Streaming Property Testing of Visibly Pushdown Languages

In the context of language recognition, we demonstrate the superiority of streaming property testers against streaming algorithms and property testers, when they are not combined. Initiated by Feigenbaum et al., a streaming property tester is a streaming algorithm recognizing a language under the property testing approximation: it must distinguish inputs of the language from those that are $\varepsilon$-far from it, while using the smallest possible memory (rather than limiting its number of input queries). Our main result is a streaming $\varepsilon$-property tester for visibly pushdown languages (VPL) with one-sided error using memory space $\mathrm{poly}((\log n) / \varepsilon)$. This constructions relies on a (non-streaming) property tester for weighted regular languages based on a previous tester by Alon et al. We provide a simple application of this tester for streaming testing special cases of instances of VPL that are already hard for both streaming algorithms and property testers. Our main algorithm is a combination of an original simulation of visibly pushdown automata using a stack with small height but possible items of linear size. In a second step, those items are replaced by small sketches. Those sketches relies on a notion of suffix-sampling we introduce. This sampling is the key idea connecting our streaming tester algorithm to property testers.Comment: 23 pages. Major modifications in the presentatio

Uniform Random Sampling of Traces in Very Large Models

This paper presents some first results on how to perform uniform random walks (where every trace has the same probability to occur) in very large models. The models considered here are described in a succinct way as a set of communicating reactive modules. The method relies upon techniques for counting and drawing uniformly at random words in regular languages. Each module is considered as an automaton defining such a language. It is shown how it is possible to combine local uniform drawings of traces, and to obtain some global uniform random sampling, without construction of the global model

Flexible RNA design under structure and sequence constraints using formal languages

The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical applications in biology, additional constraints must be taken into account, such as the presence/absence of regulatory motifs, either at a specific location or anywhere in the sequence. In this study, we investigate the design of RNA sequences from their targeted secondary structure, given these additional sequence constraints. To this purpose, we develop a general framework based on concepts of language theory, namely context-free grammars and finite automata. We efficiently combine a comprehensive set of constraints into a unifying context-free grammar of moderate size. From there, we use generic generic algorithms to perform a (weighted) random generation, or an exhaustive enumeration, of candidate sequences. The resulting method, whose complexity scales linearly with the length of the RNA, was implemented as a standalone program. The resulting software was embedded into a publicly available dedicated web server. The applicability demonstrated of the method on a concrete case study dedicated to Exon Splicing Enhancers, in which our approach was successfully used in the design of \emph{in vitro} experiments.Comment: ACM BCB 2013 - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (2013

Multi-dimensional Boltzmann Sampling of Languages

This paper addresses the uniform random generation of words from a context-free language (over an alphabet of size $k$), while constraining every letter to a targeted frequency of occurrence. Our approach consists in a multidimensional extension of Boltzmann samplers \cite{Duchon2004}. We show that, under mostly \emph{strong-connectivity} hypotheses, our samplers return a word of size in $[(1-\varepsilon)n, (1+\varepsilon)n]$ and exact frequency in $\mathcal{O}(n^{1+k/2})$ expected time. Moreover, if we accept tolerance intervals of width in $\Omega(\sqrt{n})$ for the number of occurrences of each letters, our samplers perform an approximate-size generation of words in expected $\mathcal{O}(n)$ time. We illustrate these techniques on the generation of Tetris tessellations with uniform statistics in the different types of tetraminoes.Comment: 12p

Linear Distances between Markov Chains

We introduce a general class of distances (metrics) between Markov chains, which are based on linear behaviour. This class encompasses distances given topologically (such as the total variation distance or trace distance) as well as by temporal logics or automata. We investigate which of the distances can be approximated by observing the systems, i.e. by black-box testing or simulation, and we provide both negative and positive results

Sampling Geometric Inhomogeneous Random Graphs in Linear Time

Real-world networks, like social networks or the internet infrastructure, have structural properties such as large clustering coefficients that can best be described in terms of an underlying geometry. This is why the focus of the literature on theoretical models for real-world networks shifted from classic models without geometry, such as Chung-Lu random graphs, to modern geometry-based models, such as hyperbolic random graphs. With this paper we contribute to the theoretical analysis of these modern, more realistic random graph models. Instead of studying directly hyperbolic random graphs, we use a generalization that we call geometric inhomogeneous random graphs (GIRGs). Since we ignore constant factors in the edge probabilities, GIRGs are technically simpler (specifically, we avoid hyperbolic cosines), while preserving the qualitative behaviour of hyperbolic random graphs, and we suggest to replace hyperbolic random graphs by this new model in future theoretical studies. We prove the following fundamental structural and algorithmic results on GIRGs. (1) As our main contribution we provide a sampling algorithm that generates a random graph from our model in expected linear time, improving the best-known sampling algorithm for hyperbolic random graphs by a substantial factor O(n^0.5). (2) We establish that GIRGs have clustering coefficients in {\Omega}(1), (3) we prove that GIRGs have small separators, i.e., it suffices to delete a sublinear number of edges to break the giant component into two large pieces, and (4) we show how to compress GIRGs using an expected linear number of bits.Comment: 25 page