cnnregressionmodel.java

化学图形处理软件

package org.openscience.cdk.qsar.model.R2;

import org.openscience.cdk.qsar.model.QSARModelException;
import org.openscience.cdk.tools.LoggingTool;
import org.rosuda.JRI.RBool;
import org.rosuda.JRI.REXP;
import org.rosuda.JRI.RList;

import java.io.File;
import java.util.HashMap;

/**
 * A modeling class that provides a computational neural network regression model.
 * <p/>
 * When instantiated this class ensures that the R/Java interface has been
 * initialized. The response and independent variables can be specified at construction
 * time or via the <code>setParameters</code> method.
 * The actual fitting procedure is carried out by <code>build</code> after which
 * the model may be used to make predictions, via <code>predict</code>. An example of the use
 * of this class is shown below:
 * <pre>
 * double[][] x;
 * double[] y;
 * Double[] wts;
 * Double[][] newx;
 * ...
 * try {
 *     CNNRegressionModel cnnrm = new CNNRegressionModel(x,y,3);
 *     cnnrm.setParameters("Wts",wts);
 *     cnnrm.build();
 * <p/>
 *     double fitValue = cnnrm.getFitValue();
 * <p/>
 *     cnnrm.setParameters("newdata", newx);
 *     cnnrm.setParameters("type", "raw");
 *     cnnrm.predict();
 * <p/>
 *     double[][] preds = cnnrm.getPredictPredicted();
 * } catch (QSARModelException qme) {
 *     System.out.println(qme.toString());
 * }
 * </pre>
 * The above code snippet builds a 3-3-1 CNN model.
 * Multiple output neurons are easily
 * specified by supplying a matrix for y (i.e., double[][]) with the output variables
 * in the columns.
 * <p/>
 * Nearly all the arguments to
 * <a href="http://www.maths.lth.se/help/R/.R/library/nnet/html/nnet.html" target="_top">nnet()</a> are
 * supported via the <code>setParameters</code> method. The table below lists the names of the arguments,
 * the expected type of the argument and the default setting for the arguments supported by this wrapper class.
 * <center>
 * <table border=1 cellpadding=5>
 * <THEAD>
 * <tr>
 * <th>Name</th><th>Java Type</th><th>Default</th><th>Notes</th>
 * </tr>
 * </thead>
 * <tbody>
 * <tr><td>x</td><td>Double[][]</td><td>None</td><td>This must be set by the caller via the constructors or via <code>setParameters</code></td></tr>
 * <tr><td>y</td><td>Double[][]</td><td>None</td><td>This must be set by the caller via the constructors or via <code>setParameters</code></td></tr>
 * <tr><td>weights</td><td>Double[]</td><td>rep(1,nobs)</td><td>The default case weights is a vector of 1's equal in length to the number of observations, nobs</td></tr>
 * <tr><td>size</td><td>Integer</td><td>None</td><td>This must be set by the caller via the constructors or via <code>setParameters</code></td></tr>
 * <tr><td>subset</td><td>Integer[]</td><td>1:nobs</td><td>This is supposed to be an index vector specifying which observations are to be used in building the model. The default indicates that all should be used</td></tr>
 * <tr><td>Wts</td><td>Double[]</td><td>runif(1,nwt)</td><td>The initial weight vector is set to a random vector of length equal to the number of weights if not set by the user</td></tr>
 * <tr><td>mask</td><td>Boolean[]</td><td>rep(TRUE,nwt)</td><td>All weights are to be optimized unless otherwise specified by the user</td></tr>
 * <tr><td>linout</td><td>Boolean</td><td>TRUE</td><td>Since this class performs regression this need not be changed</td></tr>
 * <tr><td>entropy</td><td>Boolean</td><td>FALSE</td><td></td></tr>
 * <tr><td>softmax</td><td>Boolean</td><td>FALSE</td><td></td></tr>
 * <tr><td>censored</td><td>Boolean</td><td>FALSE</td><td></td></tr>
 * <tr><td>skip</td><td>Boolean</td><td>FALSE</td><td></td></tr>
 * <tr><td>rang</td><td>Double</td><td>0.7</td><td></td></tr>
 * <tr><td>decay</td><td>Double</td><td>0.0</td><td></td></tr>
 * <tr><td>maxit</td><td>Integer</td><td>100</td><td></td></tr>
 * <tr><td>Hess</td><td>Boolean</td><td>FALSE</td><td></td></tr>
 * <tr><td>trace</td><td>Boolean</td><td>TRUE</td><td></td></tr>
 * <tr><td>MaxNWts</td><td>Integer</td><td>1000</td><td></td></tr>
 * <tr><td>abstol</td><td>Double</td><td>1.0e-4</td><td></td></tr>
 * <tr><td>reltol</td><td>Double</td><td>1.0e-8</td><td></td></tr>
 * </tbody>
 * </table>
 * </center>
 * <p/>
 * The values returned correspond to the various
 * values returned by the <a href="http://www.maths.lth.se/help/R/.R/library/nnet/html/nnet.html" target="_top">nnet</a> and
 * <a href="http://www.maths.lth.se/help/R/.R/library/nnet/html/predict.nnet.html" target="_top">predict.nnet</a> functions
 * in R
 * <p/>
 * See {@link org.openscience.cdk.qsar.model.R.RModel} for details regarding the R and Java environment.
 *
 * @author      Rajarshi Guha
 * @cdk.require r-project
 * @cdk.require java1.5+
 * @cdk.module  qsar
 * @cdk.keyword neural network
 * @cdk.keyword R
 */

