ICD 9/10 classification

rtrivedi

Has anyone created any pipelines that can accurately return ICD 9 /10 clinical codes from free text, any insights around this topic are much appreciated !!

lionelderkrikor

Hi @rtrivedi,

 

I'm not specialist of medecine, so I went to Internet to understand what is ICD 9 classification.

If I good understand ICD 9 is an expression like abc.d (for example 123.5) or abc.de (for example 425.23) where a,b,c,d,e are numbers, to define a disease, right ?

In this case I propose the following process : 

<?xml version="1.0" encoding="UTF-8"?><process version="9.0.003">
  <context>
    <input/>
    <output/>
    <macros/>
  </context>
  <operator activated="true" class="process" compatibility="9.0.003" expanded="true" name="Process">
    <process expanded="true">
      <operator activated="true" class="text:process_document_from_file" compatibility="8.1.000" expanded="true" height="82" name="Process Documents from Files" width="90" x="179" y="85">
        <list key="text_directories">
          <parameter key="ID9" value="C:\Users\Lionel\Documents\Formations_DataScience\Rapidminer\Tests_Rapidminer\Extract_informations"/>
        </list>
        <parameter key="file_pattern" value="*.pdf"/>
        <process expanded="true">
          <operator activated="true" class="text:tokenize" compatibility="8.1.000" expanded="true" height="68" name="Tokenize" width="90" x="179" y="34">
            <parameter key="mode" value="regular expression"/>
            <parameter key="expression" value="[ ]"/>
          </operator>
          <operator activated="false" class="text:extract_information" compatibility="8.1.000" expanded="true" height="68" name="Extract Information" width="90" x="380" y="34">
            <parameter key="query_type" value="Regular Expression"/>
            <list key="string_machting_queries"/>
            <list key="regular_expression_queries">
              <parameter key="IDx" value="/\[[0-9]+\]/"/>
            </list>
            <list key="regular_region_queries"/>
            <list key="xpath_queries"/>
            <list key="namespaces"/>
            <list key="index_queries"/>
            <list key="jsonpath_queries"/>
          </operator>
          <connect from_port="document" to_op="Tokenize" to_port="document"/>
          <connect from_op="Tokenize" from_port="document" to_port="document 1"/>
          <portSpacing port="source_document" spacing="0"/>
          <portSpacing port="sink_document 1" spacing="0"/>
          <portSpacing port="sink_document 2" spacing="0"/>
        </process>
      </operator>
      <operator activated="true" class="select_attributes" compatibility="9.0.003" expanded="true" height="82" name="Select Attributes" width="90" x="380" y="85">
        <parameter key="attribute_filter_type" value="regular_expression"/>
        <parameter key="regular_expression" value=".*\..*"/>
      </operator>
      <connect from_op="Process Documents from Files" from_port="example set" to_op="Select Attributes" to_port="example set input"/>
      <connect from_op="Select Attributes" from_port="example set output" 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>

To execute this process, you have to : 

 - Set the path where your text file is stored in the parameters of Process Documents from Files operator.

 - Eventually set the file pattern in the parameters of Process Documents from Files operator.

 

Does this process answer to your need ?

If not, can you be more explicit about what you want to do ?

 

Regards,

 

Lionel