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Diffusion Maps: A manifold learning algorithm

John Harlim

Department of Mathematics

Department of Meteorology & Atmospheric Science Institute of CyberScience.

The Pennsylvania State University

(2)

Plan of the talk:

I Principal Component Analysis

I Diffusion Maps

I Variable Bandwidth Diffusion Kernels

I Automatic estimation of manifold dimension and bandwidth parameter.

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What is manifold learning?

Given data {xi}i =1,...,N, the central task of unsupervised learning

algorithm is to be able to characterize this data set.

Under an assumption that these data lie on (or close to) a manifold M ⊆ Rn, manifold learning algorithm seeks for a set of (basis) functions, Φk : M → R to describe the data.

(4)

Principal Component Analysis (a linear manifold learning)

Given xi ∈ Rn with zero empirical mean, define

X = [x1, x2, . . . , xN] ∈ Rn×N.

Let (λk, wk) be defined as,

1 NXX

>w

k = λkwk

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Principal Component Analysis (a linear manifold learning)

Example: Uniformly distributed data on a unit circle.

x1 -1 -0.5 0 0.5 1 x 2 -1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8 1 ψ1 -1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8 1 x1 -1 -0.5 0 0.5 1 x 2 -1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8 1 ψ2 -1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8 1

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Principal Component Analysis (a linear manifold learning)

Example: Gaussian invariant density of a two-dimensional SDE’s

u -3 -2 -1 0 1 2 3 4 v -3 -2.5 -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 ~ϕ ⊤ 1U -1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8 1 u -3 -2 -1 0 1 2 3 4 v -3 -2.5 -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 ϕ~ ⊤ 2U -1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8 1

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Diffusion maps (a nonlinear manifold learning)

1

Given {xi} ∈ M ⊆ Rn with a sampling density q, the diffusion

maps algorithm is a kernel based method that produces orthonormal basis functions ϕk ∈ L2(M, q).

These basis functions are solutions of an eigenvalue problem, Lϕk(x ) = q−1div



q∇ϕk(x )



= λkϕk(x ),

with Neumann BC (if the manifold has a boundary). Remarks:

I If q = 1, then L = ∆.

I Diffusion maps approximates L with an exponentially decaying function function K(x , y ) = h

kx−y k2

4 .

1

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Diffusion maps (a nonlinear manifold learning)

1

Given {xi} ∈ M ⊆ Rn with a sampling density q, the diffusion

maps algorithm is a kernel based method that produces orthonormal basis functions ϕk ∈ L2(M, q).

These basis functions are solutions of an eigenvalue problem, Lϕk(x ) = q−1div



q∇ϕk(x )



= λkϕk(x ),

with Neumann BC (if the manifold has a boundary).

Remarks:

I If q = 1, then L = ∆.

I Diffusion maps approximates L with an exponentially decaying function function K(x , y ) = h

kx−y k2

4 .

1

(9)

Diffusion maps (a nonlinear manifold learning)

1

Given {xi} ∈ M ⊆ Rn with a sampling density q, the diffusion

maps algorithm is a kernel based method that produces orthonormal basis functions ϕk ∈ L2(M, q).

These basis functions are solutions of an eigenvalue problem, Lϕk(x ) = q−1div



q∇ϕk(x )



= λkϕk(x ),

with Neumann BC (if the manifold has a boundary). Remarks:

I If q = 1, then L = ∆.

I Diffusion maps approximates L with an exponentially decaying function function K(x , y ) = h

kx−y k2

4 .

1

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A review on diffusion maps algorithm

The key idea of diffusion maps stimulated by the following

asymptotic expansion2. For x ∈ M ⊆ Rn away from the boundary and f ∈ C3(M) Gf (x ) := −d/2 Z M K(x , y )f (y )dV (y ) = m0f (x ) + m2(ω(x )f (x ) + ∆f (x )) + O(2). where m0= R Rdh(||z|| 2)dz and m 2 = 12 R Rdy 2 1h(||z||2)dz are

constants determined by h, and ω depends on the induced geometry of M.