public class CNNRegressionModel extends RModel {
    public static int globalID = 0;
    private int noutput = 0;
    private int nvar = 0;

    private double[][] modelPredict = null;

    private static LoggingTool logger;

    private void setDefaults() {
        // lets set the default values of the arguments that are specified
        // to have default values in ?nnet

        // these params are vectors that depend on user defined stuff
        // so as a default we set them to FALSE so R can check if these
        // were not set
        this.params.put("subset", Boolean.FALSE);
        this.params.put("mask", Boolean.FALSE);
        this.params.put("Wts", Boolean.FALSE);
        this.params.put("weights", Boolean.FALSE);

        this.params.put("linout", Boolean.TRUE); // we want only regression
        this.params.put("entropy", Boolean.FALSE);
        this.params.put("softmax", Boolean.FALSE);
        this.params.put("censored", Boolean.FALSE);
        this.params.put("skip", Boolean.FALSE);
        this.params.put("rang", new Double(0.7));
        this.params.put("decay", new Double(0.0));
        this.params.put("maxit", new Integer(100));
        this.params.put("Hess", Boolean.FALSE);
        this.params.put("trace", Boolean.FALSE); // no need to see output
        this.params.put("MaxNWts", new Integer(1000));
        this.params.put("abstol", new Double(1.0e-4));
        this.params.put("reltol", new Double(1.0e-8));
    }

    /**
     * Constructs a CNNRegressionModel object.
     * <p/>
     * This constructor allows the user to simply set up an instance of a CNN
     * regression modeling class. This constructor simply sets the name for this
     * instance. It is expected all the relevent parameters for modeling will be
     * set at a later point.
     * <p/>
     * Other parameters that are required to be set should be done via
     * calls to <code>setParameters</code>. A number of parameters are set to the
     * defaults as specified in the manpage for
     * <a href="http://www.maths.lth.se/help/R/.R/library/nnet/html/nnet.html" target="_top">nnet</a>.
     */
    public CNNRegressionModel() throws QSARModelException {
        super();
        logger = new LoggingTool(this);

        params = new HashMap();
        int currentID = CNNRegressionModel.globalID;
        CNNRegressionModel.globalID++;
        setModelName("cdkCNNModel" + currentID);
        setDefaults();


    }


    /**
     * Constructs a CNNRegressionModel object.
     * <p/>
     * This constructor allows the user to specify the dependent and
     * independent variables along with the number of hidden layer neurons.
     * This constructor is suitable for cases when there is a single output
     * neuron. If the number of rows of the design matrix is not equal to
     * the number of observations in y an exception will be thrown.
     * <p/>
     * Other parameters that are required to be set should be done via
     * calls to <code>setParameters</code>. A number of parameters are set to the
     * defaults as specified in the manpage for
     * <a href="http://www.maths.lth.se/help/R/.R/library/nnet/html/nnet.html" target="_top">nnet</a>.
     *
     * @param x    An array of independent variables. Observations should be in
     *             the rows and variables in the columns.
     * @param y    An array (single column) of observed values
     * @param size The number of hidden layer neurons
     * @throws QSARModelException if the number of observations in x and y do not match
     */
    public CNNRegressionModel(double[][] x, double[] y, int size) throws QSARModelException {
        super();
        logger = new LoggingTool(this);

        params = new HashMap();
        int currentID = CNNRegressionModel.globalID;
        CNNRegressionModel.globalID++;
        setModelName("cdkCNNModel" + currentID);

        int nrow = y.length;
        int ncol = x[0].length;

        if (nrow != x.length) {
            throw new QSARModelException("The number of values for the dependent variable does not match the number of rows of the design matrix");
        }

        nvar = ncol;
        noutput = 1;

