A decorated tree approach to random permutations in substitution-closed classes

We establish a novel bijective encoding that represents permutations as forests of decorated (or enriched) trees. This allows us to prove local convergence of uniform random permutations from substitution-closed classes satisfying a criticality constraint. It also enables us to reprove and strengthen permuton limits for these classes in a new way, that uses a semi-local version of Aldous' skeleton decomposition for size-constrained Galton--Watson trees.Comment: New version including referee's corrections, accepted for publication in Electronic Journal of Probabilit

The Complexity of Rooted Phylogeny Problems

Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the literals are rooted triples, is there a rooted binary tree that satisfies the formula? If the formulas do not contain disjunctions, the problem becomes the famous rooted triple consistency problem, which can be solved in polynomial time by an algorithm of Aho, Sagiv, Szymanski, and Ullman. If the clauses in the formulas are restricted to disjunctions of negated triples, Ng, Steel, and Wormald showed that the problem remains NP-complete. We systematically study the computational complexity of the problem for all such restrictions of the clauses in the input formula. For certain restricted disjunctions of triples we present an algorithm that has sub-quadratic running time and is asymptotically as fast as the fastest known algorithm for the rooted triple consistency problem. We also show that any restriction of the general rooted phylogeny problem that does not fall into our tractable class is NP-complete, using known results about the complexity of Boolean constraint satisfaction problems. Finally, we present a pebble game argument that shows that the rooted triple consistency problem (and also all generalizations studied in this paper) cannot be solved by Datalog

Solving the intractable problem: optimal performance for worst case scenarios in XML twig pattern matching

In the history of databases, eXtensible Markup Language (XML) has been thought of as the standard format to store and exchange semi-structured data. With the advent of IoT, XML technologies can play an important role in addressing the issue of processing a massive amount of data generated from heterogeneous devices. As the number and complexity of such datasets increases there is a need for algorithms which are able to index and retrieve XML data efficiently even for complex queries. In this context twig pattern matching , finding all occurrences of a twig pattern query (TPQ), is a core operation in XML query processing. Until now holistic joins have been considered the state-of-the-art TPQ processing algorithms, but they fail to guarantee an optimal evaluation except at the expense of excessive storage costs which limit their scope in large datasets. In this article, we introduce a new approach which significantly outperforms earlier methods in terms of both the size of the intermediate storage and query running time. The approach presented here uses Child Prime Labels (Alsubai & North, 2018) to improve the filtering phase of bottom-up twig matching algorithms and a novel algorithm which avoids the use of stacks, thus improving TPQs processing efficiency. Several experiments were conducted on common benchmarks such as DBLP, XMark and TreeBank datasets to study the performance of the new approach. Multiple analyses on a range of twig pattern queries are presented to demonstrate the statistical significance of the improvements

Phylogenetic CSPs are Approximation Resistant

We study the approximability of a broad class of computational problems -- originally motivated in evolutionary biology and phylogenetic reconstruction -- concerning the aggregation of potentially inconsistent (local) information about $n$ items of interest, and we present optimal hardness of approximation results under the Unique Games Conjecture. The class of problems studied here can be described as Constraint Satisfaction Problems (CSPs) over infinite domains, where instead of values $\{0,1\}$ or a fixed-size domain, the variables can be mapped to any of the $n$ leaves of a phylogenetic tree. The topology of the tree then determines whether a given constraint on the variables is satisfied or not, and the resulting CSPs are called Phylogenetic CSPs. Prominent examples of Phylogenetic CSPs with a long history and applications in various disciplines include: Triplet Reconstruction, Quartet Reconstruction, Subtree Aggregation (Forbidden or Desired). For example, in Triplet Reconstruction, we are given $m$ triplets of the form $ij|k$ (indicating that ``items $i,j$ are more similar to each other than to $k$'') and we want to construct a hierarchical clustering on the $n$ items, that respects the constraints as much as possible. Despite more than four decades of research, the basic question of maximizing the number of satisfied constraints is not well-understood. The current best approximation is achieved by outputting a random tree (for triplets, this achieves a 1/3 approximation). Our main result is that every Phylogenetic CSP is approximation resistant, i.e., there is no polynomial-time algorithm that does asymptotically better than a (biased) random assignment. This is a generalization of the results in Guruswami, Hastad, Manokaran, Raghavendra, and Charikar (2011), who showed that ordering CSPs are approximation resistant (e.g., Max Acyclic Subgraph, Betweenness).Comment: 45 pages, 11 figures, Abstract shortened for arxi