Slide 1 of 39

Information Flow in
Interaction Networks
Aaron Gowins

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Interaction Networks
Applications:
Protein-Protein Interactions
Gene Regulatory Networks
Molecular States
Social Interactions
Each node represents an individual
Each edge represents a potential path for information

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Interaction Network

2
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SeniorProject2.nb

Adjacency Matrix
1
1
1 if Hi, jL E ,
from i 1
0 if Hi, jL E
1
0

Wij =

to j
0 0
0 0
1 0
0 0
0 1

1
3

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0
0
1
0
0

0
1
0
1
0

SeniorProject2.nb

Normalize by Row
to j

1 0 0 0 0
1
1
2 0 0 0 2
Pij =

Wij
kWik

from i

1
3
1
2

1
3

1
3

0 0 0

1
2

0 0 1 0 0

1
3

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SeniorProject2.nb

F Matrix
Let Fij(t) be the probability that information
originating at i T is absorbed in j S in t or fewer
steps.

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SeniorProject2.nb

Traveling to Vertex 1
to j

1 0 0 0 0
1
1
2 0 0 0 2
Fij(t+1)=Pij + Pik Fkj(t)
kT

from i

1
3
1
2

1
3

1
3

0 0 0

1
2

0 0 1 0 0

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One Time Step to Reach Vertex 1

Fij(1) =

1
2
1
3
1
2

1
from i

3
5

to j
1 0 0 0 0
1
1
2 0 0 0 2

1
3
1
2

1
3

1
3

0 0 0

1
2

0 0 1 0 0

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Two Time Steps to Reach Node 1

Fij(t+1)=Pij + Pik Fkj(t)
kT

F31 (2) = P31 + P32F21 + P33F31 + P34F41 + P35F51

1/3 + (1/3*1/2) + (0*1/3) + (1/3*1/2) + (0*0) = 2/3
to j
1 0 0 0 0
1
1
0
0
0
2
2
from i

1
3
1
2

1
3

1
3

0 0 0

1
2

0 0 1 0 0

1
3

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SeniorProject2.nb

Two Time Steps

F21 (2) = P21 + P22F21 + P23F31 + P24F41 + P25F51
1/2 + (0*1/3) + (0*1/3) + (0*1/2) + (1/2*0) = 1/2
F31 (2) = P31 + P32F21 + P33F31 + P34F41 + P35F51
1/3 + (1/3*1/2) + (0*1/3) + (1/3*1/2) + (0*0) = 2/3
F41 (2) =P41 + P42F21 + P43F31 + P44F41 + P45F51
1/2 + (0*1/3) + (0*1/3) + (0*1/2) + (1/2*0) = 1/2
F51 (2) =P51 + P52F21 + P53F31 + P54F41 + P55F51
0 + (0*1/3) + (1*1/3) + (0*1/2) + (0*0) = 1/3

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Two Time Steps Matrix Algebra

1
2
2
3
1
2
1
3

Fij(2) =

1
2
2
3
1
2
1
3

1
2
1
3
1
2

P=

PSS PST
PTS PTT

0 0 0

1
2

1
3

1
3

0 0 0

1
2

1 0 0 0 0
1
1
2 0 0 0 2

1
3
1
2

1
3

1
3

0 0 0 21
0 0 1 0 0
1
2
1
3
1
2

F(2) = PTS + PTT F(1)

0
0 1 0 0 0
F31 (2) = P31 + P32F21 + P33F31 + P34F41 + P35F51
1/3 + (1/3*1/2) + (0*1/3) + (1/3*1/2) + (0*0) = 2/3

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SeniorProject2.nb

Three Time Steps

F(3) = PTS + PTT F(2)

2
3
2
3
2
3
2
3

1
2
1
3
1
2

P=

0 0 0

1
2

1
3

1
3

0 0 0

1
2

+
0 1 0 0

PSS PST
PTS PTT

1
2
2
3
1
2
1
3

1 0 0 0 0
1
1
2 0 0 0 2

1
3
1
2

1
3

1
3

0 0 0 21
0 0 1 0 0

1
3

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SeniorProject2.nb

Distribution at Equilibrium
Fij(t + 1) = Pij +

Pik Fkj(t)
kT

In matrix form: F(t+1) = PTS + PTT F(t)