        Double[][] xx = new Double[nrow][ncol];
        Double[][] yy = new Double[nrow][1];

        for (int i = 0; i < nrow; i++) {
            yy[i][0] = new Double(y[i]);
            for (int j = 0; j < ncol; j++) {
                xx[i][j] = new Double(x[i][j]);
            }
        }
        params.put("x", xx);
        params.put("y", yy);
        params.put("size", new Integer(size));
        setDefaults();
    }

    /**
     * Constructs a CNNRegressionModel object.
     * <p/>
     * This constructor allows the user to specify the dependent and
     * independent variables along with the number of hidden layer neurons.
     * This constructor is suitable for cases when there are multiple output
     * neuron. If the number of rows of the design matrix is not equal to
     * the number of observations in y an exception will be thrown.
     * <p/>
     * Other parameters that are required to be set should be done via
     * calls to <code>setParameters</code>. A number of parameters are set to the
     * defaults as specified in the manpage for
     * <a href="http://www.maths.lth.se/help/R/.R/library/nnet/html/nnet.html" target="_top">nnet</a>.
     *
     * @param x    An array of independent variables. Observations should be in
     *             the rows and variables in the columns.
     * @param y    An array (multiple columns) of observed values
     * @param size The number of hidden layer neurons
     * @throws QSARModelException if the number of observations in x and y do not match
     */
    public CNNRegressionModel(double[][] x, double[][] y, int size) throws QSARModelException {
        super();
        logger = new LoggingTool(this);

        params = new HashMap();
        int currentID = CNNRegressionModel.globalID;
        CNNRegressionModel.globalID++;
        setModelName("cdkCNNModel" + currentID);

        int nrow = y.length;
        int ncol = x[0].length;

        if (nrow != x.length) {
            throw new QSARModelException("The number of values for the dependent variable does not match the number of rows of the design matrix");
        }

        nvar = ncol;
        noutput = y[0].length;

        Double[][] xx = new Double[nrow][ncol];
        Double[][] yy = new Double[nrow][noutput];

        for (int i = 0; i < nrow; i++) {
            for (int j = 0; j < ncol; j++) {
                xx[i][j] = new Double(x[i][j]);
            }
        }
        for (int i = 0; i < nrow; i++) {
            for (int j = 0; j < noutput; j++) {
                yy[i][j] = new Double(y[i][j]);
            }
        }
        params.put("x", xx);
        params.put("y", yy);
        params.put("size", new Integer(size));
        setDefaults();
    }


    /**
     * Sets parameters required for building a CNN model or using one for prediction.
     * <p/>
     * This function allows the caller to set the various parameters available
     * for the
     * <a href="http://www.maths.lth.se/help/R/.R/library/nnet/html/nnet.html" target="_top">nnet</a>
     * and
     * <a href="http://www.maths.lth.se/help/R/.R/library/nnet/html/predict.nnet.html" target="_top">predict.nnet</a>
     * R routines. See the R help pages for the details of the available
     * parameters.
     *
     * @param key A String containing the name of the parameter as described in the
     *            R help pages
     * @param obj An Object containing the value of the parameter
     * @throws QSARModelException if the type of the supplied value does not match the
     *                            expected type
     */
    public void setParameters(String key, Object obj) throws QSARModelException {
        // since we know the possible values of key we should check the coresponding
        // objects and throw errors if required. Note that this checking can't really check
        // for values (such as number of variables in the X matrix to build the model and the
        // X matrix to make new predictions) - these should be checked in functions that will
        // use these parameters. The main checking done here is for the class of obj and
        // some cases where the value of obj is not dependent on what is set before it

        if (key.equals("y")) {
            if (!(obj instanceof Double[][])) {
                throw new QSARModelException("The class of the 'y' object must be Double[][]");
            } else {
                noutput = ((Double[][]) obj)[0].length;
            }
        }
        if (key.equals("x")) {
            if (!(obj instanceof Double[][])) {
                throw new QSARModelException("The class of the 'x' object must be Double[][]");
            } else {
                nvar = ((Double[][]) obj)[0].length;
            }
        }
        if (key.equals("weights")) {
            if (!(obj instanceof Double[])) {
                throw new QSARModelException("The class of the 'weights' object must be Double[]");
            }
        }
        if (key.equals("size")) {
            if (!(obj instanceof Integer)) {
                throw new QSARModelException("The class of the 'size' object must be Integer");
            }
        }
        if (key.equals("subset")) {
            if (!(obj instanceof Integer[])) {
                throw new QSARModelException("The class of the 'size' object must be Integer[]");
            }