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Simplicial Complexes For Clouds of Data

The document summarizes different methods for constructing simplicial complexes from point cloud data: 1. The nerve of a point set allows constructing abstract simplicial complexes. 2. Čech complexes and Vietoris-Rips complexes are commonly used to construct abstract simplicial complexes from point clouds. 3. The Delaunay triangulation allows creating simplicial complexes with geometric realizations in the underlying space. 4. The alpha complex is a filtered version of the Delaunay complex, obtained by varying the parameter r.

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100 views53 pages

Simplicial Complexes For Clouds of Data

The document summarizes different methods for constructing simplicial complexes from point cloud data: 1. The nerve of a point set allows constructing abstract simplicial complexes. 2. Čech complexes and Vietoris-Rips complexes are commonly used to construct abstract simplicial complexes from point clouds. 3. The Delaunay triangulation allows creating simplicial complexes with geometric realizations in the underlying space. 4. The alpha complex is a filtered version of the Delaunay complex, obtained by varying the parameter r.

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mobius
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Simplicial complexes associated with cloud points

Seminar algorithms

Jorge Cordero

Eindhoven University of Technology

8 May 2018
Outline

1 Motivation

2 Recap

3 Nerves

4 Čech complex

5 Vietoris-Rips complex

6 Delaunay complex

7 Alpha complexes
Topological data analysis

Data can be complex in terms of size or features.

Sometimes, data has shape.


Topological data analysis
Topological data analysis (TDA) help us to understand the structure
(shape) of data.

Application:
Find coverage in networks of sensors
Understand protein interactions
Credit card fraud detection
Simplex

σ is an n-simplex spanned by n + 1 affinely independent points in P ∈ Rn .


A 0-simplex is a point
A 1-simplex is a line
A 2-simplex is a triangle
A 3-simplex is a tetrahedron
Simplicial complex
A simplicial complex K in Rn is a collection of simplices in Rn such that:
Every face of a simplex of K is in K
Every pair of distinct simplices of K has a disjoint interior
The intersection of two distinct simplices of K is a face of each of
them
ASC and Homotopy

An abstract simplicial complex is a collection of finite non-empty subsets


of S.

If A ⊆ S, each non-empty subset B ⊆ A is also in S.


ASC and Homotopy

An abstract simplicial complex is a collection of finite non-empty subsets


of S.

If A ⊆ S, each non-empty subset B ⊆ A is also in S.

For our purposes, we can think of homotopy equivalent spaces (X ' Y) as


spaces that can be deformed continuously one into another.
Simplicial representation

Our goal is to compute a simplicial representation of a set of points to


apply topological tools for data analysis.
Nerves
We can use the nerve of a finite collection of sets S to create an abstract
simplicial complex.
Nerves
We can use the nerve of a finite collection of sets S to create an abstract
simplicial complex.

The nerve of S consists of all non-empty subcollections whose sets have a


non-empty common intersection,
\
NrvS = {X ⊆ S| X 6= ∅}.
Nerves
T T
From X 6= ∅ and Y ⊆ X =⇒ Y 6= ∅, it follows that NrvS is always
an abstract simplicial complex.

We represent the nerve as an abstract simplicial complex,

NrvS = {R, B, P, G , {R, B}, {B, P}, {P, G }, {G , R}}.


Nerves

The topological space of S = {R, G , B, Y } is a disk with three holes.

NrvS has the homotopy type of a sphere.

Hence, the homotopy types for NrvS and |S| are different.
Nerves

We want to compute a nerve that resembles the structure inherent to the


set of points.
Nerves

We want to compute a nerve that resembles the structure inherent to the


set of points.

Nerve theorem
Let S be a finite collection of closed, convex sets in Euclidean space.
Then, the nerve of S and the union of the sets in S have the same
homotopy type.
Closed ball

A closed ball with center x and radius r is defined by,

Bx (r ) = x + r Bd = {y ∈ Rd | ||y − x|| ≤ r }
Čech complex

Let’s construct a simplicial complex from a set of points.


Čech complex

Let’s construct a simplicial complex from a set of points.


Čech complex

Let’s construct a simplicial complex from a set of points.


Čech complex

Let’s construct a simplicial complex from a set of points.


Čech complex
Let S be a finite set of points in Rd .

The Čech complex of S and r is given by,

Č ech(r ) = {σ ⊆ S|∩Bx (r ) 6= ∅}

The Čech complex is equivalent to the nerve of the collection of balls.


Čech complex

Čech complexes for different values of r


Čech complex

Čech complexes for different values of r


Čech complex

Some properties of the Čech complex:


When ri ≤ rj , Č ech(ri ) ⊆ Č ech(rj ).
Čech complex

Some properties of the Čech complex:


When ri ≤ rj , Č ech(ri ) ⊆ Č ech(rj ).
Č ech(r ) of a set S of points in Rd can always be represented as an
abstract simplicial complex.
Čech complex

Some properties of the Čech complex:


When ri ≤ rj , Č ech(ri ) ⊆ Č ech(rj ).
Č ech(r ) of a set S of points in Rd can always be represented as an
abstract simplicial complex.
Computing the complex takes an exponential time in the size of S.
Vietoris-Rips complex
The Vietoris-Rips VR complex of S and r consists of all subsets of
diameter at most 2r ,

VR(r ) = {σ ⊆ S|diamσ ≤ 2r }.

The diameter of σ is the supremum of all pairwise distances between


points in σ.
Comparing Čech and Vietoris-Rips complex

Čech complex

Vietoris-Rips complex
Vietoris-Rips

Notice that Č ech(r ) ⊆ VR(r ) but Č ech(r ) 6' VR(r ).

