isoak1example.java

a molecular graph kernel based on iterative graph similarity and optimal assignments

/**
 * ISOAK - Iterative similarity optimal assignment kernel.
 * 
 * Written by Matthias Rupp 2006-2007.
 * Copyright (c) 2006-2007, Matthias Rupp, Ewgenij Proschak, Gisbert Schneider.
 * 
 * All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without modification,
 * are permitted provided that the following conditions are met:
 * 
 *  * The above copyright notice, this permission notice and the following disclaimers
 *    shall be included in all copies or substantial portions of this software.
 *  * The names of the authors may not be used to endorse or promote products
 *    derived from this software without specific prior written permission.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 * 
 * Please cite
 * 
 * Matthias Rupp, Ewgenij Proschak, Gisbert Schneider:
 * A Kernel Approach to Molecular Similarity Based on Iterative Graph Similarity,
 * Journal of Chemical Information and Molecular Modeling, 47(6): 2280-2286, 2007, 
 * DOI http://dx.doi.org/10.1021/ci700274r.
 *
 * if you use this software.
 * 
 * Thanks to Samuel Wieczorek for reporting a locale related bug in parsing floating point numbers.
 */

package info.mrupp.isoak1;

import java.util.ArrayList;
import java.util.List;
import static java.lang.System.out;
import static java.lang.System.err;

/**
 * Sample program demonstrating the usage of the {@link IsoaKernel1 IsoaKernel1} class.
 * 
 * Run this class with the file 'example.sdf' in the current directory. 
 *
 */

public class Isoak1Example {
    static private void prettyPrintMatrix(Array2Float m, float prec) {
        // Determine number of digits to print.
        final int postdigits = (int) Math.round(Math.abs(Math.log10(prec)));
        int predigits = 0; for (int i = 0; i < m.elems(); ++i) predigits = Math.max(predigits, (int)Math.ceil(Math.log10(m.get(i))));
        final int totaldigits = predigits + 1 + postdigits;
        
        // Print table.
        for (int row = 0; row < m.rows(); ++row) {
            for (int col = 0; col < m.cols(); ++col) {
                out.printf(String.format("%%%d.%df ",totaldigits,postdigits), m.get(row,col) );
            }
            out.println();
        }
        out.println();
    }
    
    static private void prettyPrintAtomAssignment(int[] a) {
        StringBuilder s1 = new StringBuilder();
        StringBuilder s2 = new StringBuilder();
        for (int i = 0; i < a.length; ++i) {
            final int digits = (int) Math.ceil(Math.log10(Math.max(i+1, a[i]+1)));
            s1.append(String.format(String.format("%%%dd ", digits), i));
            s2.append(String.format(String.format("%%%dd ", digits), a[i]));
        }
        out.printf("%s\n%s\n\n", s1, s2);
    }

    static private void doKernelMatrixExperiment(List<MolecularGraph> moldb, IsoaKernel1 isoaKernel, boolean normalized, IVertexEdgeKernel vkernel, IVertexEdgeKernel ekernel, float alpha, float prec) {
        final int numMolecules = moldb.size();
        Array2Float kernelMatrix = new Array2Float(numMolecules, numMolecules);
        out.printf("Kernel matrix (%s values, vertex kernel = %s, edge kernel = %s, alpha = %f, precision = %f):\n\n",
                normalized ? "normalized" : "raw", vkernel.name(), ekernel.name(), alpha, prec);
        isoaKernel.setVertexKernel(vkernel);
        isoaKernel.setEdgeKernel(ekernel);
        for (int row = 0; row < numMolecules; ++row) {
            for (int col = row; col < numMolecules; ++col) {
                final float entry = normalized ?
                        isoaKernel.evalNorm(moldb.get(row), moldb.get(col), alpha, prec, null, null)
                        : isoaKernel.evalRaw(moldb.get(row), moldb.get(col), alpha, prec, null, null);
                kernelMatrix.set(row, col, entry);
                kernelMatrix.set(col, row, entry);  // Exploit symmetry of kernel.
            }
        }
        prettyPrintMatrix(kernelMatrix, prec);
        out.println();        
    }
    