Diffusion maps is a discretization of the following algebraic manipulation: Lf (x ) := 1 m2m−10 (G1(x ))−1Gf (x ) − f (x ) = ∆f (x ) + O() 2

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A review on diffusion maps algorithm

The key idea of diffusion maps stimulated by the following

asymptotic expansion2. For x ∈ M ⊆ Rn away from the boundary and f ∈ C3(M) Gf (x ) := −d/2 Z M K(x , y )f (y )dV (y ) = m0f (x ) + m2(ω(x )f (x ) + ∆f (x )) + O(2). where m0= R Rdh(||z|| 2)dz and m 2 = 12 R Rdy 2 1h(||z||2)dz are

constants determined by h, and ω depends on the induced geometry of M.

Diffusion maps is a discretization of the following algebraic manipulation: Lf (x ) := 1 m2m−10 (G1(x ))−1Gf (x ) − f (x ) = ∆f (x ) + O() 2

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Examples: Uniformly distributed data on a circle

Analytically, DM solves ∆ϕk(x ) = λkϕk(x ), which solutions are:

λk = −k2, ϕk(x ) = eikx. 0 1 2 3 4 5 6 -1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8 1 eix 0 1 2 3 4 5 6 -1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8 1 ei2x 0 1 2 3 4 5 6 -1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8 1 ei3x

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Example: Gaussian invariant density of a two-dimensional SDE’s -5 0 5 v -4 -2 0 2 ϕ1 -1 -0.5 0 0.5 1 -5 0 5 -4 -2 0 2 ϕ18 -1 -0.5 0 0.5 1 -5 0 5 v -4 -2 0 2 ϕ100 -1 -0.5 0 0.5 1 -5 0 5 -4 -2 0 2 ϕ250 -1 -0.5 0 0.5 1 u -5 0 5 v -4 -2 0 2 ϕ500 -1 -0.5 0 0.5 1 u -5 0 5 -4 -2 0 2 ϕ750 -1 -0.5 0 0.5 1

Essentially, we view the DM as a method to construct generalized Fourier basis on the manifold.

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Diffusion Maps Algorithm

Using this asymptotic expansion,

Gf (x ) = m0f (x ) + m2(ω(x )f (x ) + ∆f (x )) + O(2),

given data xi ∈ M with sampling density q(x), we can estimate the

Laplacian through the following procedure:

I Compute q= G(q). I Compute ˆG,α,q(f ) := G fq qα  

for some parameter α. ˆ G,α,q(f ) = m1−α0 fq 1−α1 + mω(1 − α) − mα∆q q + m ∆(fq1−α) fq1−α + O( 2), where m = m2/m0. I Compute ˆq:= ˆG,α,q(1). I Finally, L,αf := ˆ q−1Gˆ,α,q(f ) − f m = (2 − 2α)∇ log q · ∇f + ∆f + O().

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Diffusion Maps Algorithm

Using this asymptotic expansion,

Gf (x ) = m0f (x ) + m2(ω(x )f (x ) + ∆f (x )) + O(2),

given data xi ∈ M with sampling density q(x), we can estimate the

Laplacian through the following procedure:

I Compute q= G(q). I Compute ˆG,α,q(f ) := G fq qα  

for some parameter α. ˆ G,α,q(f ) = m1−α0 fq 1−α1 + mω(1 − α) − mα∆q q + m ∆(fq1−α) fq1−α + O( 2), where m = m2/m0. I Compute ˆq:= ˆG,α,q(1). I Finally, L,αf := ˆ q−1Gˆ,α,q(f ) − f m = (2 − 2α)∇ log q · ∇f + ∆f + O().

(16)

Diffusion Maps Algorithm

Using this asymptotic expansion,

Gf (x ) = m0f (x ) + m2(ω(x )f (x ) + ∆f (x )) + O(2),

given data xi ∈ M with sampling density q(x), we can estimate the

Laplacian through the following procedure:

I Compute q= G(q). I Compute ˆG,α,q(f ) := G fq qα  

for some parameter α. ˆ G,α,q(f ) = m1−α0 fq 1−α1 + mω(1 − α) − mα∆q q + m ∆(fq1−α) fq1−α + O( 2), where m = m2/m0. I Compute ˆq:= ˆG,α,q(1). I Finally, L,αf := ˆ q−1Gˆ,α,q(f ) − f m = (2 − 2α)∇ log q · ∇f + ∆f + O().