Solve for the long-term equilibrium state, where F(t+1) = F(t) = F:

F = PTS + PTT F

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14

SeniorProject2.nb

Solve for F
F = PTS + PTT F
F - PTT F = PTS
HI - PTT LF = PTS
Let G = HI - PTT L-1
F = GPTS

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39

SeniorProject2.nb

Boring...
I - PTT = G-1 :

1
0
0
0

3
5

0
1
0
0

2
5
4

GPTS = F :

1
2
1
4
1
2

3
4
3
2
3
4
3
2

0
0
1
0

0
0
1
0
3
0
0
1
0

1
4

3
4

1
2
5
4

1
2
3
4
3
2

1
2

0 0

1
2

- 21

1
3

- 31

- 31

0 0

1
2

- 21

1 0 0

-1

1
2
1
3
1
2

1
1
=
1
1
0

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16

SeniorProject2.nb

Arbitrary Graph
8

13
16

5
10

7
2

15
12
9
4
14

6
11

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SeniorProject2.nb

Adjacency Matrix

Wij =

1
0
0
1
1
0
0
0
0
0
0
0
0
0
0
0

0
1
0
0
0
0
1
1
0
0
0
0
0
0
0
0

0
0
1
1
0
0
0
0
0
0
1
0
0
0
0
0

0
0
0
0
1
0
0
0
1
0
0
0
0
0
0
0

0
0
0
0
0
1
1
0
0
1
0
0
0
0
0
0

0
0
0
0
0
1
0
1
0
1
1
0
0
0
0
0

0
0
0
0
0
0
0
0
1
0
0
0
0
0
1
0

0
0
0
0
1
0
1
0
0
0
0
1
1
0
0
0

0
0
0
0
0
0
1
0
1
0
0
0
0
1
0
0

0
0
0
0
0
0
1
0
0
1
0
0
0
0
1
0

0
0
0
0
0
0
0
0
0
0
1
1
0
0
0
1

0
0
0
0
1
0
0
0
1
0
0
0
1
1
0
0

0
0
0
0
0
0
0
0
0
1
0
0
0
0
1
1

0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0

0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0

0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0

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18

SeniorProject2.nb

Normalized by Row
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
1

0 0 0 0 0 0 0 0 0 0 0 0 0
2

2
1

0 0

0 0 0
4

0 0 0 0 0 0 0 0 0 0
3
1

0 0
5
1

0 0

0 0 0 0 0 0

0 0 0 0 0 0 0 0 0 0
1

0 0
5
1

5
1

0 0 0
0

0 0
5

0 0 0 0
5

0 0 0

0 0
4

0
5

1
5

2
1

1
5

1
5

0 0

0 0 0

Pij =

0 0 0 0
4

0 0 0

0 0 0
4

0 0
5
1

0 0 0 0
4

0 0 0 0 0 0

0 0 0 0 0 0

0 0 0 0 0
2
1

0 0
2
1

0 0 0 0 0
2
1

0 0 0
2

0 0 0 0 0 0 0

0 0 0 0 0

0 0
2

0 0 0 0
2

0 0
3

0 0 0 0
2
1

0 0
3

0 0 0 0 0 0 0 0 0

0 0 0
3
1

0 0 0
5

0
2

0 0 0
2

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39

SeniorProject2.nb

Partitioned Matrix
1 0 0 0
0 1 0 0
0 0 1 0
1
1
0 2 0
2

0
0
0
0

0
0
0
0

0
0
0
0

0
0
0
0

0
0
0
0

0
0
0
0

0
0
0
0

1
4

0 0 0

1
4

0 0 0

1
4

0 0 0 0

0 0

1
4

0 0 0 0
0

PSS PST
P =
PTS PTT

1
5
1
2

0 0

0 0 0

0 0 0

1
5

0 0 0 0
0 0

1
3
1
5

1
4

0
0
0
0

2
3

0 0
1
5

0 0

1
5
1
4

0
0
0
0

0
0
0
0

1
5

1
5

1
5

0 0 0 0 0 0

0 0 0 0 0 0 0 0 0 0
1
5

2
5

0 0 0

0 0
2
5

0 0 0 0

0 0 0 0 0 0 0
0 0 0 0 0 0 0

1
2
1
2

0 0 0 0 0 0 0 0
0 0 0 0 0 0

0
0
0
0

0 0 0 0 0 0 0 0 0 0

0 0
1
2

0
0
0
0

1
3

0 0

0 0
1
2
1
2

0 0 0
1
2

0 0

0 0
1
3

0 0 0 0 0 0 0 0 0 0

1
5

1
5

0 0 0

0 0 0 0 0
0 0 0 0 0
1
2
1
2

0 0
1
2

0 0 0 0

0 0 0 0
0 0 0 0
1
3
1
2

0 0 0
0 0 0

