imbalanced data

hi

how can I solve imbalanced problem?

I used adaboostm1 weka, but it doesn't work at all,
1. I used sampling method to balance data and performance developed but as far as I know it should be by far better methods to solve imbalanced problem.
2. Moreover, libsvm can be used in weighted mode, but I do not know how use it and tune libsvm parameters like cost weight ,....
and how it can be used in metacost?

I'd appreciate if you help me

Regards
REZA

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land

Hi Reza,
just put the LibSVM learner inside the MetaCost learner. The metaCost learner is a so called Meta Learner using another, inner learning scheme.
This time you could have simply read the manual. This is why haddock repeats it so many times. And although this IS a help forum, other people have to spend their time for giving you hints. So I think it's fair that you made your best efforts to cope with the problem yourself. And this always should include the (admittedly spare) documentation.

Greetings,
Sebastian

m_r_nour

Hi

thanks Sebastian

my code is :

<operator name="Root" class="Process" expanded="yes">
    <operator name="CSVExampleSource" class="CSVExampleSource">
        <parameter key="filename"	value="data_ver5_all.csv"/>
        <parameter key="label_name"	value="CellCycle"/>
    </operator>
    <operator name="ExampleFilter" class="ExampleFilter" breakpoints="after">
        <parameter key="condition_class"	value="attribute_value_filter"/>
        <parameter key="parameter_string"	value="label=anaA||label=anaB||label=prometa"/>
    </operator>
    <operator name="Normalization" class="Normalization">
    </operator>
    <operator name="Random Optimizer" class="RandomOptimizer" expanded="yes">
        <parameter key="iterations"	value="100"/>
        <operator name="Xvalidation" class="XValidation" expanded="yes">
            <parameter key="keep_example_set"	value="true"/>
            <parameter key="create_complete_model"	value="true"/>
            <operator name="MetaCost" class="MetaCost" expanded="yes">
                <parameter key="keep_example_set"	value="true"/>
                <parameter key="cost_matrix"	value="[0.0 3.0 1.0;1.0 0.0 1.0;1.0 1.0 0.0]"/>
                <operator name="LibSVMLearner" class="LibSVMLearner">
                    <list key="class_weights">
                    </list>
                </operator>
            </operator>
            <operator name="OperatorChain (2)" class="OperatorChain" expanded="yes">
                <operator name="ModelApplier (2)" class="ModelApplier">
                    <parameter key="keep_model"	value="true"/>
                    <list key="application_parameters">
                    </list>
                    <parameter key="create_view"	value="true"/>
                </operator>
                <operator name="Performance (2)" class="Performance">
                    <parameter key="keep_example_set"	value="true"/>
                </operator>
            </operator>
        </operator>
        <operator name="AverageBuilder" class="AverageBuilder">
        </operator>
        <operator name="Performance (3)" class="Performance">
            <parameter key="keep_example_set"	value="true"/>
        </operator>
        <operator name="ProcessLog" class="ProcessLog">
            <parameter key="filename"	value="output_%{a}.log"/>
            <list key="log">
              <parameter key="File"	value="operator.CSVExampleSource.parameter.filename"/>
              <parameter key="Learner"	value="operator.Classifier.parameter.select_which"/>
              <parameter key="Performance"	value="operator.Xvalidation.value.performance"/>
              <parameter key="Deviation"	value="operator.Xvalidation.value.deviation"/>
              <parameter key="Feature Selection On|Off"	value="operator.FS SAM.parameter.enable"/>
              <parameter key="Pro_meta merging"	value="operator.Class merging.parameter.enable"/>
            </list>
            <parameter key="sorting_dimension"	value="3"/>
        </operator>
    </operator>
</operator>

but it halts by "process failed " massage and I donot know why

I'd appreciate if help me about this matter

Regards
REZA

haddock

<operator name="Root" class="Process" expanded="yes">
    <operator name="CSVExampleSource" class="CSVExampleSource" activated="no">
        <parameter key="filename"	value="data_ver5_all.csv"/>
        <parameter key="label_name"	value="CellCycle"/>
    </operator>
    <operator name="ExampleFilter" class="ExampleFilter" breakpoints="after" activated="no">
        <description text="This will not work - we've alreeady discussed why - wake up"/>
        <parameter key="condition_class"	value="attribute_value_filter"/>
        <parameter key="parameter_string"	value="label=anaA||label=anaB||label=prometa"/>
    </operator>
    <operator name="ExampleSetGenerator" class="ExampleSetGenerator">
        <parameter key="target_function"	value="simple non linear classification"/>
    </operator>
    <operator name="Normalization" class="Normalization">
    </operator>
    <operator name="Random Optimizer" class="RandomOptimizer" expanded="yes">
        <parameter key="iterations"	value="10"/>
        <operator name="Xvalidation" class="XValidation" expanded="yes">
            <parameter key="keep_example_set"	value="true"/>
            <parameter key="create_complete_model"	value="true"/>
            <operator name="MetaCost" class="MetaCost" expanded="yes">
                <parameter key="keep_example_set"	value="true"/>
                <parameter key="cost_matrix"	value="[0.0 3.0 1.0;1.0 0.0 1.0;1.0 1.0 0.0]"/>
                <operator name="LibSVMLearner" class="LibSVMLearner">
                    <list key="class_weights">
                    </list>
                </operator>
            </operator>
            <operator name="OperatorChain (2)" class="OperatorChain" expanded="yes">
                <operator name="ModelApplier (2)" class="ModelApplier">
                    <parameter key="keep_model"	value="true"/>
                    <list key="application_parameters">
                    </list>
                    <parameter key="create_view"	value="true"/>
                </operator>
                <operator name="Performance (2)" class="Performance">
                    <parameter key="keep_example_set"	value="true"/>
                </operator>
            </operator>
        </operator>
        <operator name="AverageBuilder" class="AverageBuilder" activated="no">
        </operator>
        <operator name="Performance (3)" class="Performance" activated="no">
            <description text="Why on earth is this here? Disable it."/>
            <parameter key="keep_example_set"	value="true"/>
        </operator>
        <operator name="ProcessLog" class="ProcessLog">
            <parameter key="filename"	value="output_%{a}.log"/>
            <list key="log">
              <parameter key="File"	value="operator.CSVExampleSource.parameter.filename"/>
              <parameter key="Performance"	value="operator.Xvalidation.value.performance"/>
              <parameter key="Deviation"	value="operator.Xvalidation.value.deviation"/>
            </list>
            <parameter key="sorting_dimension"	value="3"/>
        </operator>
    </operator>
</operator>

