Frontiers of Membrane Computing: Open Problems and Research Topics

This is a list of open problems and research topics collected after the Twelfth Conference on Membrane Computing, CMC 2012 (Fontainebleau, France (23 - 26 August 2011), meant initially to be a working material for Tenth Brainstorming Week on Membrane Computing, Sevilla, Spain (January 30 - February 3, 2012). The result was circulated in several versions before the brainstorming and then modified according to the discussions held in Sevilla and according to the progresses made during the meeting. In the present form, the list gives an image about key research directions currently active in membrane computing

AI Methods in Algorithmic Composition: A Comprehensive Survey

Algorithmic composition is the partial or total automation of the process of music composition by using computers. Since the 1950s, different computational techniques related to Artificial Intelligence have been used for algorithmic composition, including grammatical representations, probabilistic methods, neural networks, symbolic rule-based systems, constraint programming and evolutionary algorithms. This survey aims to be a comprehensive account of research on algorithmic composition, presenting a thorough view of the field for researchers in Artificial Intelligence.This study was partially supported by a grant for the MELOMICS project (IPT-300000-2010-010) from the Spanish Ministerio de Ciencia e Innovación, and a grant for the CAUCE project (TSI-090302-2011-8) from the Spanish Ministerio de Industria, Turismo y Comercio. The first author was supported by a grant for the GENEX project (P09-TIC- 5123) from the Consejería de Innovación y Ciencia de Andalucía

Analysis of communication topologies by partner abstraction

Dynamic communication systems are hard to verify due to inherent unboundedness. Unbounded creation and destruction of objects and a dynamically evolving communication topology are characteristic features. Prominent examples include traffic control systems based on wireless communication and ad hoc networks. As dynamic communication systems have to meet safety-critical requirements, this thesis develops appropriate specification and verification techniques for them. It is shown that earlier attempts at doing so have failed. Partner graph grammars are presented as an adequate specification formalism for dynamic communication systems. They form a novel variant of the single pushout approach to algebraic graph transformation equipped with a special kind of negative application conditions: Partner constraints that allow to reason about communication partners are specifically tailored to dynamic communication systems. A novel verification technique based on abstract interpretation of partner graph grammars is proposed. It is based on a two-layered abstraction that keeps precise information about objects and the kinds of their communication partners. The analysis is formally proven sound. Some statically checkable cases are defined for which the analysis results are even complete. The analysis has been implemented in the hiralysis tool. A complex case study - car platooning originally developed in the California PATH project - is modeled using partner graph grammars. An experimental evaluation using the tool discovered many flaws in the PATH specification of car platooning that had not been discovered earlier due to insufficient specification and verification methods. Many interesting properties can be automatically proven for a corrected implementation of car platooning using hiralysis.Aufgrund ihres unbeschränkten Verhaltens sind dynamisch kommunizierende Systeme schwierig zu verifizieren. Sie zeichnen sich durch unbegrenztes Erzeugen und Zerstören von Objekten sowie eine sich ständig ändernde Kommunikationstopologie aus. Funkbasierte Verkehrskontrollsysteme und drahtlose Ad-hoc Netzwerke sind bekannte Beispiele dynamisch kommunizierender Systeme. Da diese außerdem sicherheitskritischen Anforderungen genügen müssen, werden in dieser Arbeit Spezifikations- und Verifikationsmethoden für dynamisch kommunizierende Systeme entwickelt. Es wird gezeigt, dass frühere Versuche in dieser Richtung fehlgeschlagen sind. Partner-Graphgrammatiken stellen einen geeigneten Formalismus zur Beschreibung solcher Systeme dar. Sie bilden eine neue Form des "single pushout" Ansatzes für algebraische Graphtransformationen erweitert um besondere negative Anwendungsbedingungen. "Partner constraints", die speziell für die Spezifikation dynamisch kommunizierender Systeme entwickelt wurden, erlauben, Nebenbedingungen an Objekte und ihre Kommunikationspartner zu formulieren. Es wird eine neuartige Verifikationstechnik vorgeschlagen, die auf der abstrakten Interpretation von Partner-Graphgrammatiken beruht. Diese fußt auf einer Abstraktion, die präzise Informationen über Objekte und ihre Kommunikationspartner erhält. Die Analyse wird korrekt bewiesen, und es werden statisch erkennbare Fälle aufgezeigt, in denen die Analyse sogar vollständige Resultate liefert. Die Analyse wurde in dem hiralysis Werkzeug implementiert. Eine komplexe Fallstudie - "car platooning", welche ursprünglich im Rahmen des California PATH Projektes entwickelt wurde - wird durch Partner-Graphgrammatiken modelliert. Eine experimentelle Auswertung mithilfe desWerkzeugs deckte zahlreiche Fehler in der ursprünglichen Modellierung auf, welche ihre Ursache in unzureichenden Spezifikations- und Verifikationsmethoden haben. Viele interessante Eigenschaften eines verbesserten Modells konnten mittels hiralysis automatisch bewiesen werden

