Paper Info
Title
Gene Set Cultural Algorithm: A Cultural Algorithm Approach to Reconstruct Networks from Gene Sets
Abstract
With the increasing availability of gene sets, novel approaches that focus on reconstructing networks from gene sets are of interest. Currently, few computational approaches explore the search space of candidate networks using a parallel search. As such, novel methods that employ search agents are needed to help better escape local optima. In particular, gene sets may model signal transduction events, which refer to linear chains or cascades of reactions starting at the cell membrane and ending at the cell nucleus. These events may be indirectly observed as a set of unordered and overlapping gene sets. Thus, the underlying goal is to reverse engineer the order information within each gene set to reconstruct the underlying source network. To achieve this goal, we developed the Gene Set Cultural Algorithm to discover the true order of the gene sets and to reconstruct the underlying network. In a proof of concept study, we show that the Gene Set Cultural Algorithm can satisfactorily reconstruct three E. coli networks from the DREAM initiative using simulated and unordered gene sets as the input.
Year
DOI
Venue
2013
10.1145/2506583.2506650
BCB
Keywords
Field
DocType
underlying network,underlying source network,reconstruct networks,search space,gene sets,underlying goal,parallel search,overlapping gene set,cultural algorithm approach,gene set,unordered gene set,search agent,gene set cultural algorithm,cultural algorithm
Data mining,Gene,Computer science,Parallel search,Local optimum,Reverse engineering,Proof of concept,Artificial intelligence,Cultural algorithm,Bioinformatics,Overlapping gene,Machine learning
Conference
Citations 
PageRank 
References 
1
0.36
9
Authors
5
Name
Order
Citations
PageRank
Thair Judeh1102.20
Thaer Jayyousi2141.42
Lipi Acharya331.50
Robert G. Reynolds4610188.20
Dongxiao Zhu516725.91