Operators
Related Doc:
package manifold
Isometric feature mapping.
Isometric feature mapping. Isomap is a widely used low-dimensional embedding methods, where geodesic distances on a weighted graph are incorporated with the classical multidimensional scaling. Isomap is used for computing a quasi-isometric, low-dimensional embedding of a set of high-dimensional data points. Isomap is highly efficient and generally applicable to a broad range of data sources and dimensionalities.
To be specific, the classical MDS performs low-dimensional embedding based on the pairwise distance between data points, which is generally measured using straight-line Euclidean distance. Isomap is distinguished by its use of the geodesic distance induced by a neighborhood graph embedded in the classical scaling. This is done to incorporate manifold structure in the resulting embedding. Isomap defines the geodesic distance to be the sum of edge weights along the shortest path between two nodes. The top n eigenvectors of the geodesic distance matrix, represent the coordinates in the new n-dimensional Euclidean space.
The connectivity of each data point in the neighborhood graph is defined as its nearest k Euclidean neighbors in the high-dimensional space. This step is vulnerable to "short-circuit errors" if k is too large with respect to the manifold structure or if noise in the data moves the points slightly off the manifold. Even a single short-circuit error can alter many entries in the geodesic distance matrix, which in turn can lead to a drastically different (and incorrect) low-dimensional embedding. Conversely, if k is too small, the neighborhood graph may become too sparse to approximate geodesic paths accurately.
This class implements C-Isomap that involves magnifying the regions of high density and shrink the regions of low density of data points in the manifold. Edge weights that are maximized in Multi-Dimensional Scaling(MDS) are modified, with everything else remaining unaffected.
the data set.
the dimension of the manifold.
k-nearest neighbor.
C-Isomap algorithm if true, otherwise standard algorithm.
Laplacian Eigenmap.
Laplacian Eigenmap. Using the notion of the Laplacian of the nearest neighbor adjacency graph, Laplacian Eigenmap compute a low dimensional representation of the dataset that optimally preserves local neighborhood information in a certain sense. The representation map generated by the algorithm may be viewed as a discrete approximation to a continuous map that naturally arises from the geometry of the manifold.
The locality preserving character of the Laplacian Eigenmap algorithm makes it relatively insensitive to outliers and noise. It is also not prone to "short circuiting" as only the local distances are used.
the data set.
the dimension of the manifold.
k-nearest neighbor.
the smooth/width parameter of heat kernel e-||x-y||2 / t. Non-positive value means discrete weights.
Locally Linear Embedding.
Locally Linear Embedding. It has several advantages over Isomap, including faster optimization when implemented to take advantage of sparse matrix algorithms, and better results with many problems. LLE also begins by finding a set of the nearest neighbors of each point. It then computes a set of weights for each point that best describe the point as a linear combination of its neighbors. Finally, it uses an eigenvector-based optimization technique to find the low-dimensional embedding of points, such that each point is still described with the same linear combination of its neighbors. LLE tends to handle non-uniform sample densities poorly because there is no fixed unit to prevent the weights from drifting as various regions differ in sample densities.
the data set.
the dimension of the manifold.
k-nearest neighbor.
t-distributed stochastic neighbor embedding.
t-distributed stochastic neighbor embedding. t-SNE is a nonlinear dimensionality reduction technique that is particularly well suited for embedding high-dimensional data into a space of two or three dimensions, which can then be visualized in a scatter plot. Specifically, it models each high-dimensional object by a two- or three-dimensional point in such a way that similar objects are modeled by nearby points and dissimilar objects are modeled by distant points.
input data. If X is a square matrix, it is assumed to be the squared distance/dissimilarity matrix.
the dimension of the manifold.
the perplexity of the conditional distribution.
the learning rate.
the number of iterations.
High level manifold learning operators.