Approximate comparison of distance automata

Distance automata are automata weighted over the semiring (N∪ {∞}, min,+) (the tropical semiring). Such automata compute functions from words to N ∪{∞} such as the number of occurrences of a given letter. It is known that testing f 0 and two functions f,g computed by distance automata, answers "yes" if f <= (1-ε ) g, "no" if f \not\leq g, and may answer "yes" or "no" in all other cases. This result highly refines previously known decidability results of the same type. The core argument behind this quasi-decision procedure is an algorithm which is able to provide an approximated finite presentation to the closure under products of sets of matrices over the tropical semiring. We also provide another theorem, of affine domination, which shows that previously known decision procedures for cost-automata have an improved precision when used over distance automata

Approximate Comparison of Functions Computed by Distance Automata

Distance automata are automata weighted over the semiring (N∪{∞},min,+) (the tropical semiring). Such automata compute functions from words to N∪{∞}. It is known from Krob that the problems of deciding ‘ f≤g’ or ‘ f=g’ for f and g computed by distance automata is an undecidable problem. The main contribution of this paper is to show that an approximation of this problem is decidable. We present an algorithm which, given ε>0 and two functions f,g computed by distance automata, answers “yes” if f≤(1−ε)g, “no” if f≦̸g, and may answer “yes” or “no” in all other cases. The core argument behind this quasi-decision procedure is an algorithm which is able to provide an approximated finite presentation of the closure under products of sets of matrices over the tropical semiring. Lastly, our theorem of affine domination gives better bounds on the precision of known decision procedures for cost automata, when restricted to distance automata

Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS

Vector Addition Systems with States (VASS) provide a well-known and fundamental model for the analysis of concurrent processes, parameterized systems, and are also used as abstract models of programs in resource bound analysis. In this paper we study the problem of obtaining asymptotic bounds on the termination time of a given VASS. In particular, we focus on the practically important case of obtaining polynomial bounds on termination time. Our main contributions are as follows: First, we present a polynomial-time algorithm for deciding whether a given VASS has a linear asymptotic complexity. We also show that if the complexity of a VASS is not linear, it is at least quadratic. Second, we classify VASS according to quantitative properties of their cycles. We show that certain singularities in these properties are the key reason for non-polynomial asymptotic complexity of VASS. In absence of singularities, we show that the asymptotic complexity is always polynomial and of the form $\Theta(n^k)$, for some integer $k\leq d$, where $d$ is the dimension of the VASS. We present a polynomial-time algorithm computing the optimal $k$. For general VASS, the same algorithm, which is based on a complete technique for the construction of ranking functions in VASS, produces a valid lower bound, i.e., a $k$ such that the termination complexity is $\Omega(n^k)$. Our results are based on new insights into the geometry of VASS dynamics, which hold the potential for further applicability to VASS analysis.Comment: arXiv admin note: text overlap with arXiv:1708.0925

Containment and equivalence of weighted automata: Probabilistic and max-plus cases

This paper surveys some results regarding decision problems for probabilistic and max-plus automata, such as containment and equivalence. Probabilistic and max-plus automata are part of the general family of weighted automata, whose semantics are maps from words to real values. Given two weighted automata, the equivalence problem asks whether their semantics are the same, and the containment problem whether one is point-wise smaller than the other one. These problems have been studied intensively and this paper will review some techniques used to show (un)decidability and state a list of open questions that still remain

Assessing associations between the AURKAHMMR-TPX2-TUBG1 functional module and breast cancer risk in BRCA1/2 mutation carriers

While interplay between BRCA1 and AURKA-RHAMM-TPX2-TUBG1 regulates mammary epithelial polarization, common genetic variation in HMMR (gene product RHAMM) may be associated with risk of breast cancer in BRCA1 mutation carriers. Following on these observations, we further assessed the link between the AURKA-HMMR-TPX2-TUBG1 functional module and risk of breast cancer in BRCA1 or BRCA2 mutation carriers. Forty-one single nucleotide polymorphisms (SNPs) were genotyped in 15,252 BRCA1 and 8,211 BRCA2 mutation carriers and subsequently analyzed using a retrospective likelihood appr

