A Python wrapper of the dimensionality reduction algorithm Neighbor Retrieval Visualizer (NeRV)
Set up the paths in Makefile then make.
import numpy as np
import matplotlib.pyplot as plt
from nerv import NeRV
data = np.genfromtxt('dredviz-1.0.2/spheredata.dat', skip_header=1)
color = np.genfromtxt('dredviz-1.0.2/spheredata.col', skip_header=1)
nerv_obj = NeRV(random_state=0)
nerv_obj.fit(data)
print('Final cost = %g' % nerv_obj.cost_)
plt.scatter(*nerv_obj.embedding_.T, c=color)
plt.show()
which shows (right)
@article{venna2010information,
title={Information retrieval perspective to nonlinear dimensionality reduction for data visualization},
author={Venna, Jarkko and Peltonen, Jaakko and Nybo, Kristian and Aidos, Helena and Kaski, Samuel},
journal={Journal of Machine Learning Research},
volume={11},
number={Feb},
pages={451--490},
year={2010}
}