(17)

Diffusion Maps Algorithm

Using this asymptotic expansion,

Gf (x ) = m0f (x ) + m2(ω(x )f (x ) + ∆f (x )) + O(2),

given data xi ∈ M with sampling density q(x), we can estimate the

Laplacian through the following procedure:

I Compute q= G(q). I Compute ˆG,α,q(f ) := G fq qα  

for some parameter α. ˆ G,α,q(f ) = m1−α0 fq 1−α1 + mω(1 − α) − mα∆q q + m ∆(fq1−α) fq1−α + O( 2), where m = m2/m0. I Compute ˆq:= ˆG,α,q(1). I Finally, L,αf := ˆ q−1Gˆ,α,q(f ) − f m = (2 − 2α)∇ log q · ∇f + ∆f + O().

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Diffusion Maps Algorithm

Using this asymptotic expansion,

Gf (x ) = m0f (x ) + m2(ω(x )f (x ) + ∆f (x )) + O(2),

given data xi ∈ M with sampling density q(x), we can estimate the

Laplacian through the following procedure:

I Compute q= G(q). I Compute ˆG,α,q(f ) := G fq qα  

for some parameter α. ˆ G,α,q(f ) = m1−α0 fq 1−α1 + mω(1 − α) − mα∆q q + m ∆(fq1−α) fq1−α + O( 2), where m = m2/m0. I Compute ˆq:= ˆG,α,q(1). I Finally, L,αf := ˆ q−1Gˆ,α,q(f ) − f m = (2 − 2α)∇ log q · ∇f + ∆f + O().

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Diffusion Maps Algorithm

Numerically, we can repeat this procedure as follows.

Given {xi}Ni =1 ∼ q(x) that lie on M ∈ Rn, choose a Gaussian

kernel, K(x , y ) = exp  −kx − y k 2 4  , such that m = m2/m0 = 1.

We can approximate the operator Gf as a discrete sum,

d /2G(fq)(x ) = Z M K(x , y )f (y )q(y )dV (y ) = lim N→∞ 1 N N X i =1 K(x , xi)f (xi).

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Diffusion Maps Algorithm

With the Monte-Carlo discretization, the numerical approximation of operator L,α is given as:

I Compute q(xi) = N1 PNj =1K(xi, xj).

I Construct the kernel of ˆG,α,q(f ) := G

 fq qα   : ˆ K(xi, xj) = K(xi, xj) q(xi)αq(xj)α .

This is called “right” normalization

I Compute ˆq(xi) = N1

PN

j =1Kˆ(xi, xj).

I Then matrix representation of L,α is given as,

h L,α i i ,j = 1   ˆK(xi, xj) ˆ q(xi) − δi ,j  .

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Diffusion Maps Algorithm

With the Monte-Carlo discretization, the numerical approximation of operator L,α is given as:

I Compute q(xi) = N1 PNj =1K(xi, xj).

I Construct the kernel of ˆG,α,q(f ) := G

 fq qα   : ˆ K(xi, xj) = K(xi, xj) q(xi)αq(xj)α .

This is called “right” normalization

I Compute ˆq(xi) = N1

PN

j =1Kˆ(xi, xj).

I Then matrix representation of L,α is given as,

h L,α i i ,j = 1   ˆK(xi, xj) ˆ q(xi) − δi ,j  .

(22)

Diffusion Maps Algorithm

With the Monte-Carlo discretization, the numerical approximation of operator L,α is given as:

I Compute q(xi) = N1 PNj =1K(xi, xj).

I Construct the kernel of ˆG,α,q(f ) := G

 fq qα   : ˆ K(xi, xj) = K(xi, xj) q(xi)αq(xj)α .

