Complex networks are at the core of an intense research activity. However, in most cases, intricate and costly measurement procedures are needed to explore their structure. In some cases, these measurements rely on link queries: given two nodes, it is possible to test the existence of a link between them. These tests may be costly, and thus minimizing their number while maximizing the number of discovered links is a key issue. This paper studies this problem: we observe that properties classically observed on real-world complex networks give hints for their efficient measurement; we derive simple principles and several measurement strategies based on this, and experimentally evaluate their efficiency on real-world cases. In order to do so, we introduce methods to evaluate the efficiency of strategies. We also explore the bias that different measurement strategies may induce.

Motivated from parallel network mapping, we provide efficient query complexity and round complexity bounds for graph reconstruction using distance queries, including a bound that improves a previous sequential complexity bound. Our methods use a high-probability parametric parallelization of a graph clustering technique of Thorup and Zwick, which may be of independent interest.

In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer security settings, which can be abstracted in terms of two parties, a responder, Alice, who must correctly answer queries of a given type regarding a degree-d tree, T, and a querier, Bob, who issues batches of queries, with each query in a batch being independent of the others, so as to eventually infer the structure of T. We show that a querier can efficiently reconstruct an n-node degree-d tree, T, with a logarithmic number of rounds and quasilinear number of queries, with high probability, for various types of queries, including relative-distance queries and path queries. Our results are all asymptotically optimal and improve the asymptotic (sequential) query complexity for one of the problems we study. Moreover, through an experimental analysis using both real-world and synthetic data, we provide empirical evidence that our algorithms provide significant parallel speedups while also improving the total query complexities for the problems we study.

We study the parallel query complexity of reconstructing binary trees from simple queries involving their nodes. We show that a querier can efficiently reconstruct a binary tree with a logarithmic number of rounds and quasilinear number of queries, with high probability, for various types of queries.

We consider the NP-complete problem of tracking paths in a graph, first introduced by Banik et. al. [3]. Given an undirected graph with a source $s$ and a destination $t$, find the smallest subset of vertices whose intersection with any $s-t$ path results in a unique sequence. In this paper, we show that this problem remains NP-complete when the graph is planar and we give a 4-approximation algorithm in this setting. We also show, via Courcelle's theorem, that it can be solved in linear time for graphs of bounded-clique width, when its clique decomposition is given in advance.

We show new applications of the nearest-neighbor chain algorithm, a technique that originated in agglomerative hierarchical clustering. We apply it to a diverse class of geometric problems: we construct the greedy multi-fragment tour for Euclidean TSP in $O(n\log n)$ time in any fixed dimension and for Steiner TSP in planar graphs in $O(n\sqrt{n}\log n)$ time; we compute motorcycle graphs (which are a central part in straight skeleton algorithms) in $O(n^{4/3+\varepsilon})$ time for any $\varepsilon>0$; we introduce a narcissistic variant of the $k$-attribute stable matching model, and solve it in $O(n^{2-4/(k(1+\varepsilon)+2)})$ time; we give a linear-time $2$-approximation for a 1D geometric set cover problem with applications to radio station placement.

MOTIVATION: In this article, we consider the bicriteria pairwise sequence alignment problem and propose extensions of dynamic programming algorithms for several problem variants with a novel pruning technique that efficiently reduces the number of states to be processed. Moreover, we present a method for the construction of phylogenetic trees based on this bicriteria framework. Two exemplary cases are discussed. RESULTS: Numerical results on a real dataset show that this approach is very fast in practice. The pruning technique saves up to 90% in memory usage and 80% in CPU time. Based on this method, phylogenetic trees are constructed from real-life data. In addition of providing complementary information, some of these trees match those obtained by the Maximum Likelihood method. AVAILABILITY AND IMPLEMENTATION: Source code is freely available for download at URL http://eden.dei.uc.pt/paquete/MOSAL, implemented in C and supported on Linux, MAC OS and MS Windows.