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 |
|
3.1.2. Dual Descent
Algorithm 2: DualDescent |
|
3.1.3. Overall Method
Algorithm 3: Natalie |
|
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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El-Kebir, M.; Heringa, J.; Klau, G.W. Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment. Algorithms 2015, 8, 1035-1051. https://doi.org/10.3390/a8041035
El-Kebir M, Heringa J, Klau GW. Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment. Algorithms. 2015; 8(4):1035-1051. https://doi.org/10.3390/a8041035
Chicago/Turabian StyleEl-Kebir, 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: 1035-1051. https://doi.org/10.3390/a8041035