This is called “right” normalization

I Compute ˆq(xi) = N1

PN

j =1Kˆ(xi, xj).

I Then matrix representation of L,α is given as,

h L,α i i ,j = 1   ˆK(xi, xj) ˆ q(xi) − δi ,j  .

(23)

Diffusion Maps Algorithm

With the Monte-Carlo discretization, the numerical approximation of operator L,α is given as:

I Compute q(xi) = N1 PNj =1K(xi, xj).

I Construct the kernel of ˆG,α,q(f ) := G

 fq qα   : ˆ K(xi, xj) = K(xi, xj) q(xi)αq(xj)α .

This is called “right” normalization

I Compute ˆq(xi) = N1

PN

j =1Kˆ(xi, xj).

I Then matrix representation of L,α is given as,

h L,α i i ,j = 1   ˆK(xi, xj) ˆ q(xi) − δi ,j  .

(24)

Diffusion Maps Algorithm

With the Monte-Carlo discretization, the numerical approximation of operator L,α is given as:

I Compute q(xi) = N1 PNj =1K(xi, xj).

I Construct the kernel of ˆG,α,q(f ) := G

 fq qα   : ˆ K(xi, xj) = K(xi, xj) q(xi)αq(xj)α .

This is called “right” normalization

I Compute ˆq(xi) = N1

PN

j =1Kˆ(xi, xj).

I Then matrix representation of L,α is given as,

h L,α i i ,j = 1   ˆK(xi, xj) ˆ q(xi) − δi ,j  .

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Remarks:

Recall that L,αf = (2 − 2α)∇ log q · ∇f + ∆f + O().

I If α = 0 and q(x ) = 1/Vol (M) is uniform, then we approximate the Laplace-Beltrami on M; this is the

”Laplacian eigenmaps” introduced by Belkin and Niyogi 2003.

I If α = 1, we also get Laplace-Beltrami on M even if the sampling measure is non-uniform.

I If α = 1/2, we approximate,

L,1/2= ∇ log q · ∇ + ∆ + O() = q−1div 

q∇ 

+ O(), which is the generator of a gradient system with an isotropic diffusion:

dx = −∇U(x )dt +√2 dWt,

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Remarks:

For the estimation of ∆, the eigenfunctions ϕk form an

orthonormal basis of L2(M) correspond to eigenvalues λk ≥ 0.

Definition

Let S(x , y ) = e∆δy(x ) be the heat kernel of ∆. The diffusion

distance is defined as,

D(x , y )2 := kS(x , ·) − S(y , ·)k2L2(M).

Representing the heat kernel with the basis functions, we have

D(x , y )2= ∞ X k=1 e2λk ϕ k(x ) − ϕk(y ) 2 .

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Remarks:

Diffusion Maps3 is defined as a map, Φ,M : M → RM, as

Φ,M(x ) := (eλ1ϕ1(x ), . . . , eλMϕM(x )).

Then for appropriate choices of  and M, the map Φ,M is an

isometric embedding, in the sense of:

D(x , y )2≈ kΦ,M(x ) − Φ,M(y )kRM

preserving the diffusion distance.

Compare to PCA, Φk(x ) = wk>x .

3

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Remarks:

Diffusion Maps3 is defined as a map, Φ,M : M → RM, as

Φ,M(x ) := (eλ1ϕ1(x ), . . . , eλMϕM(x )).

Then for appropriate choices of  and M, the map Φ,M is an

isometric embedding, in the sense of:

D(x , y )2≈ kΦ,M(x ) − Φ,M(y )kRM

preserving the diffusion distance. Compare to PCA, Φk(x ) = wk>x .

3

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Restriction on compact manifold

Consider estimating generator of Ornstein-Uhlenbeck process on a line M = R, which is a gradient flow with potential U(x) = x2/2.

−3 −2 −1 0 1 2 3 −8 −6 −4 −2 0 2 4 6 8 x 4th Eigenfunction Analytic ε=0.05 ε=0.025 ε=0.005 ε=0.002 −3 −2 −1 0 1 2 3 −8 −6 −4 −2 0 2 4 6 8 x 4th Eigenfunction Analytic N=1000 N=10000 N=100000

Figure : Left: Estimation of the third eigenfunction of the generator of the OU process with 2000 data points. Right: Various number of data points where√N outliers are removed.

