Site-Directed Insertion: Decision Problems, Maximality and Minimality

Site-directed insertion is an overlapping insertion operation that can be viewed as analogous to the overlap assembly or chop operations that concatenate strings by overlapping a suffix and a prefix of the argument strings. We consider decision problems and language equations involving site-directed insertion. By relying on the tools provided by semantic shuffle on trajectories we show that one variable equations involving site-directed insertion and regular constants can be solved. We consider also maximal and minimal variants of the site-directed insertion operation

From Finite Automata to Regular Expressions and Back--A Summary on Descriptional Complexity

The equivalence of finite automata and regular expressions dates back to the seminal paper of Kleene on events in nerve nets and finite automata from 1956. In the present paper we tour a fragment of the literature and summarize results on upper and lower bounds on the conversion of finite automata to regular expressions and vice versa. We also briefly recall the known bounds for the removal of spontaneous transitions (epsilon-transitions) on non-epsilon-free nondeterministic devices. Moreover, we report on recent results on the average case descriptional complexity bounds for the conversion of regular expressions to finite automata and brand new developments on the state elimination algorithm that converts finite automata to regular expressions.Comment: In Proceedings AFL 2014, arXiv:1405.527

Word Blending and Other Formal Models of Bio-operations

As part of ongoing efforts to view biological processes as computations, several formal models of DNA-based processes have been proposed and studied in the formal language literature. In this thesis, we survey some classical formal language word and language operations, as well as several bio-operations, and we propose a new operation inspired by a DNA recombination lab protocol known as Cross-pairing Polymerase Chain Reaction, or XPCR. More precisely, we define and study a word operation called word blending which models a special case of XPCR, where two words x w p and q w y sharing a non-empty overlap part w generate the word x w y. Properties of word blending that we study include closure properties of the Chomsky families of languages under this operation and its iterated version, existence of solution to equations involving this operation, and its state complexity

Real-time and Probabilistic Temporal Logics: An Overview

Over the last two decades, there has been an extensive study on logical formalisms for specifying and verifying real-time systems. Temporal logics have been an important research subject within this direction. Although numerous logics have been introduced for the formal specification of real-time and complex systems, an up to date comprehensive analysis of these logics does not exist in the literature. In this paper we analyse real-time and probabilistic temporal logics which have been widely used in this field. We extrapolate the notions of decidability, axiomatizability, expressiveness, model checking, etc. for each logic analysed. We also provide a comparison of features of the temporal logics discussed

Techniques for searching, parsing, and matching (fourth edition)

These lecture notes present some basic techniques for: (i) exploring search spaces, (ii) parsing context-free languages, and (iii) matching patterns in strings. These techniques are taught in a course on Automata, Languages, and Translators at the University of Roma "Tor Vergata''. We assume that the reader is familiar with the basic notions of Automata Theory and Formal Languages. These notions can be found in many books such as [Har78,HoU79,Pet13a]. Some of the algorithms we have presented in these notes are written in Java 1.5 and some others in Prolog. For the Java language the reader may refer to the Java Tutorial at http://java.sun.com/docs/books/tutorial/} . (Recall that this Java version allows the use of parameterized types, also called generics.) All Java programs have been compiled using the Java compiler 1.5.0-13 running under Mac OS X 10.4.11 Darwin 8.11.1. For the Prolog language the reader may refer to [ClM84]. The Prolog language incorporates a backtracking mechanism which is useful for exploring search spaces and solving parsing and matching problems