Lossless Compression of Semi-Ordered Trees

In this paper, authors are interested in the problem of lossless compression of unlabeled semi-ordered trees. Semi-ordered trees are a class of trees that present an order between some sibling while some other sibling are unordered. They offer a wide possibility of applications especially for the representation of plants architecture. Authors show that these trees present remarkable compression properties covering those of ordered and unordered trees. To illustrate this approach, authors apply these notions to a particular class of semi-ordered trees which is the most studied branching structure particularly for a botanical motivation, namely axial trees.

Extremal Values of the Sackin Tree Balance Index

Tree balance plays an important role in different research areas like theoretical computer science and mathematical phylogenetics. For example, it has long been known that under the Yule model, a pure birth process, imbalanced trees are more likely than balanced ones. Also, concerning ordered search trees, more balanced ones allow for more efficient data structuring than imbalanced ones. Therefore, different methods to measure the balance of trees were introduced. The Sackin index is one of the most frequently used measures for this purpose. In many contexts, statements about the minimal and maximal values of this index have been discussed, but formal proofs have only been provided for some of them, and only in the context of ordered binary (search) trees, not for general rooted trees. Moreover, while the number of trees with maximal Sackin index as well as the number of trees with minimal Sackin index when the number of leaves is a power of 2 are relatively easy to understand, the number of trees with minimal Sackin index for all other numbers of leaves has been completely unknown. In this manuscript, we extend the findings on trees with minimal and maximal Sackin indices from the literature on ordered trees and subsequently use our results to provide formulas to explicitly calculate the numbers of such trees. We also extend previous studies by analyzing the case when the underlying trees need not be binary. Finally, we use our results to contribute both to the phylogenetic as well as the computer scientific literature using the new findings on Sackin minimal and maximal trees to derive formulas to calculate the number of both minimal and maximal phylogenetic trees as well as minimal and maximal ordered trees both in the binary and non-binary settings. All our results have been implemented in the Mathematica package SackinMinimizer, which has been made publicly available.

Tree limits and limits of random trees

We explore the tree limits recently defined by Elek and Tardos. In particular, we find tree limits for many classes of random trees. We give general theorems for three classes of conditional Galton–Watson trees and simply generated trees, for split trees and generalized split trees (as defined here), and for trees defined by a continuous-time branching process. These general results include, for example, random labelled trees, ordered trees, random recursive trees, preferential attachment trees, and binary search trees.

From Relation Algebra to Semi-join Algebra: An Approach to Graph Query Optimization

Many graph query languages rely on composition to navigate graphs and select nodes of interest, even though evaluating compositions of relations can be costly. Often, this need for composition can be reduced by rewriting toward queries using semi-joins instead, resulting in a significant reduction of the query evaluation cost. We study techniques to recognize and apply such rewritings. Concretely, we study the relationship between the expressive power of the relation algebras, which heavily rely on composition, and the semi-join algebras, which replace composition in favor of semi-joins. Our main result is that each fragment of the relation algebras where intersection and/or difference is only used on edges (and not on complex compositions) is expressively equivalent to a fragment of the semi-join algebras. This expressive equivalence holds for node queries evaluating to sets of nodes. For practical relevance, we exhibit constructive rules for rewriting relation algebra queries to semi-join algebra queries and prove that they lead to only a well-bounded increase in the number of steps needed to evaluate the rewritten queries. In addition, on sibling-ordered trees, we establish new relationships among the expressive power of Regular XPath, Conditional XPath, FO-logic and the semi-join algebra augmented with restricted fixpoint operators.

Supermodular ordering of Poisson and binomial random vectors by tree-based correlations

We construct a dependence structure for binomial, Poisson and Gaussian random vectors, based on partially ordered binary trees and sums of independent random variables. Using this construction, we characterize the supermodular ordering of such random vectors via the componentwise ordering of their covariance matrices. For this, we apply Möbius inversion techniques on partially ordered trees, which allow us to connect the Lévy measures of Poisson random vectors on the discrete d-dimensional hypercube to their covariance matrices.

Counting, Generating, Analyzing and Sampling Tree Alignments

Pairwise ordered tree alignment are combinatorial objects that appear in important applications, such as RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical sets of matches between identical pairs of trees. This ambiguity is uninformative, and detrimental to any probabilistic analysis. In this work, we consider tree alignments up to equivalence. Our first result is a precise asymptotic enumeration of tree alignments, obtained from a context-free grammar by mean of basic analytic combinatorics. Our second result focuses on alignments between two given ordered trees [Formula: see text] and [Formula: see text]. By refining our grammar to align specific trees, we obtain a decomposition scheme for the space of alignments, and use it to design an efficient dynamic programming algorithm for sampling alignments under the Gibbs-Boltzmann probability distribution. This generalizes existing tree alignment algorithms, and opens the door for a probabilistic analysis of the space of suboptimal alignments.

Spurious Ambiguity and Focalization

Spurious ambiguity is the phenomenon whereby distinct derivations in grammar may assign the same structural reading, resulting in redundancy in the parse search space and inefficiency in parsing. Understanding the problem depends on identifying the essential mathematical structure of derivations. This is trivial in the case of context free grammar, where the parse structures are ordered trees; in the case of type logical categorial grammar, the parse structures are proof nets. However, with respect to multiplicatives, intrinsic proof nets have not yet been given for displacement calculus, and proof nets for additives, which have applications to polymorphism, are not easy to characterize. In this context we approach here multiplicative-additive spurious ambiguity by means of the proof-theoretic technique of focalization.