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SeniorProject2.nb

Fundamental Matrix
F = GPTS

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39

SeniorProject2.nb

Analysis
G = HI - PTT L-1
4

1.0
0.33

0
1.3

0
1.0

0
0

0
0.50

0
0

6
7

0.33

1.3

4.0

0.50

0.25 0.71 1.3

1.1

0.57 0.36

8
9

0.17 0.67 2.0

4
5

1.3

0.47 0.46 1.1 0.36 0.44

1.1

10
0
0
0
0.36

1.8

0.12

11

12

13

14 15 16

0
0
0.33 0.33

0
0

0
0

0
0

0
0

0.33 0.33

0.29 0.29 0.071

0.17 0.17

0.48 0.48 0.024

0.44 0.44

0.33

10
11
12
13

0.28

2.3

0.67

1.7

0.17 0.67 2.0

0.25

2.2

0.17

0.17 0.67 2.0

0.75

1.2

1.2

0.17 0.67 2.0

1.0

1.0

14

0.32 0.56 1.5 0.18 0.60 0.89 0.060 0.83 0.83 0.012 1.0

15

0.23 0.83 1.9 0.36 0.75 0.12

16

0.17 0.67 2.0

0.63

0.67
0

0.67 0.67

0.47 0.47
1.4

0.42

0.47

1.0

0.50

1.0

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SeniorProject2.nb

Distributions
F = GPTS
4
5
6
7
8
9
10
11
12
13
14
15
16

0.50
0.50
0.50
0.30
0.25
0.35
0.42
0.25
0.25
0.25
0.30
0.32
0.25

0
0.25
0.25
0.50
0.63
0.29
0.33
0.13
0.38
0.50
0.33
0.44
0.31

3
0.50
0.25
0.25
0.20
0.13
0.36
0.25
0.63
0.38
0.25
0.37
0.23
0.44

16

13

1
5

10
7
15

12
9
4

14

6
11

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39

SeniorProject2.nb

Distributions
Distribution of information originating at any source

SINK 1

SINK 2

SINK 3

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SeniorProject2.nb

Information Dissipation
Dissipation:
Technique to account for loss or gain of
information at a transient node.
~

Pij = i j Pij
i gives the proportion of the signal leaving i that is retained,
j gives the proportion of the signal entering j that is retained.
~

~~

Then F = GPTS

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SeniorProject2.nb

Dissipation
~

Pij = i j Pij

Ex: 8= 0.1

ORIGINAL DISSIPATED ORIGINAL DISSIPATED ORIGINAL DISSIPATED

SINK 3
SINK 2
SINK 1

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25

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SeniorProject2.nb

Dissipation
~

Pij = i j Pij

Ex: 5= 0.1

ORIGINAL DISSIPATED ORIGINAL DISSIPATED ORIGINAL DISSIPATED

SINK 3
SINK 2
SINK 1

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39

SeniorProject2.nb

Dissipation
~

Pij = i j Pij

Ex: 8= 0.1, 5= 0.1

ORIGINAL DISSIPATED ORIGINAL DISSIPATED ORIGINAL DISSIPATED

SINK 2
SINK 3
SINK 1

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SeniorProject2.nb

Direct the Flow

Potentials:
Technique to direct the flow of information
toward selected nodes.
Q(j) =

k (( j,k));
kR

where denotes the path-metric on the

Adjacency Matrix

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39

SeniorProject2.nb

Potentials Q
is the sum of the weights of the edges
forming the shortest directed path from i to j.

