Just give them as separate strings in the array, instead of combining the last two into "val_31 val_32":

String[] command = {"script.py", "run",
                    "-arg1", "val1", 
                    "-arg2", "val2" ,          
                    "-arg3" , "val_31", "val_32",
       };

Otherwise it will escape the space in between val_31 and val_32 because you are telling it that they're a single parameter. Incidentally, you can also use the varargs constructor and skip having to create an array, if you want:

ProcessBuilder probuilder = new ProcessBuilder( "script.py", "run",
                    "-arg1", "val1", 
                    "-arg2", "val2" ,          
                    "-arg3" , "val_31", "val_32");

Usually when executing commands using ProcessBuilder, PATH variable is not taken into consideration. Your python C:/Machine_Learning/Text_Analysis/Ontology_based.py is directly working in your CMD shell because it can locate the python executable using the PATH variable. Please provide the absolute path to python command in your Java code. In below code replace <Absolute Path to Python> with the path to python command and its libraries. Usually it will something like C:\Python27\python in Windows by default

package text_clustering;

import java.io.*;

public class Similarity {

    /**
     * 
     * @param args
     * 
     */
    public static void main(String[] args){
        try{
            String pythonPath = "C:/Machine_Learning/Text_Analysis/Ontology_based.py";
            //String pythonExe = "C:/Users/AppData/Local/Continuum/Anaconda/python.exe";
            ProcessBuilder pb = new ProcessBuilder(Arrays.asList("<Absolute Path to Python>/python", pythonPath));
            Process p = pb.start();

            BufferedReader bfr = new BufferedReader(new InputStreamReader(p.getInputStream()));
            String line = "";
            System.out.println("Running Python starts: " + line);
            int exitCode = p.waitFor();
            System.out.println("Exit Code : "+exitCode);
            line = bfr.readLine();
            System.out.println("First Line: " + line);
            while ((line = bfr.readLine()) != null){
                System.out.println("Python Output: " + line);


            }

        }catch(Exception e){System.out.println(e);}
    }

}

I don't think reading the executable (a series of binary numbers) will do any good. Also, The class java.lang.ProcessBuilder, in Java 1.5, is used to create operating system processe. Instead you should use the jython API: http://www.jython.org/javadoc/org/python/util/PythonInterpreter.html

Particularly: PyInstance and PythonInterpreter;

I haven't found a solution yet, however I've implemented workaround/cleaner solution. I've decided to separate totally java and python code and created microservice for data retrieving. I use flask for rest webservice (followed this tutorial https://docs.dataplicity.com/docs/control-gpios-using-rest-api) and call it directly from java.
Since this does not resolve my initial question I do not mark it as an answer, however it might help someone.