m_r_nour

hi

but it doesn't work, it seems you just disabled averagebuilder and performance of it, I do it in my data, but again process failed message . however thanks for your time and consideration

<operator name="Root" class="Process" expanded="yes">
    <operator name="CSVExampleSource" class="CSVExampleSource">
        <parameter key="filename"	value="I:\WORK\ver5\RM\DATA\data_ver5_all.csv"/>
        <parameter key="label_name"	value="CellCycle"/>
    </operator>
    <operator name="ExampleFilter" class="ExampleFilter">
        <description text="This will not work - we've alreeady discussed why - wake up"/>
        <parameter key="condition_class"	value="attribute_value_filter"/>
        <parameter key="parameter_string"	value="label=anaA||label=anaB||label=prometa"/>
    </operator>
    <operator name="Normalization" class="Normalization">
    </operator>
    <operator name="Random Optimizer" class="RandomOptimizer" expanded="yes">
        <parameter key="iterations"	value="10"/>
        <operator name="Xvalidation" class="XValidation" expanded="yes">
            <parameter key="keep_example_set"	value="true"/>
            <parameter key="create_complete_model"	value="true"/>
            <operator name="MetaCost" class="MetaCost" expanded="yes">
                <parameter key="keep_example_set"	value="true"/>
                <parameter key="cost_matrix"	value="[0.0 3.0 1.0;1.0 0.0 1.0;1.0 1.0 0.0]"/>
                <operator name="LibSVMLearner" class="LibSVMLearner">
                    <list key="class_weights">
                    </list>
                </operator>
            </operator>
            <operator name="OperatorChain (2)" class="OperatorChain" expanded="yes">
                <operator name="ModelApplier (2)" class="ModelApplier">
                    <parameter key="keep_model"	value="true"/>
                    <list key="application_parameters">
                    </list>
                    <parameter key="create_view"	value="true"/>
                </operator>
                <operator name="Performance (2)" class="Performance">
                    <parameter key="keep_example_set"	value="true"/>
                </operator>
            </operator>
        </operator>
        <operator name="ProcessLog" class="ProcessLog">
            <parameter key="filename"	value="output_%{a}.log"/>
            <list key="log">
              <parameter key="File"	value="operator.CSVExampleSource.parameter.filename"/>
              <parameter key="Performance"	value="operator.Xvalidation.value.performance"/>
              <parameter key="Deviation"	value="operator.Xvalidation.value.deviation"/>
            </list>
            <parameter key="sorting_dimension"	value="3"/>
        </operator>
    </operator>
</operator>

haddock

It really helps if you include the error message. This code works on generated examples on my machine right now. I disabled the average builder and final performance operator because that was causing the failure on the original code, as detailed in your original post.

m_r_nour

G Nov 28, 2009 5:50:44 PM: [Fatal] ArrayIndexOutOfBoundsException occured in 1st application of ModelApplier (2) (ModelApplier)
G Nov 28, 2009 5:50:44 PM: [Fatal] Process failed: operator cannot be executed (3). Check the log messages...
Root[1] (Process)
+- CSVExampleSource[1] (CSVExampleSource)
+- ExampleFilter[1] (ExampleFilter)
+- Normalization[1] (Normalization)
+- Random Optimizer[1] (RandomOptimizer)
+- Xvalidation[1] (XValidation)
| +- MetaCost[1] (MetaCost)
| | +- LibSVMLearner[10] (LibSVMLearner)
| +- OperatorChain (2)[1] (OperatorChain)
here ==> | +- ModelApplier (2)[1] (ModelApplier)
| +- Performance (2)[0] (Performance)
+- ProcessLog[0] (ProcessLog)

haddock

Must be the data then, as the generator version works. My guess is that your filter doesn't work as you think, because you use '||' where you should use '|'.

m_r_nour

Hi Haddock

no, even I changed the code to as you think, but again same problem

but:

number of classes are 7 and by filter I reduced them to 3, but classifier apply to data as if it has 7 group because when I changed size of matrix 7
it works.?

so.... how can ....?

thanks for your time

regards
REZA