Regular Expressions for Data Words

Abstract. In data words, each position carries not only a letter form a finite alphabet, as the usual words do, but also a data value coming from an infinite domain. There has been a renewed interest in them due to applications in querying and reasoning about data models with complex structural properties, notably XML, and more recently, graph databases. Logical formalisms designed for querying such data often require concise and easily understandable presentations of regular languages over data words. Our goal, therefore, is to define and study regular expressions for data words. As the automaton model, we take register automata, which are a natural analog of NFAs for data words. We first equip standard regular expressions with limited memory, and show that they capture the class of data words defined by register automata. The complexity of the main decision problems for these expressions (nonemptiness, membership) also turns out to be the same as for register automata. We then look at a subclass of these regular expressions that can define many properties of interest in applications of data words, and show that the main decision problems can be solved efficiently for it.

PPR proteins - orchestrators of organelle RNA metabolism.

Pentatricopeptide repeat (PPR) proteins are important RNA regulators in chloroplasts and mitochondria, aiding in RNA editing, maturation, stabilisation or intron splicing, and in transcription and translation of organellar genes. In this review, we summarise all PPR proteins documented so far in plants and the green alga Chlamydomonas. By further analysis of the known target RNAs from Arabidopsis thaliana PPR proteins, we find that all organellar-encoded complexes are regulated by these proteins, although to differing extents. In particular, the orthologous complexes of NADH dehydrogenase (Complex I) in the mitochondria and NADH dehydrogenase-like (NDH) complex in the chloroplast were the most regulated, with respectively 60 and 28% of all characterised A. thaliana PPR proteins targeting their genes

Arabidopsis CaM Binding Protein CBP60g Contributes to MAMP-Induced SA Accumulation and Is Involved in Disease Resistance against Pseudomonas syringae

Salicylic acid (SA)-induced defense responses are important factors during effector triggered immunity and microbe-associated molecular pattern (MAMP)-induced immunity in plants. This article presents evidence that a member of the Arabidopsis CBP60 gene family, CBP60g, contributes to MAMP-triggered SA accumulation. CBP60g is inducible by both pathogen and MAMP treatments. Pseudomonas syringae growth is enhanced in cbp60g mutants. Expression profiles of a cbp60g mutant after MAMP treatment are similar to those of sid2 and pad4, suggesting a defect in SA signaling. Accordingly, cbp60g mutants accumulate less SA when treated with the MAMP flg22 or a P. syringae hrcC strain that activates MAMP signaling. MAMP-induced production of reactive oxygen species and callose deposition are unaffected in cbp60g mutants. CBP60g is a calmodulin-binding protein with a calmodulin-binding domain located near the N-terminus. Calmodulin binding is dependent on Ca2+. Mutations in CBP60g that abolish calmodulin binding prevent complementation of the SA production and bacterial growth defects of cbp60g mutants, indicating that calmodulin binding is essential for the function of CBP60g in defense signaling. These studies show that CBP60g constitutes a Ca2+ link between MAMP recognition and SA accumulation that is important for resistance to P. syringae

Tight polynomial bounds for Loop programs in polynomial space

We consider the following problem: given a program, find tight asymptotic bounds on the values of some variables at the end of the computation (or at any given program point) in terms of its input values. We focus on the case of polynomially-bounded variables, and on a weak programming language for which we have recently shown that tight bounds for polynomially-bounded variables are computable. These bounds are sets of multivariate polynomials. While their computability has been settled, the complexity of this program-analysis problem remained open. In this paper, we show the problem to be PSPACE-complete. The main contribution is a new, space-efficient analysis algorithm. This algorithm is obtained in a few steps. First, we develop an algorithm for univariate bounds, a sub-problem which is already PSPACE-hard. Then, a decision procedure for multivariate bounds is achieved by reducing this problem to the univariate case; this reduction is orthogonal to the solution of the univariate problem and uses observations on the geometry of a set of vectors that represent multivariate bounds. Finally, we transform the univariate-bound algorithm to produce multivariate bounds