    /** Just run the {@link #main #main} method of this class. */
    public Isoak1Example() {}
    
    /** Run this class with the file 'example.sdf' in the current directory. */
    public static void main(String[] args) {
        // Check input arguments & initialize.
        String filename = "example.sdf";
        IsoaKernel1 isoaKernel = new IsoaKernel1();

        // Load sdf file into memory.
        out.printf("Loading file '%s'... ", filename);
        List<MolecularGraph> moldb = new ArrayList<MolecularGraph>();
        try {
            java.io.LineNumberReader sdfReader = 
                new java.io.LineNumberReader(
                new java.io.InputStreamReader(
                new java.io.FileInputStream(
                new java.io.File(filename))));
            while (sdfReader.ready()) { moldb.add(new MolecularGraph(sdfReader, MolecularGraph.FileFormat.MDL_MOL)); }
            sdfReader.close();
        } catch (java.io.FileNotFoundException e) {
            err.printf("The file '%s' could not be found.", e.getMessage());
            return;     
        } catch (java.io.IOException e) {
            err.printf("An error occurred while loading file '%s': '%s'.", filename, e.getMessage());
            return;
        } catch (java.text.ParseException e) {
            err.printf("An error occurred while parsing file '%s': '%s'.", filename, e.getMessage());
            return;
        }
        out.printf("Done\n\n");

        // Do experiments.
        final float alpha1 = 0.875f;
        final float prec1 = 0.001f;
        final IVertexEdgeKernel vkernel1 = VertexEdgeKernel.NONE.create(null);
        final IVertexEdgeKernel ekernel1 = VertexEdgeKernel.NONE.create(null);
        float[] args1 = {0.f, 0.f};
        float[] args2 = {1.f, 0.f};

        // Compute some kernel matrices.
        doKernelMatrixExperiment(moldb, isoaKernel, false, VertexEdgeKernel.NONE.create(null), VertexEdgeKernel.NONE.create(null), alpha1, prec1);
        doKernelMatrixExperiment(moldb, isoaKernel, true, VertexEdgeKernel.NONE.create(null), VertexEdgeKernel.NONE.create(null), alpha1, prec1);
        doKernelMatrixExperiment(moldb, isoaKernel, true, VertexEdgeKernel.DIRACV.create(args1), VertexEdgeKernel.DIRACE.create(args1), alpha1, prec1);
        doKernelMatrixExperiment(moldb, isoaKernel, true, VertexEdgeKernel.DIRACV.create(args2), VertexEdgeKernel.NONE.create(null), alpha1, prec1);
       
        // Compute assignment details for one molecule pair.
        final MolecularGraph molA = moldb.get(3);
        final MolecularGraph molB = moldb.get(2);
        int[] assignment1 = new int[Math.min(molA.numAtoms(), molB.numAtoms())];
        Array2Float atomMatrix1 = new Array2Float(molA.numAtoms(), molB.numAtoms());
        out.printf("Atom assignment and atom similarities (%s vs. %s, normalized values, vertex kernel = %s, edge kernel = %s, alpha = %f, precision = %f):\n\n",
            molA.name(), molB.name(), vkernel1.name(), ekernel1.name(), alpha1, prec1);
        isoaKernel.setVertexKernel(vkernel1);
        isoaKernel.setEdgeKernel(ekernel1);
        isoaKernel.evalNorm(molA, molB, alpha1, prec1, assignment1, atomMatrix1);
        out.printf("Atom assignments:\n\n"); prettyPrintAtomAssignment(assignment1);
        out.printf("Atom similarities:\n\n"); prettyPrintMatrix(atomMatrix1, prec1);
        
        out.println("Done.");
    }
}