Accurate reconstruction of insertion-deletion histories by statistical phylogenetics

The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.Comment: 28 pages, 15 figures. arXiv admin note: text overlap with arXiv:1103.434

Finite Model Finding for Parameterized Verification

In this paper we investigate to which extent a very simple and natural "reachability as deducibility" approach, originated in the research in formal methods in security, is applicable to the automated verification of large classes of infinite state and parameterized systems. The approach is based on modeling the reachability between (parameterized) states as deducibility between suitable encodings of states by formulas of first-order predicate logic. The verification of a safety property is reduced to a pure logical problem of finding a countermodel for a first-order formula. The later task is delegated then to the generic automated finite model building procedures. In this paper we first establish the relative completeness of the finite countermodel finding method (FCM) for a class of parameterized linear arrays of finite automata. The method is shown to be at least as powerful as known methods based on monotonic abstraction and symbolic backward reachability. Further, we extend the relative completeness of the approach and show that it can solve all safety verification problems which can be solved by the traditional regular model checking.Comment: 17 pages, slightly different version of the paper is submitted to TACAS 201

Generalizing input-driven languages: theoretical and practical benefits

Regular languages (RL) are the simplest family in Chomsky's hierarchy. Thanks to their simplicity they enjoy various nice algebraic and logic properties that have been successfully exploited in many application fields. Practically all of their related problems are decidable, so that they support automatic verification algorithms. Also, they can be recognized in real-time. Context-free languages (CFL) are another major family well-suited to formalize programming, natural, and many other classes of languages; their increased generative power w.r.t. RL, however, causes the loss of several closure properties and of the decidability of important problems; furthermore they need complex parsing algorithms. Thus, various subclasses thereof have been defined with different goals, spanning from efficient, deterministic parsing to closure properties, logic characterization and automatic verification techniques. Among CFL subclasses, so-called structured ones, i.e., those where the typical tree-structure is visible in the sentences, exhibit many of the algebraic and logic properties of RL, whereas deterministic CFL have been thoroughly exploited in compiler construction and other application fields. After surveying and comparing the main properties of those various language families, we go back to operator precedence languages (OPL), an old family through which R. Floyd pioneered deterministic parsing, and we show that they offer unexpected properties in two fields so far investigated in totally independent ways: they enable parsing parallelization in a more effective way than traditional sequential parsers, and exhibit the same algebraic and logic properties so far obtained only for less expressive language families

A multi-paradigm language for reactive synthesis

This paper proposes a language for describing reactive synthesis problems that integrates imperative and declarative elements. The semantics is defined in terms of two-player turn-based infinite games with full information. Currently, synthesis tools accept linear temporal logic (LTL) as input, but this description is less structured and does not facilitate the expression of sequential constraints. This motivates the use of a structured programming language to specify synthesis problems. Transition systems and guarded commands serve as imperative constructs, expressed in a syntax based on that of the modeling language Promela. The syntax allows defining which player controls data and control flow, and separating a program into assumptions and guarantees. These notions are necessary for input to game solvers. The integration of imperative and declarative paradigms allows using the paradigm that is most appropriate for expressing each requirement. The declarative part is expressed in the LTL fragment of generalized reactivity(1), which admits efficient synthesis algorithms, extended with past LTL. The implementation translates Promela to input for the Slugs synthesizer and is written in Python. The AMBA AHB bus case study is revisited and synthesized efficiently, identifying the need to reorder binary decision diagrams during strategy construction, in order to prevent the exponential blowup observed in previous work.Comment: In Proceedings SYNT 2015, arXiv:1602.0078