A parallelizable Model for Cancer Tissue Heterogeneity

Submitted by: Anik Chaudhuri

Literature review:
An important problem in systems biology is to model gene regulatory networks which can then be
utilized to develop novel therapeutic methods for cancer treatment. Knowledge about which
proteins/genes are dysregulated in a regulatory network, such as in the Mitogen Activated Protein
Kinase (MAPK) Network, can be used not only to decide upon which therapy to use for a particular
case of cancer, but also help in discovering effective targets for new drugs. This problem can be solved
by using the message passing algorithm.

Factor Graphs:
Factor Graphs are an important tool used in various applications such as signal processing and
telecommunications. Many algorithms can be easily understood and derived using the factor graph
approach. These include Kalman Filters, the Viterbi Algorithm, the Forward Backward algorithm and
Turbo Codes to name a few. The approach involves first representing the probability model as a factor
graph and then applying the message passing algorithm along the edges.
The message passing algorithm terminates and gives exact marginals for the cases where the factor
graph has no cycles. But the most interesting applications are for those cases where the factor graph has
cycles, where the marginals are calculated by iteratively updating the messages. A similar approach was
used in Mohanty et. al, 2014 to approximate the marginal posterior distribution of the unknown
parameters. Here, the unknown parameters are the probability of the fault locations in the Boolean
network.

14/11/2020