(i, j) =

1
1
2
2
3
2
2
3
4
4
3
3
4

2
3
1
1
2
3
4
2
2
3
2
3

0
1
2
3
3
4
2
3
1
2
3
3
4
2

0
1
2
2
3
1
2
3
4
4
2
3
4

0
1
1
2
2
1
2
3
3
3
2
3

2
0
2
1
3
1
1
2
2
3
2
2

2
1

1
2
1
0
2
2
3
1
1
2
2
2

1
2

2
0

3
1

2
3
3
4
2
3
0
1
2
2
3
1

1
2
2
3
1
2
3
0
1
1
2
2

3
1

0
4
1
1

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SeniorProject2.nb

Potentials
Choose R, a subset of V, and for x = (i, j), set
k (x)=

0.8181 x
if 0 < x 2,
0.8181 x + 0.05 Hx - 2L2 if x > 2,

define Q(j) =

k (( j,k))
kR

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SeniorProject2.nb

Potentials

W ij = Wij (-QH jL)

Direct the flow from each vertex towards
the vertices adjacent to it that have lower
potential relative to other adjacent vertices.

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SeniorProject2.nb

Lets try this

With R={1,2,3,11}
8

13
16

5
10

7
2

15
12
9
4
14

6
11

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SeniorProject2.nb

Potentials Matrix
define Q(j) =

k (( j,k))
kR

W ij = Wij (-QH jL)

0.0074
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.0074
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.0074
0.
0.
0.
0.
0.
0.
0.
0.
0.0074
0.
0.0074
0.
0.
0.
0.
0.
0.
0.
0.
0.0074
0.
0.
0.0074
0.
0.
0.
0.000035
0.
0.
0.
0.
0.
0.
0.
0.0033 0.00011
0.
0.
0.
0.
0.
0.
0.0074
0.
0.
0.0033
0.
0.
0.000035 0.0014 0.00011
0.
0.
0.0074
0.
0.
0.
0.00011
0.
0.
0.
0.
0.
0.
0.
0.
0.0074
0.
0.
0.00057
0.
0.0014
0.
0.
0.
0.
0.
0.
0.0033 0.00011
0.
0.
0.
0.00011
0.
0.
0.
0.0074
0.
0.
0.00011
0.
0.
0.
0.
0.0011
0.
0.
0.
0.
0.
0.
0.
0.000035
0.
0.
0.0011
0.
0.
0.
0.
0.
0.
0.
0.000035
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.0014
0.
0.
0.
0.
0.
0.
0.
0.
0.00057
0.
0.
0.00011
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.
0.0011

Printed by Wolfram Mathematica Student Edition

0.
0.
0. 0. 0.
0.
0.
0. 0. 0.
0.
0.
0. 0. 0.
0.
0.
0. 0. 0.
0.00052
0.
0. 0. 0.
0.
0.
0. 0. 0.
0.
0.
0. 0. 0.
0.
0.
0. 0. 0.
0.00052
0.
0. 0. 0.
0.
0.000096 0. 0. 0.
0.
0.
0. 0. 0.
0.
0.
0. 0. 0.
0.00052
0.
0. 0. 0.
0.00052
0.
0. 0. 0.
0.
0.000096 0. 0. 0.
0.
0.000096 0. 0. 0.

33

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SeniorProject2.nb

Normalize
1.
0.
0.
0.5

0.
1.
0.
0.

0.
0.
1.
0.5

0.
0.
0.
0.

0.
0.
0.
0.

0.
0.
0.
0.

0.
0.
0.
0.

0.
0.
0.
0.

0.
0.
0.
0.

