This is my presentation in WaFIS last year, about the use of complex networks on data mining in genetic databases.

1. Who’s this guy?
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex
Knowledge Discovery in Databases through
Complex Networks: application to
phylodynamics
Luiz Max F. de Carvalho
Scientific Computing Programme (PROCC), Fiocruz
Pan American Center for Foot-and-Mouth Disease
(PAHO/WHO)
WaFiS 2012
September 28, 2012

2. Outline
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
1 Knowledge Discovery in Databases (KDD)
2 Complex Networks
3 Example 1: Chitin pathway phylogeny
4 Example 2: Foot-and-mouth disease virus in South America
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex

3. Knowledge Discovery in Databases (KDD)
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex
Lots of data
human brain very limited processing capacity
Information → Knowledge
Increasing number of molecular data (sequences, 3D
structures, antigenicity,. . . )
Is it possible to explore these databases to discover useful
stuff?

4. Well. . . Let’s see
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex

5. [We may use] Complex Networks
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex
Graphs → G = (V , E )

6. Yeah, but how?
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex
We can explore the ”dynamic signature” of these Complex
Networks, i.e., study and compare their structural properties.
Some useful formulas:
Clustering Coefficient < c >:
Degree distribution PK =
Diameter: max(d(i, j))
3×#triangles
#triples
∞
K =K
pK

7. Ok, Let’s work then
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex
1
Grab n sequences;
2
Create an n × n matrix using some kind of (normalized)
distance (say, S);
3
For each σ ∈ [0, 1] build M(σ) such that:
mij (σ) =
1 if Sij > σ,
0 if Sij < σ.
In a sense, we are transforming a single network in a family of
networks.

8. Analysis
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex
We shall explore the relationships between these networks:
First, define a higher-order neighborhood indicator function,
such that you binarize the adjacency matrix with regard the
ˆ
path length , obtaining a matrix M = D M( ). Then
=1
δ(α, β) =
1
N2
N
N
(
i=1 j=1
ˆ
mij (α) mij (β)
ˆ
−
)
D(α)
D(β)
Evaluating δ(σ, σ + ∆σ) can give some interesting insights.
(1)

9. Example 1: Chitin pathway phylogeny
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
Proteins related to the chitin metabolic pathway from
1605 complete genomes;
WaFiS 2012
BLAST distances (which are asymmetric);
Knowledge
Discovery in
Databases
(KDD)
Complex
Search for phylogenetic relationships

10. Example 1: Some results
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex

11. Example 1: Some more results
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex

12. Example 1: The expected Network(s)
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex

13. Example 2: Foot-and-mouth disease virus in South
America
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
S was built with phylogenetic (TN93) distances for NT
and JTT distances for AA;
Try to make sense of a somewhat big data set (167 seqs);
Extract some nice patterns;
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex

14. Indexes × σ
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
(a)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex
(b)

15. A nice network
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex

16. Some more developments
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex

17. Related Work
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex
Identify transmission clusters (HIV, HCV) (Lewis et al,
2008,Plos Medicine)
Explore scale-free behavior in phylodynamics (Shiino,
2012, Frontiers in Microbiology)

18. Future Directions
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex
Explore the spatial aspect in the construction of S
ˆ
Maybe S = µ + S(G )α
Power law analysis
Implement assortativity
Suggestions. . .

19. Thank You!
Knowledge
Discovery in
Databases
through
Complex
Networks:
application to
phylodynamics
Luiz Max F.
de Carvalho
Scientific
Computing
Programme
(PROCC),
Fiocruz
Pan American
Center for
Foot-andMouth Disease
(PAHO/WHO)
WaFiS 2012
Knowledge
Discovery in
Databases
(KDD)
Complex