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);}
    }

}

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");

You can check the ProcessBuilder documentation over at Sunoracle, but basically, you can run the interpreter for the scripting language and pass the script you want to run to it.

For example, let's say you have a script in /home/myuser/py_script.py, and python is in /usr/bin/

class ProcessRunner
{
    public static void main(String [] args)
    {
        ProcessBuilder pb = new ProcessBuilder("/usr/bin/python", "/home/myuser/py_script.py");
        Process p = pb.start();
    }
}

An extremely basic example, you can get fancier with changing the working directory and change the environment.

You can also construct ProcessBuilder with a String array or a subtype of List<String>. The first item in the list should be the program/executable you want to run, and all the following items are arguments to the program.

String pbCommand[] = { "/usr/bin/python", "/home/myuser/py_script.py" };
ProcessBuilder pb = new ProcessBuilder(pbCommand);
Process p = pb.start();

Pass two separate arguments to ProcessBuilder instead of concatenating --arg1 and argumentValue:

ProcessBuilder builder = new ProcessBuilder("C:\\Python33\\python.exe",
                                            "-u",
                                            "C:\\...\\script.py,
                                            "--arg1",
                                            "argumentValue");

Otherwise the program to be executed will see a single argument --arg1 argumentValue that it does not recognise.

You can use like this also:

String command = "python /c start python path\to\script\script.py";
Process p = Runtime.getRuntime().exec(command + param );

or

String prg = "import sys";
BufferedWriter out = new BufferedWriter(new FileWriter("path/a.py"));
out.write(prg);
out.close();
Process p = Runtime.getRuntime().exec("python path/a.py");
BufferedReader in = new BufferedReader(new InputStreamReader(p.getInputStream()));
String ret = in.readLine();
System.out.println("value is : "+ret);

Run Python script from Java