Quantifying the degree of self-nestedness of trees. Application to the structural analysis of plants

17 pagesInternational audienceIn this paper we are interested in the problem of approximating trees by trees with a particular self-nested structure. Self-nested trees are such that all their subtrees of a given height are isomorphic. We show that these trees present remarkable compression properties, with high compression rates. In order to measure how far a tree is from being a self-nested tree, we then study how to quantify the degree of self-nestedness of any tree. For this, we define a measure of the self-nestedness of a tree by constructing a self-nested tree that minimizes the distance of the original tree to the set of self-nested trees that embed the initial tree. We show that this measure can be computed in polynomial time and depict the corresponding algorithm. The distance to this nearest embedding self-nested tree (NEST) is then used to define compression coefficients that reflect the compressibility of a tree. To illustrate this approach, we then apply these notions to the analysis of plant branching structures. Based on a database of simulated theoretical plants in which different levels of noise have been introduced, we evaluate the method and show that the NESTs of such branching structures restore partly or completely the original, noiseless, branching structures. The whole approach is then applied to the analysis of a real plant (a rice panicle) whose topological structure was completely measured. We show that the NEST of this plant may be interpreted in biological terms and may be used to reveal important aspects of the plant growth

Sublinear DTD Validity

International audienceWe present an efficient algorithm for testing approximate DTD validity modulo the strong tree edit distance. Our algorithm inspects XML documents in a probabilistic manner. It detects with high probability the nonvalidity of XML documents with a large fraction of errors, measured in terms of the strong tree edit distance from the DTD. The run time depends polynomially on the depth of the XML document tree but not on its size, so that it is sublinear in most cases. Therefore, our algorithm can be used to speed up exact DTD validators that run in linear time. We also prove a negative result showing that the run time of any approximate DTD validity tester must depend on the depth of the input tree. A long version is available here.</p

Overlaying Circuit Clauses for Secure Computation

Given a set S = {C_1,...,C_k } of Boolean circuits, we show how to construct a universal for S circuit C_0, which is much smaller than Valiant’s universal circuit or a circuit incorporating all C_1,...,C_k. Namely, given C_1,...,C_k and viewing them as directed acyclic graphs (DAGs) D_1,...,D_k, we embed them in a new graph D_0. The embedding is such that a GC garbling of any of C_1,...,C_k could be implemented by a corresponding garbling of a circuit corresponding to D_0. We show how to improve Garbled Circuit (GC) and GMW-based secure function evaluation (SFE) of circuits with if/switch clauses using such S-universal circuit. The most interesting case here is the application to the GMW approach. We provide a novel observation that in GMW the cost of processing a gate is almost the same for 5 (or more) Boolean inputs, as it is for the usual case of 2 Boolean inputs. While we expect this observation to greatly improve general GMW-based computation, in our context this means that GMW gates can be programmed almost for free, based on the secret-shared programming of the clause. Our approach naturally and cheaply supports nested clauses. Our algorithm is a heuristic; we show that solving the circuit embedding problem is NP-hard. Our algorithms are in the semi-honest model and are compatible with Free-XOR. We report on experimental evaluations and discuss achieved performance in detail. For 32 diverse circuits in our experiment, our construction results 6.1x smaller circuit than prior techniques

The complexity of counting models of linear-time temporal logic

We determine the complexity of counting models of bounded size of specifications expressed in Linear-time Temporal Logic. Counting word-models is #P-complete, if the bound is given in unary, and as hard as counting accepting runs of nondeterministic polynomial space Turing machines, if the bound is given in binary. Counting tree-models is as hard as counting accepting runs of nondeterministic exponential time Turing machines, if the bound is given in unary. For a binary encoding of the bound, the problem is at least as hard as counting accepting runs of nondeterministic exponential space Turing machines. On the other hand, it is not harder than counting accepting runs of nondeterministic doubly-exponential time Turing machines

Grammar Boosting: A New Technique for Proving Lower Bounds for Computation over Compressed Data

Grammar compression is a general compression framework in which a string $T$ of length $N$ is represented as a context-free grammar of size $n$ whose language contains only $T$. In this paper, we focus on studying the limitations of algorithms and data structures operating on strings in grammar-compressed form. Previous work focused on proving lower bounds for grammars constructed using algorithms that achieve the approximation ratio $\rho=\mathcal{O}(\text{polylog }N)$. Unfortunately, for the majority of grammar compressors, $\rho$ is either unknown or satisfies $\rho=\omega(\text{polylog }N)$. In their seminal paper, Charikar et al. [IEEE Trans. Inf. Theory 2005] studied seven popular grammar compression algorithms: RePair, Greedy, LongestMatch, Sequential, Bisection, LZ78, and $\alpha$-Balanced. Only one of them ($\alpha$-Balanced) is known to achieve $\rho=\mathcal{O}(\text{polylog }N)$. We develop the first technique for proving lower bounds for data structures and algorithms on grammars that is fully general and does not depend on the approximation ratio $\rho$ of the used grammar compressor. Using this technique, we first prove that $\Omega(\log N/\log \log N)$ time is required for random access on RePair, Greedy, LongestMatch, Sequential, and Bisection, while $\Omega(\log\log N)$ time is required for random access to LZ78. All these lower bounds hold within space $\mathcal{O}(n\text{ polylog }N)$ and match the existing upper bounds. We also generalize this technique to prove several conditional lower bounds for compressed computation. For example, we prove that unless the Combinatorial $k$-Clique Conjecture fails, there is no combinatorial algorithm for CFG parsing on Bisection (for which it holds $\rho=\tilde{\Theta}(N^{1/2})$) that runs in $\mathcal{O}(n^c\cdot N^{3-\epsilon})$ time for all constants $c>0$ and $\epsilon>0$. Previously, this was known only for $c<2\epsilon$