17,442 research outputs found
Scalable global alignment for multiple biological networks
<p>Abstract</p> <p>Background</p> <p>Advances in high-throughput technology has led to an increased amount of available data on protein-protein interaction (PPI) data. Detecting and extracting functional modules that are common across multiple networks is an important step towards understanding the role of functional modules and how they have evolved across species. A global protein-protein interaction network alignment algorithm attempts to find such functional orthologs across multiple networks.</p> <p>Results</p> <p>In this article, we propose a scalable global network alignment algorithm based on clustering methods and graph matching techniques in order to detect conserved interactions while simultaneously attempting to maximize the sequence similarity of nodes involved in the alignment. We present an algorithm for multiple alignments, in which several PPI networks are aligned. We empirically evaluated our algorithm on three real biological datasets with 6 different species and found that our approach offers a significant benefit both in terms of quality as well as speed over the current state-of-the-art algorithms.</p> <p>Conclusion</p> <p>Computational experiments on the real datasets demonstrate that our multiple network alignment algorithm is a more efficient and effective algorithm than the state-of-the-art algorithm, IsoRankN. From a qualitative standpoint, our approach also offers a significant advantage over IsoRankN for the multiple network alignment problem.</p
An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner.
Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological networks holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology-the "structure" of the network-is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment-which is an essentially solved problem-network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used.Here we introduce SANA, the Simulated Annealing Network Aligner. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between two or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks
Stochastic Block Coordinate Frank-Wolfe Algorithm for Large-Scale Biological Network Alignment
With increasingly "big" data available in biomedical research, deriving
accurate and reproducible biology knowledge from such big data imposes enormous
computational challenges. In this paper, motivated by recently developed
stochastic block coordinate algorithms, we propose a highly scalable randomized
block coordinate Frank-Wolfe algorithm for convex optimization with general
compact convex constraints, which has diverse applications in analyzing
biomedical data for better understanding cellular and disease mechanisms. We
focus on implementing the derived stochastic block coordinate algorithm to
align protein-protein interaction networks for identifying conserved functional
pathways based on the IsoRank framework. Our derived stochastic block
coordinate Frank-Wolfe (SBCFW) algorithm has the convergence guarantee and
naturally leads to the decreased computational cost (time and space) for each
iteration. Our experiments for querying conserved functional protein complexes
in yeast networks confirm the effectiveness of this technique for analyzing
large-scale biological networks
Data-driven network alignment
Biological network alignment (NA) aims to find a node mapping between
species' molecular networks that uncovers similar network regions, thus
allowing for transfer of functional knowledge between the aligned nodes.
However, current NA methods do not end up aligning functionally related nodes.
A likely reason is that they assume it is topologically similar nodes that are
functionally related. However, we show that this assumption does not hold well.
So, a paradigm shift is needed with how the NA problem is approached. We
redefine NA as a data-driven framework, TARA (daTA-dRiven network Alignment),
which attempts to learn the relationship between topological relatedness and
functional relatedness without assuming that topological relatedness
corresponds to topological similarity, like traditional NA methods do. TARA
trains a classifier to predict whether two nodes from different networks are
functionally related based on their network topological patterns. We find that
TARA is able to make accurate predictions. TARA then takes each pair of nodes
that are predicted as related to be part of an alignment. Like traditional NA
methods, TARA uses this alignment for the across-species transfer of functional
knowledge. Clearly, TARA as currently implemented uses topological but not
protein sequence information for this task. We find that TARA outperforms
existing state-of-the-art NA methods that also use topological information,
WAVE and SANA, and even outperforms or complements a state-of-the-art NA method
that uses both topological and sequence information, PrimAlign. Hence, adding
sequence information to TARA, which is our future work, is likely to further
improve its performance
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