- dynamo.tl.DDRTree(X, maxIter, sigma, gamma, eps=0, dim=2, Lambda=1.0, ncenter=None, keep_history=False)
Provides an implementation of the framework of reversed graph embedding (RGE).
This function is a python version of the DDRTree algorithm originally written in R. (https://cran.r-project.org/web/packages/DDRTree/DDRTree.pdf)
ndarray) – the matrix on which DDRTree would be implemented.
int) – the max number of iterations.
float) – the bandwidth parameter.
float) – regularization parameter for k-means.
int) – the threshold of convergency to stop the iteration. Defaults to 0.
int) – the number of dimensions reduced to. Defaults to 2.
float) – regularization parameter for inverse praph embedding. Defaults to 1.0.
bool) – wether to keep relative parameters during each iteration and return. Defaults to False.
- Return type:
A dataframe containing W, Z, Y, stree, R, objs for each iterations if keep_history is True. Otherwise, a tuple (Z, Y, stree, R, W, Q, C, objs). The items in the tuple is from the last iteration. Z is the reduced dimension; Y is the latent points as the center of Z; stree is the smooth tree graph embedded in the low dimension space; R is used to transform the hard assignments used in K-means into soft assignments; W is the orthogonal set of d (dimensions) linear basis; Q is (I + lambda L)^(-1), where L = diag(B1) - B, a Laplacian matrix. C equals to XQ^(-1)X^T; objs is a list containing convergency conditions during the iterations.