Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment^{ †}
Abstract
:1. Introduction
1.1. Previous Work
1.2. Contribution
2. Preliminaries
3. Methods
3.1. Solving Strategies
3.1.1. Subgradient Optimization
Algorithm 1: SubgradientOpt$(\lambda ,M,N)$ 

3.1.2. Dual Descent
Algorithm 2: DualDescent$(\lambda ,L)$ 

3.1.3. Overall Method
Algorithm 3: Natalie$(K,L,M,N)$ 

4. Experimental Evaluation
Species  Nodes  Annotated  Interactions 

cel (c)  5948  4694  23,496 
sce (s)  6018  5703  131,701 
dme (d)  7433  6006  26,829 
rno (r)  8002  6786  32,527 
mmu (m)  9109  8060  38,414 
hsa (h)  11,512  9328  67,858 
4.1. Topological Measures
4.2. GO Similarity
5. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
References
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ElKebir, M.; Heringa, J.; Klau, G.W. Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment. Algorithms 2015, 8, 10351051. https://doi.org/10.3390/a8041035
ElKebir M, Heringa J, Klau GW. Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment. Algorithms. 2015; 8(4):10351051. https://doi.org/10.3390/a8041035
Chicago/Turabian StyleElKebir, Mohammed, Jaap Heringa, and Gunnar W. Klau. 2015. "Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment" Algorithms 8, no. 4: 10351051. https://doi.org/10.3390/a8041035