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Nonlinear
Dimensionality
Reduction
Presented by Dragana Veljkovic
Overview
Curse-of-dimensionality
 Dimension reduction techniques
 Isomap
 Locally linear embedding (LLE)
 Problems and improvements
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Problem description
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Large amount of data being collected leads to
creation of very large databases
Most problems in data mining involve data with a
large number of measurements (or dimensions)
E.g. Protein matching, fingerprint recognition,
meteorological predictions, satellite image
repositories
Reducing dimensions increases capability of
extracting knowledge
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Problem definition
Original high dimensional data:
X = (x1, …, xn) where xi=(xi1,…,xip)T
 underlying low dimensional data:
Y = (y1, …, yn) where yi=(yi1,…,yiq)T and q<<p
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Assume X forms a smooth low dimensional manifold in
high dimensional space
Find the mapping that captures the important features
Determine q that can best describe the data
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Different approaches
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Local or Shape preserving
Global or Topology preserving
Local embeddings
Local – simplify representation of each object
regardless of the rest of the data
 Features
selected retain most of the information
 Fourier decomposition, wavelet decomposition,
piecewise constant approximation, etc.
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Global or Topology preserving
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Mostly used for visualization and
classification
 PCA or
KL decomposition
 MDS
 SVD
 ICA
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Local embeddings (LE)
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Overlapping local neighborhoods, collectively
analyzed, can provide information on global
geometry
LE preserves the local neighborhood of each
object
preserving the global distances through the nonneighboring objects
Isomap and LLE
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Another classification
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Linear and Non Linear methods
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Neighborhood
Two ways to select neighboring objects:
nearest neighbors (k-NN) – can make nonuniform neighbor distance across the dataset
 ε-ball – prior knowledge of the data is needed
to make reasonable neighborhoods; size of
neighborhood can vary
k
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Isomap – general idea
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Only geodesic distances reflect the true low dimensional
geometry of the manifold
MDS and PCA see only Euclidian distances and there for
fail to detect intrinsic low-dimensional structure
Geodesic distances are hard to compute even if you
know the manifold
In a small neighborhood Euclidian distance is a good
approximation of the geodesic distance
For faraway points, geodesic distance is approximated
by adding up a sequence of “short hops” between
neighboring points
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Isomap algorithm
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Find neighborhood of each object by computing
distances between all pairs of points and
selecting closest
Build a graph with a node for each object and an
edge between neighboring points. Euclidian
distance between two objects is used as edge
weight
Use a shortest path graph algorithm to fill in
distance between all non-neighboring points
Apply classical MDS on this distance matrix
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Isomap
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Isomap on face images
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Isomap on hand images
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Isomap on written two-s
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Isomap - summary
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Inherits features of MDS and PCA:
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guaranteed asymptotic convergence to true structure
Polynomial runtime
Non-iterative
Ability to discover manifolds of arbitrary dimensionality
Perform well when data is from a single well sampled
cluster
Few free parameters
Good theoretical base for its metrics preserving
properties
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Problems with Isomap
Embeddings are biased to preserve the
separation of faraway points, which can
lead to distortion of local geometry
 Fails to nicely project data spread among
multiple clusters
 Well-conditioned algorithm but
computationally expensive for large
datasets
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Improvements to Isomap
Conformal Isomap – capable of learning
the structure of certain curved manifolds
 Landmark Isomap – approximates large
global computations by a much smaller set
of calculation
 Reconstruct distances using k/2 closest
objects, as well as k/2 farthest objects
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Locally Linear Embedding (LLE)
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Isomap attempts to preserve geometry on all
scales, mapping nearby points close and distant
points far away from each other
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LLE attempts to preserve local geometry of the
data by mapping nearby points on the manifold
to nearby points in the low dimensional space
Computational efficiency
Representational capacity
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LLE – general idea
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Locally, on a fine enough
scale, everything looks
linear
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Represent object as linear
combination of its neighbors
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Representation indifferent to
affine transformation
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Assumption: same linear
representation will hold in
the low dimensional space
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LLE – matrix representation
X = W*X where
 X is p*n matrix of original data
 W is n*n matrix of weights and
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Wij =0 if Xj is not neighbor of Xi
rows of W sum to one
Need to solve system Y = W*Y
 Y is q*n matrix of underlying low dimensional data
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 Minimize error:
 (Y)   Yi   WijYj
i
j
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LLE - algorithm
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Find k nearest neighbors in X space
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Solve for reconstruction weights W
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Compute embedding coordinates Y using
weights W:
 create sparse matrix M = (I-W)'*(I-W)
 Compute bottom q+1 eigenvectors of
M
 Set i-th row of Y to be i+1 smallest eigen vector
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Numerical Issues
Covariance matrix used to compute W
can be ill-conditioned, regularization needs
to be used
 Small eigen values are subject to
numerical precision errors and to getting
mixed
 But, sparse matrices used in this algorithm
make it much faster then Isomap
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LLE
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LLE – effect of neighborhood size
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LLE – with face picture
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LLE – Lips pictures
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PCA vs. LLE
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Problems with LLE
If data is noisy, sparse or weakly
connected coupling between faraway
points can be attenuated
 Most common failure of LLE is mapping
close points that are faraway in original
space – arising often if manifold is
undersampled
 Output strongly depends on selection of k
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References
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Roweis, S. T. and L. K. Saul (2000). "Nonlinear dimensionality reduction by
locally linear embedding " Science 290(5500): 2323-2326.
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Tenenbaum, J. B., V. de Silva, et al. (2000). "A global geometric framework
for nonlinear dimensionality reduction " Science 290(5500): 2319-2323.
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Vlachos, M., C. Domeniconi, et al. (2002). "Non-linear dimensionality
reduction techniques for classification and visualization." Proc. of 8th
SIGKDD, Edmonton, Canada.
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de Silva, V. and Tenenbaum, J. (2003). “Local versus global methods for
nonlinear dimensionality reduction”, Advances in Neural Information
Processing Systems,15.
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Questions?
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