Documentation of 'jsat.datatransform.visualization.Isomap' Java class
Isomap
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jsat.datatransform.visualization

Class Isomap

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, VisualizationTransform

    public class Isomap
extends java.lang.Object
implements VisualizationTransform
    Isomap is an extension of MDS. It uses a geodesic distance made from a nearest neighbor search of all the points in the data set. This implementation also includes the extension C-Isomap, which further weights distances by density.

    Note, that Isomap normally will fail on some datasets when two or more regions can not be connected in the induced neighbor graph. While increasing the number of neighbors considered will eventually resolve this problem, the separated groups may be desirable in practice. This implementation includes a non-standard addition that will forcibly connect such isolated regions with very large values, hoping to preserve the farther distances in the given dataset while maintaining local structure.

    See:
    • Tenenbaum, J. B., Silva, V. De, & Langford, J. C. (2000). A Global Geometric Framework for Nonlinear Dimensionality Reduction. Science, 290, 2319–2323. doi:10.1126/science.290.5500.2319
    • De Silva, V., & Tenenbaum, J. B. (2003). Global Versus Local Methods in Nonlinear Dimensionality Reduction. In Advances in Neural Information Processing Systems 15 (pp. 705–712). MIT Press. Retrieved from here
    See Also:
    Serialized Form

    • Constructor Summary

      Constructors 
      Constructor and Description
      Isomap() 
      Isomap(int searchNeighbors) 
      Isomap(int searchNeighbors, boolean c_isomap) 

    • Constructor Detail

      • Isomap

        public Isomap()

      • Isomap

        public Isomap(int searchNeighbors)
        Parameters:
        searchNeighbors - the number of nearest neighbors to consider

      • Isomap

        public Isomap(int searchNeighbors,
              boolean c_isomap)
        Parameters:
        searchNeighbors - the number of nearest neighbors to consider
        c_isomap - true to use the C-Isomap extension, false for normal Isomap.

    • Method Detail

      • setNeighbors

        public void setNeighbors(int searchNeighbors)
        Set the number of neighbors to consider for the initial graph in Isomap
        Parameters:
        searchNeighbors - the number of nearest neighbors to consider

      • getNeighbors

        public int getNeighbors()
        Returns:
        the number of neighbors used when creating the initial graph

      • setCIsomap

        public void setCIsomap(boolean c_isomap)
        Controls whether the C-Isomap extension is used. If set true, the initial distances will also be scaled based on the density of the region between the points. If false, normal Isomap will be used.
        Parameters:
        c_isomap - true to use the C-Isomap extension, false for normal Isomap.

      • isCIsomap

        public boolean isCIsomap()
        Returns:
        true if the C-Isomap extension is in use, false for normal Isomap.

      • transform

        public <Type extends DataSet> Type transform(DataSet<Type> d,
                                             boolean parallel)
        Description copied from interface: VisualizationTransform
        Transforms the given data set, returning a dataset of the same type.
        Specified by:
        transform in interface VisualizationTransform
        Type Parameters:
        Type - the dataset type
        Parameters:
        d - the data set to transform
        parallel - true if transform should be done in parallel, or false if it should use a single thread.
        Returns:
        the lower dimension dataset for visualization.

      • setTargetDimension

        public boolean setTargetDimension(int target)
        Description copied from interface: VisualizationTransform
        Sets the target dimension to embed new dataset to. Many visualization methods may only support a target of 2 or 3 dimensions, or only one of those options. For that reason a boolean value will be returned indicating if the target size was acceptable. If not, no change to the object will occur.
        Specified by:
        setTargetDimension in interface VisualizationTransform
        Parameters:
        target - the new target dimension size when VisualizationTransform.transform(jsat.DataSet) is called.
        Returns:
        true if this transform supports that dimension and it was set, false if the target dimension is unsupported and the previous value will be used instead.
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