Biomedical Engineering Reference
In-Depth Information
the ATPG formulation, allowing for different control strategies depending on desired
specifications (i.e. selection with fewest drugs or fewest side effects). Unlike [
13
],
[
14
], our method can also determine the
best
drug selection for a BN, where the
faulty gene location is unknown.
5.3
Method
In this section, we present our SAT-based ATPG method. Before the method is
described in detail, we first provide definitions for fault modeling and Boolean
Satisfiability.
5.3.1
Fault Terminology
Definition V.1:
A manifestation of a defect at the abstracted function level is called
a
fault
.
In an IC, the difference between a defect and a fault can be explained as imperfec-
tions in the hardware and function, respectively. A defect is an incorrectly fabricated
circuit (with a short circuit, open circuit, etc.) and the fault is the resulting change in
circuit functionality. While in genomics, examples of biological defects can include
mutations in the gene activation site, malformation of the protein folding, and prob-
lems in the gene product transport. Likewise, an example of a biological fault is a
modification of the logical function of a gene, producing the incorrect output.
Definition V.2:
A
stuck-at fault
is modeled by assigning a fixed (0 or 1) value to a
signal line (input or output of a logic gate) in the circuit.
Definition V.3:
An
untestable fault
is a fault which no test can detect. Untestable
faults appear in two situations.
Faults that are
redundant
, whose presence does not change the output function
(behavior) of the circuit.
Faults that change the output behavior of the circuit, but no test (drug vector in
the context of cancer therapy) can be generated to rectify the fault.
5.3.2
Stuck-at Fault Modeling
In the Boolean network model for a GRN, the activity of genes is modeled as a
Boolean circuit. We assume the circuit is modeled as an interconnection of Boolean
gates. A stuck-at fault is assumed to only affect interconnections (wires or nets)
between gates. Each net can have one of two types of faults: stuck-at-1 or stuck-at-0