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Variable bandwidth diffusion kernels

4

I We consider variable bandwidth diffusion kernels for data lie on non-compact domain without boundary of the following form, KS(x , y ) = exp− kx − y k 2 4ρ(x )ρ(y )  .

I If we choose ρ(x ) = q(x )β+ O() and β = −1/2, and apply DM with α = −d /4, where d = dim(M), then we can approximate the generator L,1/2that takes functions on

L2(M, q) ∩ C3(M).

4

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Back to the OU example

With the variable bandwidth kernel.

−3 −2 −1 0 1 2 3 −8 −6 −4 −2 0 2 4 6 8 x 4th Eigenfunction Analytic ε=0.001 ε=0.0005 ε=0.0001 ε=4e−05 10−6 10−5 10−4 10−3 10−2 10−1 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2 ε MSE, 4th Eigenfunction Variable Bandwidth Fixed Bandwidth

Figure : Left: VB estimation of the fourth eigenfunction of the generator of the OU process with 2000 data points. Right: The mean squared error between the analytic fourth eigenfunction and the kernel based

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Variable Bandwidth Diffusion Kernels

5 Given data xi∼ q(x), KS(xi, xj) = exp  −||xi− xj||2 4ρ(xi)ρ(xj)  qS(xi) = N X j =1 K(xi, xj) ρ(xi)d K,αS (xi, xj) = KS (xi, xj) qS (xi)αqS(xj)α q,αS (xi) = N X j =1 K,αS (xi, xj) ˆ K,αS (xi, xj) = KS ,α(xi, xj) qS ,α(xi) LS,α(xi, xj) = ˆ KS ,α(xi, xj) − δij ρ(xi)2 ,

We proved that for each x ,

LS,αf (x ) → ∆f (x ) + 2(1 − α)∇f (x ) ·∇q(x) q(x ) + (d + 2)∇f (x ) · ∇ρ(x) ρ(x ) in probability. 5

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Variable Bandwidth Diffusion Kernels

6

Choosing ρ = qβ+ O(), we have at each xi,

LS,αf (xi) = ∆f (xi) + c1∇f (xi) · ∇q(xi) q(xi) +O ,q(xi) (1−d β)/2 √ N2+d /4 , ||∇f (x i)||q(xi)−c2 N1/2+d /4 ! , with c1 = 2 − 2α + d β + 2β and c2= 1/2 − 2α + 2d α + d β/2 + β.

Remarks: A natural choice for β = −1/2.

I For gradient flow, we want c1= 1 and α = −d /4. In this

case, c2 = d /2(1/2 − d ) < 0 for d > 0.

I In contrast, the fixed bandwidth with β = 0, we have α = 1/2 and c2= d − 1/2 > 0 for d > 0.

6

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Automatic estimation of  and d

Note that S () ≡ 1 N2 X i ,j K(xi, xj) ≈ 1 Vol (M) Z M Z TxiM K(xi, y ) dy dV (x ) ≈ Z M (4π)d /2 Vol (M)dV (x ) = (4π) d /2 such that, dlogS dlog  = d /2 (1)

Remark: As  → 0, S →N1 and as  → ∞, S → 1 and in these extreme cases, the slopes of log S are zero. Our strategy is to determine  and d that maximize (1).

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Example: Estimation of ∆ on S

2

∈ R

3

with N = 3000.

