EE 5940: Circuits, Computation and Biology

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EE 5940 Circuits, Computation and Biology
Marc D. Riedel
Assistant Professor, ECE University of Minnesota
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Design Scenario
Bacteria are engineered to produce an anti-cancer
drug
triggering compound
drug
E. Coli
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Design Scenario
Bacteria invade the cancerous tissue
cancerous tissue
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Design Scenario
The trigger elicits the bacteria to produce the
drug
Bacteria invade the cancerous tissue
cancerous tissue
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Design Scenario
The trigger elicits the bacteria produce the
drug
Problem patient receives too high of a dose of
the drug.
cancerous tissue
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Design Scenario
Conceptual design problem.
Constraints

• Bacteria are all identical.
• Population density is fixed.
• Exposure to triggering compound is uniform.

Requirement

• Control quantity of drug that is produced.

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Design Scenario
Approach elicit a fractional response.
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Synthesizing Stochasticity
Approach engineer a probabilistic response in
each bacterium.
produce drug
with Prob. 0.3
triggering compound
dont produce drug
with Prob. 0.7
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Synthesizing Stochasticity
Generalization engineer a probability
distribution on logical combinations of different
outcomes.
A
with Prob. 0.3
B
with Prob. 0.2
cell
C
with Prob. 0.5
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Synthesizing Stochasticity
Generalization engineer a probability
distribution on logical combinations of different
outcomes.
A
with Prob. 0.3
B
with Prob. 0.2
cell
C
with Prob. 0.5
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Synthesizing Stochasticity
Generalization engineer a probability
distribution on logical combinations of different
outcomes.
X
Y
cell
Further program probability distribution with
(relative) quantity of input compounds.
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Engineering vs. Biology vs. Mathematics
Papa
Beaker
Dilbert
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Its not a bug, its a feature.
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Jargon vs.Terminology
Now this end is called the thagomizer, after the
late Thag Simmons.
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Communicating Ideas
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Domains of Expertise

• Vision
• Language
• Abstract Reasoning
• Farming

• Number Crunching
• Mining Data
• Iterative Calculations

Human
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(No Transcript)
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Circuits Computers as a Window into our
Linguistic Brains
Conceives of circuits and computation by
applying language.
?
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If You Dont Know the Answer
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Feedback in Digital Circuits
Acyclic (i.e., feed-forward) circuits are always
combinational.
1
1
0
1
0
0
0
1
0
1
1
1
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Combinational Circuits
Acyclic (i.e., feed-forward) circuits are always
combinational.
Are combinational circuits always acyclic?
Combinational networks can never have feedback
loops.
A combinational circuit is a directed acyclic
graph (DAG)...
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Combinational Circuits
Acyclic (i.e., feed-forward) circuits are always
combinational.
Are combinational circuits always acyclic?
Combinational networks can never have feedback
loops.
A combinational circuit is a directed acyclic
graph (DAG)...
Designers and EDA tools follow this practice.
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Feedback in Digital Circuits
x
a




)))
(
(
(
f
x
c
d
x
a
b
f
1
1
b
x
c
d
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Feedback in Digital Circuits
0
0
x
AND
a
OR




x
0
)))
(
(
(
f
c
d
x
a
b
f
0
1
1
b
AND
0
x
OR
c
AND
d
OR
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Feedback in Digital Circuits
0
0
x
AND
a
OR




x
)))
(
(
(
f
x
c
d
a
b
f
1
1
b
AND
0
x
OR
c
AND
d
OR
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Feedback in Digital Circuits
1
x
AND
a
OR




x
1
x
1
)))
(
(
(
f
c
d
a
b
f
1
1
b
AND
1
1
x
OR
c
AND
d
OR
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Feedback in Digital Circuits
Circuit is cyclic yet combinational computes
functions f1 and f2 with 6 gates.
1
x
AND
An acyclic circuit computing these functions
requires 8 gates.
a
OR



x
))
(
(
c
d
a
b
f
1
b
AND
1
1
x
OR
c
AND



)
(
a
b
x
c
d
f
2
d
OR
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Feedback in Digital Circuits
Circuit is cyclic yet combinational computes
functions f1 and f2 with 6 gates.
There is no feedback in a functional sense.
x
A cyclic topology permits greater overlap in the
computation of the two functions
AND
An acyclic circuit computing these functions
requires 8 gates.
a
OR



x
))
(
(
c
d
a
b
f
1
b
AND
x
OR
c
AND



)
(
a
b
x
c
d
f
2
d
OR
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Feedback in Biology
Thomas Knight et. al.
no output protein
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Feedback in Biology
Thomas Knight et. al.
no input repressor protein
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Feedback in Biology
Example Genetic regulatory system.
input A
output Z
repression
transcription
translation
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Feedback in Biology
View that logical dependencies cannot be cyclic
is prevalent Nature knows better!