0.
0.
0.
0.

0.
0.
0.
0.

0.
0.
0.
0.

0.
0.
0.
0.

0.
0.
0.
0.

0.48

0.

0.

0.48

0.

0.

0.

0.

0.97 0.032

0.

0.60

0.

0.

0.27

0.

0.

0.

0.

0.

0.0023

0.

0.

0.

0.034

0.

0. 0. 0.

0.

0.

0.

0.

0.

0.

0.

0. 0. 0.

0.

0.

0.

0.

0.99

0.

0.

0.

0.014

0.

0.

0.

0. 0. 0.

0.

0.

0.

0.

0.

0.

0.

0.74

0.

0.

0.058

0.

0. 0. 0.

0.15

0.

0.

0.052

0.

0.

0.

0.

0.

0.

0. 0. 0.

0.

0.

0.030

0.

0.

0.

0.

0.86

0.

0.

0.012

0.

0.

0.

0.

0.13

0.

0.

0. 0. 0.

0.

0.

0.

0.

0.

0.

0.

0.

0.

0.

0.

0.

0.030

0.

0.

0.97

0.

0.

0. 0. 0.

0.

0.

0.063

0.

0.

0.

0.94

0.

0.

0.

0.

0.

0. 0. 0.

0.

0.

0.

0.

0.73

0.

0.

0.27

0.

0.

0.

0.

0. 0. 0.

0.

0.

0.

0.74

0.

0.

0.14

0.

0.

0.12

0.

0.

0.

0. 0. 0.

0.

0.

0.

0.

0.

0.

0.

0.92

0.

0.91 0.030

0.0028 0.12 0.0087

Printed by Wolfram Mathematica Student Edition

0.
0.
0.
0.

0.
0.
0.
0.

0.027 0. 0. 0.

0.079 0. 0. 0.

39

SeniorProject2.nb

Distributions
With R={1,2,3,11}
1
2

F=

4
5
6
7
8
9
10
11
12
13
14
15
16

0.5
0.
0.5
0.72
0.0032
0.27
0.72
0.0032
0.27
0.25
0.61
0.13
0.010
0.99
0.0039
0.45
0.043
0.50
0.70
0.0056
0.29
0.010 0.000046 0.99
0.010
0.030
0.96
0.010
0.090
0.90
0.34
0.040
0.62
0.28
0.47
0.25
0.010 0.0071
0.99

Printed by Wolfram Mathematica Student Edition

35

39

36

SeniorProject2.nb

Directed Flow
With R={1,2,3,11}

ORIGINAL POTENTIAL
SINK 1

ORIGINAL POTENTIAL
SINK 2

ORIGINAL POTENTIAL
SINK 3

Printed by Wolfram Mathematica Student Edition

39

SeniorProject2.nb

Potentials
8

13
16

5
10

7
2

15
12
9
4
14

6
11

Printed by Wolfram Mathematica Student Edition

37

39

38

SeniorProject2.nb

Potentials
With R={1,2,3,5,9}
1 2
3

F=

0.5
0.
0.5
0.74 0.016 0.25
0.74 0.016 0.25
0.51
0.27
0.22
0.053 0.93 0.018
0.50
0.14
0.36
0.73 0.018 0.25
0.053 0.0012 0.95
0.053 0.47
0.48
0.053 0.79
0.16
0.50
0.14
0.36
0.52
0.26
0.22
0.053 0.12
0.82

Printed by Wolfram Mathematica Student Edition

39

SeniorProject2.nb

Potentials
With R={1,2,3,10}

ORIGINAL POTENTIAL
SINK 1

ORIGINAL POTENTIAL
SINK 2

ORIGINAL POTENTIAL
SINK 3

Printed by Wolfram Mathematica Student Edition

39

40

SeniorProject2.nb

Literature Cited :
Stojmirovic, A. and Yu, Y.-K. 2007. Information flow in interaction Networks.
J. Comput. Biol. 14, 1115-1143.
National Center for Biotechnology Information, National Library of Medicine,
National Institutes of Health, Bethesda, Maryland.

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