−0.5 0 0.5 −0.5 0 0.5 −0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 10−4 10−2 100 10−2 10−1 ε MSE, 2nd Eigenfunction Variable Bandwidth Fixed Bandwidth Automatic ε, Variable Bandwidth Automatic ε, Fixed Bandwidth

10−4 10−2 100 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 ε

Power law exponent, a, S

∝ ε a Variable bandwidth Fixed bandwidth −1 −0.5 0 0.5 −1 −0.5 0 0.5 1 −0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 −2 −1.5 −1 −0.5 0 0.5 1 −1 −0.5 0 0.5 −0.5 0 0.5 1 1.5 −1 −0.5 0 0.5 −1 −0.5 0 0.5 1 −1 −0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8

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Other automatic estimation of  and d

Let X = [X1, . . . , XN] and xi ∈ M ⊆ Rm, where

Xj = D(x )−1/2exp  − kxj − xk 2 4  (xj − x) D(x ) = N X i =1 exp  −kxi − xk 2 2  We showed7 that lim N→0 1 XX >

= I(x )>I(x) + O(),

where I : Rm → TxM is a projection onto the tangent space. Remarks: This means that for ν ∈ TxM,

lim

N→0ν >

XX>ν = kνk2+ O(2),

7

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Other automatic estimation of  and d

This means that, for ν ∈ TxM, the singular value of X

σν := lim N→∞ √ ν>XX>ν kνk = √  + O().

and if ν ∈ TxM⊥, then σν = O().

Thus, one can estimate the dimension using

d ≈ 1 Trace(XX >), or even using,  det(XX>)  = d Y j =1 σj ≈ d ⇔ d ≈ d  det(XX>)  d 

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Example: 2D torus embedded in R

30

.

ǫ 10-4 10-2 100 102 Dimension 0 0.5 1 1.5 2 2.5 3 3.5

Dimension from Kernel Sum Dimension from SVD Metric of agreement to minimize Best ǫ and dimension

ǫ 10-4 10-2 100 102 Dimension 0 0.5 1 1.5 2 2.5 3 3.5

Dimension from Kernel Sum Dimension from SVD Metric of agreement to minimize Best ǫ and dimension

Figure : Dimension measures d1(blue) and d2(red) as functions of the

bandwidth  corresponding to the data set sampled from the torus embedded in 30-dim (left) and with 30-dim Gaussian noisy torus (right). The metric of agreement, M(), is shown as the dotted black curve. The solid black dot represents the bandwidth that minimizes the metric along with the average dimension at the optimal .

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Discussion:

For junior participants:

I Convince yourself that the differential operator

L = q−1div(q∇ ) that is being estimated is symmetric

negative definite with respect to an appropriate Hilbert space.

I In the construction of matrix L,α, notice that this N × N

matrix is not symmetric. Can you find a similarity

transformation to a symmetric matrix since we have a more stable algorithm for spd matrix.

I When N is large, you can store the matrix L,α and the entries

of the matrix is mostly zero since the kernel is local with bandwidth . How do you get around of the storing and avoid computing zero entries.

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Discussion:

A general research problem:

I Solving eigenvalue problem of such large system is very expensive. The amount of required data of any

non-parametric method grows exponentially as a function of intrinsic dimension. Now, are there any computationally cheaper alternatives to get basis of the range of L,α?

I I had explored one with QR decomposition8 which is cheap but the problem is that QR basis does not reveal rank. Eigenbasis has a special properties since its corresponding eigenvalues 0 = λ0≥ λ1 ≥ . . ., and they satisfy

−λk = arg min f ∈H2(M,q)∩H⊥ k−1 k∇f kq where Hk−1 = span{ϕ0, . . . , ϕj −1}. 8

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References:

I T. Berry and J. Harlim, Variable bandwidth diffusion kernels, Appl. Comput. Harmon. Anal. 40(1), 68-96, 2016.

I T. Berry and J. Harlim, Iterated diffusion maps for feature identification, Appl. Comput. Harmon. Anal. 45(1), 84-119, 2018.

I J. Harlim, Data-driven computational methods: Parameter and operator estimations, Cambridge University Press, UK, 2018. (with supplementary MATLAB codes for VBDM)

I J. Harlim and H. Yang, Diffusion forecasting model with basis functions from QR decomposition, J. Nonlinear Sci 28, 847-872, 2018.

Collaborators:

I Tyrus Berry, Assistant Professor at Department of Mathematical Sciences, George Mason University.

I Haizhao Yang, Assistant Professor at Department of Mathematics National University of Singapore.

References

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