      <portSpacing port="sink_result 1" spacing="0"/>
      <portSpacing port="sink_result 2" spacing="0"/>

MariusHelf

Hi,

please post the complete process xml using the steps described in the post which is linked in my signature.

Best,
Marius

sinae

Marius wrote:
Hi, please post the complete process xml using the steps described in the post which is linked in my signature. Best, Marius

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<process version="5.2.008">
  <context>
    <input/>
    <output/>
    <macros/>
  </context>
  <operator activated="true" class="process" compatibility="5.2.008" expanded="true" name="Process">
    <process expanded="true" height="650" width="1090">
      <operator activated="true" class="retrieve" compatibility="5.2.008" expanded="true" height="60" name="Retrieve (3)" width="90" x="45" y="30">
        <parameter key="repository_entry" value="MSN2AR/filter_BasicTSAR_MSN2AR_descriptor"/>
      </operator>
      <operator activated="true" class="parallel:optimize_selection_parallel" compatibility="5.1.000" expanded="true" height="94" name="Optimize Selection (2)" width="90" x="246" y="30">
        <parameter key="generations_without_improval" value="2"/>
        <parameter key="limit_number_of_generations" value="true"/>
        <parameter key="keep_best" value="2"/>
        <parameter key="maximum_number_of_generations" value="5"/>
        <parameter key="user_result_individual_selection" value="true"/>
        <parameter key="number_of_threads" value="8"/>
        <process expanded="true" height="650" width="858">
          <operator activated="true" class="bootstrapping_validation" compatibility="5.2.008" expanded="true" height="112" name="Validation (2)" width="90" x="313" y="165">
            <parameter key="use_local_random_seed" value="true"/>
            <process expanded="true" height="668" width="404">
              <operator activated="true" class="weka:W-PLSClassifier" compatibility="5.1.001" expanded="true" height="76" name="W-PLSClassifier (2)" width="90" x="179" y="30">
                <parameter key="filter" value="weka.filters.supervised.attribute.PLSFilter  -C 8  -A PLS1 -P standardize"/>
                <parameter key="D" value="true"/>
              </operator>
              <connect from_port="training" to_op="W-PLSClassifier (2)" to_port="training set"/>
              <connect from_op="W-PLSClassifier (2)" from_port="model" to_port="model"/>
              <connect from_op="W-PLSClassifier (2)" from_port="exampleSet" to_port="through 1"/>
              <portSpacing port="source_training" spacing="0"/>
              <portSpacing port="sink_model" spacing="0"/>
              <portSpacing port="sink_through 1" spacing="0"/>
              <portSpacing port="sink_through 2" spacing="0"/>
            </process>
            <process expanded="true" height="668" width="404">
              <operator activated="true" class="apply_model" compatibility="5.2.008" expanded="true" height="76" name="Apply Model (2)" width="90" x="45" y="30">
                <list key="application_parameters"/>
              </operator>
              <operator activated="true" class="performance_regression" compatibility="5.2.008" expanded="true" height="76" name="Performance (2)" width="90" x="224" y="30">
                <parameter key="main_criterion" value="root_mean_squared_error"/>
                <parameter key="absolute_error" value="true"/>
                <parameter key="squared_correlation" value="true"/>
              </operator>
              <connect from_port="model" to_op="Apply Model (2)" to_port="model"/>
              <connect from_port="test set" to_op="Apply Model (2)" to_port="unlabelled data"/>
              <connect from_op="Apply Model (2)" from_port="labelled data" to_op="Performance (2)" to_port="labelled data"/>
              <connect from_op="Performance (2)" from_port="performance" to_port="averagable 1"/>
              <portSpacing port="source_model" spacing="0"/>
              <portSpacing port="source_test set" spacing="0"/>
              <portSpacing port="source_through 1" spacing="0"/>
              <portSpacing port="source_through 2" spacing="0"/>
              <portSpacing port="sink_averagable 1" spacing="0"/>
              <portSpacing port="sink_averagable 2" spacing="0"/>
            </process>
          </operator>
          <connect from_port="example set" to_op="Validation (2)" to_port="training"/>
          <connect from_op="Validation (2)" from_port="averagable 1" to_port="performance"/>
          <portSpacing port="source_example set" spacing="0"/>
          <portSpacing port="source_through 1" spacing="0"/>
          <portSpacing port="sink_performance" spacing="0"/>
        </process>
      </operator>
      <operator activated="true" class="weka:W-PLSClassifier" compatibility="5.1.001" expanded="true" height="76" name="W-PLSClassifier" width="90" x="447" y="30">
        <parameter key="filter" value="weka.filters.supervised.attribute.PLSFilter  -C 8  -A PLS 1 -P standardize"/>
        <parameter key="D" value="true"/>
      </operator>
      <operator activated="true" class="apply_model" compatibility="5.2.008" expanded="true" height="76" name="Apply Model" width="90" x="581" y="30">
        <list key="application_parameters"/>
      </operator>
      <operator activated="true" class="performance_regression" compatibility="5.2.008" expanded="true" height="76" name="Performance" width="90" x="715" y="30">
        <parameter key="main_criterion" value="root_mean_squared_error"/>
        <parameter key="absolute_error" value="true"/>
        <parameter key="squared_correlation" value="true"/>
      </operator>
      <connect from_op="Retrieve (3)" from_port="output" to_op="Optimize Selection (2)" to_port="example set in"/>
      <connect from_op="Optimize Selection (2)" from_port="example set out" to_op="W-PLSClassifier" to_port="training set"/>
      <connect from_op="W-PLSClassifier" from_port="model" to_op="Apply Model" to_port="model"/>
      <connect from_op="W-PLSClassifier" from_port="exampleSet" to_op="Apply Model" to_port="unlabelled data"/>
      <connect from_op="Apply Model" from_port="labelled data" to_op="Performance" to_port="labelled data"/>
      <connect from_op="Performance" from_port="performance" to_port="result 1"/>
      <portSpacing port="source_input 1" spacing="0"/>
      <portSpacing port="sink_result 1" spacing="0"/>
      <portSpacing port="sink_result 2" spacing="0"/>
    </process>
  </operator>
</process>

thank you.

MariusHelf

Hm, the process setup looks fine. Does the error occur every time you run the process? Where exactly does it occur? Do you have a longer error message? If you get a message dialog which allows you to send a bug report, please do it - it will help us greatly to find the cause of the problem.

One remark on your process: after the feature selection, you create the model on the training data, but you also apply it and evaluate the performance on the training data - instead you should use a X-Validation here.

Best,
Marius