Every alignment algorithm consists of two orthogonal components: an objective function M measuring the quality an alignment, and a search algorithm that explores the space of alignments looking for ones scoring well according to M . We introduce a new search algorithm called SANA (Simulated Annealing Network Aligner) and apply it to protein-protein interaction networks using S 3 as the the topological measure. Compared against 12 recent algorithms, SANA produces 5-10 times as many correct node mappings as the others when the correct answer is known. We expose an anti-correlation in many existing aligners between their ability to produce good topological vs. functional similarity scores, whereas SANA usually outscores other methods in both measures. If given the perfect objective function encoding the identity mapping, SANA quickly converges to the perfect solution while many other algorithms falter. We observe that when aligning networks with a known mapping and optimizing only S 3 , SANA creates alignments that are not perfect and yet whose S 3 scores match that of the perfect alignment. We call this phenomenon saturation of the topological score. Saturation implies that a measure's correlation with alignment correctness falters before the perfect alignment is reached. This, combined with SANA's ability to produce the perfect alignment if given the perfect objective function, suggests that better objective functions may lead to dramatically better alignments. We conclude that future work should focus on finding better objective functions, and offer SANA as the search algorithm of choice.
Supplementary data are available at Bioinformatics online.
We introduce a novel method for defining geographic districts in road networks using stable matching. In this approach, each geographic district is defined in terms of a center, which identifies a location of interest, such as a post office or polling place, and all other network vertices must be labeled with the center to which they are associated. We focus on defining geographic districts that are equitable, in that every district has the same number of vertices and the assignment is stable in terms of geographic distance. That is, there is no unassigned vertex-center pair such that both would prefer each other over their current assignments. We solve this problem using a version of the classic stable matching problem, called symmetric stable matching, in which the preferences of the elements in both sets obey a certain symmetry. In our case, we study a graph-based version of stable matching in which nodes are stably matched to a subset of nodes denoted as centers, prioritized by their shortest-path distances, so that each center is apportioned a certain number of nodes. We show that, for a planar graph or road network with n nodes and k centers, the problem can be solved in O(n √ n log n) time, which improves upon the O(nk) runtime of using the classic Gale-Shapley stable matching algorithm when k is large. Finally, we provide experimental results on road networks for these algorithms and a heuristic algorithm that performs better than the Gale-Shapley algorithm for any range of values of k.
We introduce models and algorithmic foundations for graph watermarking. Our frameworks include security definitions and proofs, as well as characterizations when graph watermarking is algorithmically feasible, in spite of the fact that the general problem is NP-complete by simple reductions from the subgraph isomorphism or graph edit distance problems. In the digital watermarking of many types of files, an implicit step in the recovery of a watermark is the mapping of individual pieces of data, such as image pixels or movie frames, from one object to another. In graphs, this step corresponds to approximately matching vertices of one graph to another based on graph invariants such as vertex degree. Our approach is based on characterizing the feasibility of graph watermarking in terms of keygen, marking, and identification functions defined over graph families with known distributions. We demonstrate the strength of this approach with exemplary watermarking schemes for two random graph models, the classic Erdős-Rényi model and a random power-law graph model, both of which are used to model real-world networks.
We consider data structures for graphs where we maintain a subset of the nodes called sites, and allow proximity queries, such as asking for the closest site to a query node, and update operations that enable or disable nodes as sites. We refer to a data structure that can efficiently react to such updates as reactive. We present novel reactive proximity data structures for graphs of polynomial expansion, i.e., the class of graphs with small separators, such as planar graphs and road networks. Our data structures can be used directly in several logistical problems and geographic information systems dealing with real-time data, such as emergency dispatching. We experimentally compare our data structure to Dijkstra's algorithm in a system emulating random queries in a real road network.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.