For appropriate values of ra and rb , we have VR(ra ) ⊆ Č ech(rb ).

Vietoris-Rips Lemma
√ in some Euclidean space and r ≥ 0. It
Let S be a finite set of points
follows that VR(r ) ⊆ Č ech( 2r ).
Vietoris-Rips

Properties of VR complexes:
VR complexes avoid the intersection test used in Čech.
Vietoris-Rips

Properties of VR complexes:
VR complexes avoid the intersection test used in Čech.
VR complexes also take exponential time to compute.
Vietoris-Rips

Properties of VR complexes:
VR complexes avoid the intersection test used in Čech.
VR complexes also take exponential time to compute.
VR complexes might not have a geometric representation in the
underlying space of S.
Voronoi diagram
What if we want the simplicial complex to have a geometric
representation?.

Delaunay complexes can be used for this task.

To explore Delaunay complexes, we first introduce the Voronoi diagram.


Voronoi diagram

Consider a finite set of points S = {v1 , v2 , ..., vn } in Rd :


The Voronoi cell of vi ∈ S is the set of points in Rd closest to vi ,

Vvi = {x ∈ Rd | ||x − vi || ≤ ||x − vj ||, ∀vj ∈ S}.

Together, the Voronoi cells of all points vi cover the entire space.
Voronoi diagram

For a set of points in a plane:


Encode proximity information useful for answering point queries.
Voronoi diagram

For a set of points in a plane:


Encode proximity information useful for answering point queries.
Can be computed in time O(nlogn) using Fortune’s algorithm.
Voronoi diagram

For a set of points in a plane:


Encode proximity information useful for answering point queries.
Can be computed in time O(nlogn) using Fortune’s algorithm.
It uses O(n) space.
Delaunay complex
The Delaunay complex of a finite set of points S ⊆ Rd is equivalent to the
nerve of the Voronoi diagram,
\
Delaunay (S) = {σ ⊆ S| Vui 6= ∅}.
ui ∈σ
Delaunay complex

The Delaunay complex seems to always create triangles in R2 .


Delaunay complex

The Delaunay complex seems to always create triangles in R2 .

Is this always the case?


Delaunay complex

The Delaunay complex seems to always create triangles in R2 .

Is this always the case?

No, unless the set of points is in general position.


Delaunay complex

A set of points S is in general position if not d + 2 points lie on a common


(d − 1)-sphere.

For a finite set of points S ∈ Rd , assuming general position, the geometric


realization of a Delaunay complex fits in Rd .
Delaunay complex

For a set of points in the plane:


It can be computed from the Voronoi diagram.
It takes expected O(nlogn) time.
It uses O(n) space.
Alpha complexes
Let S be a finite set of points in Rd and r ≥ 0.

Let Ru (r ) = Bu (r ) ∩ Vu , with Vu being the Voronoi cell of u.

The alpha complex is defined as


\
Alpha(r ) = {σ ⊆ S| Ru (r ) 6= ∅}.
u∈σ
Delaunay filtration

Different values of r to create different alpha complexes.


Delaunay filtration

Eventually, we obtain the Delaunay complex.


Delaunay filtration

The filtration of Km = Delaunay is represented as,

∅ = K0 ⊆ ... ⊆ Ki ⊆ ... ⊆ Km .

Ki corresponds to the i-th alpha complex from the sequence of different


alpha complexes obtained by varying r .
Summary

The nerve of a set of points S allows us to compute simplicial


complexes.
Summary

The nerve of a set of points S allows us to compute simplicial


complexes.
Čech complexes and Vietoris-Rips complexes allows us to construct
abstract simplicial complexes from S.
Summary

The nerve of a set of points S allows us to compute simplicial


complexes.
Čech complexes and Vietoris-Rips complexes allows us to construct
abstract simplicial complexes from S.
The Delaunay triangulation allows to create simplicial complexes with
geometric realizations.
Summary

The nerve of a set of points S allows us to compute simplicial


complexes.
Čech complexes and Vietoris-Rips complexes allows us to construct
abstract simplicial complexes from S.
The Delaunay triangulation allows to create simplicial complexes with
geometric realizations.
The alpha complex can be seen as a filtered version of the Delaunay
complex.
Sources

H. Edelsbrunner, J. L. Harer, Computational topology. An


introduction. American Mathematical Society, Providence, RI, 2010.
Mark de Berg, Otfried Cheong, Marc van Kreveld, and Mark
Overmars. 2008. Computational Geometry: Algorithms and
Applications (3rd ed.).
Lecture notes and videos on Computational Topology. Lectures 11,
12, and 13.
Topological data analysis of genes
Čech and Vietoris-Rips complex
Persistent homology
Images

https://mathematica.stackexchange.com/questions/61021/
triangulated-mesh-from-voronoi-diagram
https:
//www.researchgate.net/figure/Delaunay-Triangulation_fig3_44897706
http://www.pnas.org/content/pnas/113/26/7035/F10.large.jpg
http://www.ugc.edu.hk/minisite/rgc_newsletter/rgcnews18/eng/05.htm
http://www.pnas.org/content/pnas/113/26/7035/F10.large.jpg
http://www.dei.unipd.it/~schenato/pics/SensorNetwork.jpg
https://www.johndcook.com/persistent_homology.png
https:
//upload.wikimedia.org/wikipedia/commons/thumb/5/50/Simplicial_
complex_example.svg/532px-Simplicial_complex_example.svg.png
https://s3.amazonaws.com/cdn.ayasdi.com/wp-content/uploads/2017/05/
09112616/srep43845-f2.jpg

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