Reconstructing Biological and Digital Phylogenetic Trees in Parallel

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

Optimal distance query reconstruction for graphs without long induced cycles

Let $G=(V,E)$ be an $n$-vertex connected graph of maximum degree $\Delta$. Given access to $V$ and an oracle that given two vertices $u,v\in V$, returns the shortest path distance between $u$ and $v$, how many queries are needed to reconstruct $E$? We give a simple deterministic algorithm to reconstruct trees using $\Delta n\log_\Delta n+(\Delta+2)n$ distance queries and show that even randomised algorithms need to use at least $\frac1{100} \Delta n\log_\Delta n$ queries in expectation. The best previous lower bound was an information-theoretic lower bound of $\Omega(n\log n/\log \log n)$. Our lower bound also extends to related query models including distance queries for phylogenetic trees, membership queries for learning partitions and path queries in directed trees. We extend our deterministic algorithm to reconstruct graphs without induced cycles of length at least $k$ using $O_{\Delta,k}(n\log n)$ queries, which includes various graph classes of interest such as chordal graphs, permutation graphs and AT-free graphs. Since the previously best known randomised algorithm for chordal graphs uses $O_{\Delta}(n\log^2 n)$ queries in expectation, we both get rid off the randomness and get the optimal dependency in $n$ for chordal graphs and various other graph classes. Finally, we build on an algorithm of Kannan, Mathieu, and Zhou [ICALP, 2015] to give a randomised algorithm for reconstructing graphs of treelength $k$ using $O_{\Delta,k}(n\log^2n)$ queries in expectation.Comment: 35 page

Fully dynamic maintenance of Euclidean minimum spanning trees and maxima of decomposable functions

We maintain the minimum spanning tree of a point set in the plane, subject to point insertions and deletions, in time O(n^1/2 log^2 n) per update operation. We reduce the problem to maintaining bichromatic closest pairs, which we solve in time O(n^E) per update. Our algorithm uses a novel construction, the ordered nearest neighbors of a sequence of points. Any point set or bichromatic point set can be ordered so that this graph is a simple path. Our results generalize to higher dimensions, and to fully dynamic algorithms for maintaining maxima of decomposable functions, including the diameter of a point set and the bichromatic farthest pair

Distance Oracles for Time-Dependent Networks

We present the first approximate distance oracle for sparse directed networks with time-dependent arc-travel-times determined by continuous, piecewise linear, positive functions possessing the FIFO property. Our approach precomputes $(1+\epsilon)-$approximate distance summaries from selected landmark vertices to all other vertices in the network. Our oracle uses subquadratic space and time preprocessing, and provides two sublinear-time query algorithms that deliver constant and $(1+\sigma)-$approximate shortest-travel-times, respectively, for arbitrary origin-destination pairs in the network, for any constant $\sigma > \epsilon$. Our oracle is based only on the sparsity of the network, along with two quite natural assumptions about travel-time functions which allow the smooth transition towards asymmetric and time-dependent distance metrics.Comment: A preliminary version appeared as Technical Report ECOMPASS-TR-025 of EU funded research project eCOMPASS (http://www.ecompass-project.eu/). An extended abstract also appeared in the 41st International Colloquium on Automata, Languages, and Programming (ICALP 2014, track-A