Use of a novel grammatical inference approach in classification of amyloidogenic hexapeptides

The present paper is a novel contribution to the field of bioinformatics by using grammatical inference in the analysis of data. We developed an algorithm for generating star-free regular expressions which turned out to be good recommendation tools, as they are characterized by a relatively high correlation coefficient between the observed and predicted binary classifications. The experiments have been performed for three datasets of amyloidogenic hexapeptides, and our results are compared with those obtained using the graph approaches, the current state-of-the-art methods in heuristic automata induction, and the support vector machine. The results showed the superior performance of the new grammatical inference algorithm on fixed-length amyloid datasets

Minimal Synthesis of String To String Functions From Examples

We study the problem of synthesizing string to string transformations from a set of input/output examples. The transformations we consider are expressed using deterministic finite automata (DFA) that read pairs of letters, one letter from the input and one from the output. The DFA corresponding to these transformations have additional constraints, ensuring that each input string is mapped to exactly one output string. We suggest that, given a set of input/output examples, the smallest DFA consistent with the examples is a good candidate for the transformation the user was expecting. We therefore study the problem of, given a set of examples, finding a minimal DFA consistent with the examples and satisfying the functionality and totality constraints mentioned above. We prove that, in general, this problem (the corresponding decision problem) is NP-complete. This is unlike the standard DFA minimization problem which can be solved in polynomial time. We provide several NP-hardness proofs that show the hardness of multiple (independent) variants of the problem. Finally, we propose an algorithm for finding the minimal DFA consistent with input/output examples, that uses a reduction to SMT solvers. We implemented the algorithm, and used it to evaluate the likelihood that the minimal DFA indeed corresponds to the DFA expected by the user.Comment: SYNT 201

PAC learning of Probabilistic Automaton based on the Method of Moments

International audienceProbabilitic Finite Automata (PFA) are gener-ative graphical models that define distributions with latent variables over finite sequences of symbols, a.k.a. stochastic languages. Traditionally , unsupervised learning of PFA is performed through algorithms that iteratively improves the likelihood like the Expectation-Maximization (EM) algorithm. Recently, learning algorithms based on the so-called Method of Moments (MoM) have been proposed as a much faster alternative that comes with PAC-style guarantees. However, these algorithms do not ensure the learnt automata to model a proper distribution , limiting their applicability and preventing them to serve as an initialization to iterative algorithms. In this paper, we propose a new MoM-based algorithm with PAC-style guarantees that learns automata defining proper distributions. We assess its performances on synthetic problems from the PAutomaC challenge and real datasets extracted from Wikipedia against previous MoM-based algorithms and EM algorithm

Model-based quality assurance of instrumented context-free systems

The ever-growing complexity of today’s software and hardware systems makes quality assurance (QA) a challenging task. Abstraction is a key technique for dealing with this complexity because it allows one to skip non-essential properties of a system and focus on the important ones. Crucial for the success of this approach is the availability of adequate abstraction models that strike a fine balance between simplicity and expressiveness. This thesis presents the formalisms of systems of procedural automata (SPAs), systems of behavioral automata (SBAs), and systems of procedural Mealy machines (SPMMs). The three model types describe systems which consist of multiple procedures that can mutually call each other, including recursion. While the individual procedures are described by regular automata and therefore are easy to understand, the aggregation of procedures towards systems captures the semantics of context-free systems, offering the expressiveness necessary for representing procedural systems. A central concept of the proposed model types is an instrumentation that exposes the internal structure of systems by making calls to and returns from procedures observable. This instrumentation allows for a notion of rigorous (de-) composition which enables a translation between local (procedural) views and global (holistic) views on a system. On the basis of this translation, this thesis presents algorithms for the verification, testing, and learning of (instrumented) context-free systems, covering a broad spectrum of practical QA tasks. Starting with SPAs as a “base” formalism for context-free systems, the flexibility of this concept is shown by including features such as prefix-closure (SBAs) and dialog-based transductions (SPMMs). In a comparison with related formalisms, this thesis shows that the simplicity of the proposed model types not only increases the understandability of models but can also improve the performance of QA tasks. This makes SPAs, SBAs, and SPMMs a powerful tool for tackling the practical challenges of assuring the quality of today’s software and hardware systems

On the Use of Quasiorders in Formal Language Theory

In this thesis we use quasiorders on words to offer a new perspective on two well-studied problems from Formal Language Theory: deciding language inclusion and manipulating the finite automata representations of regular languages. First, we present a generic quasiorder-based framework that, when instantiated with different quasiorders, yields different algorithms (some of them new) for deciding language inclusion. We then instantiate this framework to devise an efficient algorithm for searching with regular expressions on grammar-compressed text. Finally, we define a framework of quasiorder-based automata constructions to offer a new perspective on residual automata.Comment: PhD thesi

Tools and Algorithms for the Construction and Analysis of Systems

This open access book constitutes the proceedings of the 28th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2022, which was held during April 2-7, 2022, in Munich, Germany, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2022. The 46 full papers and 4 short papers presented in this volume were carefully reviewed and selected from 159 submissions. The proceedings also contain 16 tool papers of the affiliated competition SV-Comp and 1 paper consisting of the competition report. TACAS is a forum for researchers, developers, and users interested in rigorously based tools and algorithms for the construction and analysis of systems. The conference aims to bridge the gaps between different communities with this common interest and to support them in their quest to improve the utility, reliability, exibility, and efficiency of tools and algorithms for building computer-controlled systems

Tools and Algorithms for the Construction and Analysis of Systems

This open access book constitutes the proceedings of the 28th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2022, which was held during April 2-7, 2022, in Munich, Germany, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2022. The 46 full papers and 4 short papers presented in this volume were carefully reviewed and selected from 159 submissions. The proceedings also contain 16 tool papers of the affiliated competition SV-Comp and 1 paper consisting of the competition report. TACAS is a forum for researchers, developers, and users interested in rigorously based tools and algorithms for the construction and analysis of systems. The conference aims to bridge the gaps between different communities with this common interest and to support them in their quest to improve the utility, reliability, exibility, and efficiency of tools and algorithms for building computer-controlled systems

Tools and Algorithms for the Construction and Analysis of Systems

This open access two-volume set constitutes the proceedings of the 27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2021, which was held during March 27 – April 1, 2021, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2021. The conference was planned to take place in Luxembourg and changed to an online format due to the COVID-19 pandemic. The total of 41 full papers presented in the proceedings was carefully reviewed and selected from 141 submissions. The volume also contains 7 tool papers; 6 Tool Demo papers, 9 SV-Comp Competition Papers. The papers are organized in topical sections as follows: Part I: Game Theory; SMT Verification; Probabilities; Timed Systems; Neural Networks; Analysis of Network Communication. Part II: Verification Techniques (not SMT); Case Studies; Proof Generation/Validation; Tool Papers; Tool Demo Papers; SV-Comp Tool Competition Papers