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

Formal Verification of P Systems

Membrane systems, also known as P systems, constitute an innovative computational paradigm inspired by the structure and dynamics of the living cell. A P system consists of a hierarchical arrangement of compartments and a finite set of multiset rewriting and communication rules, which operate in a maximally parallel manner. The organic vision of concurrent dynamics captured by membrane systems stands in antithesis with conventional formal modelling methods which focus on algebraic descriptions of distributed systems. As a consequence, verifying such models in a mathematically rigorous way is often elusive and indeed counter-intuitive when considering established approaches, which generally require sequential process representations or highly abstract theoretical frameworks. The prevalent investigations with this objective in the field of membrane computing are ambivalent and inconclusive in the wider application scope of P systems. In this thesis we directly address the formal verification of membrane systems by means of model checking. A fundamental distinction between the agnostic perspective on parallelism, advocated by process calculi, and P systems' emblematic maximally parallel execution strategy is identified. On this basis, we establish that an intuitional translation to traditional process models is inadequate for the purpose of formal verification, due to a state space growth disparity. The observation is essential for this research project: on one hand it implies the feasibility of model checking P systems, and on the other hand it underlines the suitability of this formal verification technique in the context of membrane computing. Model checking entails an exhaustive state space exploration and does not derive inferences based on the independent instructions comprising a state transition. In this respect, we define a new sequential modelling strategy which is optimal for membrane systems and targets the SPIN formal verification tool. We introduce elementary P systems, a distributed computational model which subsumes the feature diversity of the membrane computing paradigm and distils its functional vocabulary. A suite of supporting software tools which gravitate around this formalism has also been developed, comprising of 1. the eps modelling language for elementary P systems; 2. a parser for the eps specification; 3. a model simulator and 4. a translation tool which targets the Promela specification of the SPIN model checker. The formal verification approach proposed in this thesis is progressively demonstrated in four heterogeneous case studies, featuring 1. a parallel algorithm applicable to a structured model; 2. a linear time solution to an NP-complete problem; 3. an innovative implementation of the Dining Philosophers scenario (a synchronisation problem) using an elementary P system and 4. a quantitative analysis of a simple random process implemented without the support of a probabilistic model

Construction of Hierarchical Neural Architecture Search Spaces based on Context-free Grammars

The discovery of neural architectures from simple building blocks is a long-standing goal of Neural Architecture Search (NAS). Hierarchical search spaces are a promising step towards this goal but lack a unifying search space design framework and typically only search over some limited aspect of architectures. In this work, we introduce a unifying search space design framework based on context-free grammars that can naturally and compactly generate expressive hierarchical search spaces that are 100s of orders of magnitude larger than common spaces from the literature. By enhancing and using their properties, we effectively enable search over the complete architecture and can foster regularity. Further, we propose an efficient hierarchical kernel design for a Bayesian Optimization search strategy to efficiently search over such huge spaces. We demonstrate the versatility of our search space design framework and show that our search strategy can be superior to existing NAS approaches. Code is available at https://github.com/automl/hierarchical_nas_construction

Verification problems for timed and probabilistic extensions of Petri Nets

In the first part of the thesis, we prove the decidability (and PSPACE-completeness) of the universal safety property on a timed extension of Petri Nets, called Timed Petri Nets. Every token has a real-valued clock (a.k.a. age), and transition firing is constrained by the clock values that have integer bounds (using strict and non-strict inequalities). The newly created tokens can either inherit the age from an input token of the transition or it can be reset to zero. In the second part of the thesis, we refer to systems with controlled behaviour that are probabilistic extensions of VASS and One-Counter Automata. Firstly, we consider infinite state Markov Decision Processes (MDPs) that are induced by probabilistic extensions of VASS, called VASS-MDPs. We show that most of the qualitative problems for general VASS-MDPs are undecidable, and consider a monotone subclass in which only the controller can change the counter values, called 1-VASS-MDPs. In particular, we show that limit-sure control state reachability for 1-VASS-MDPs is decidable, i.e., checking whether one can reach a set of control states with probability arbitrarily close to 1. Unlike for finite state MDPs, the control state reachability property may hold limit surely (i.e. using an infinite family of strategies, each of which achieving the objective with probability ≥ 1-e, for every e > 0), but not almost surely (i.e. with probability 1). Secondly, we consider infinite state MDPs that are induced by probabilistic extensions of One-Counter Automata, called One-Counter Markov Decision Processes (OC-MDPs). We show that the almost-sure {1;2;3}-Parity problem for OC-MDPs is at least as hard as the limit-sure selective termination problem for OC-MDPs, in which one would like to reach a particular set of control states and counter value zero with probability arbitrarily close to 1

Algorithms and Software for Biological MP Modeling by Statistical and Optimization Techniques

I sistemi biologici sono gruppi di entit\ue0 biologiche (es. molecole ed organismi), che interagiscono producendo specifiche dinamiche. Questi sistemi sono solitamente caratterizzati da una elevata complessit\ue0 perch\ue8 coinvolgono un elevato numero di componenti con molte interconnessioni. La comprensione dei meccanismi che governano i sistemi biologici e la previsione dei loro comportamenti in condizioni normali e patologiche \ue8 una sfida cruciale della biologia dei sistemi (in inglese detta systems biology), un'area di ricerca al confine tra biologia, medicina, matematica ed informatica. In questa tesi i P sistemi metabolici, detti brevemente sistemi MP, sono stati utilizzati come modello discreto per l'analisi di dinamiche biologiche. Essi sono una classe deterministica dei P sistemi classici, che utilizzano regole di riscrittura per rappresentare le reazioni chimiche e "funzioni di regolazioni di flusso" per regolare la reattivit\ue0 di ciascuna reazione rispetto alla quantita' di sostanze presenti istantaneamente nel sistema. Dopo un excursus sulla letteratura relativa ad alcuni modelli convenzionali (come le equazioni differenziali ed i modelli stocastici proposti da Gillespie) e non-convenzionali (come i P sistemi ed i P sistemi metabolici), saranno presentati i risultati della mia ricerca. Essi riguardano tre argomenti principali: i) l'equivalenza tra sistemi MP e reti di Petri ibride funzionali, ii) le prospettive statistiche e di ottimizzazione nella generazione di sistemi MP a partire da dati sperimentali, iii) lo sviluppo di un laboratorio virtuale chiamato MetaPlab, un software Java basato sui sistemi MP. L'equivalenza tra i sistemi MP e le reti di Petri ibride funzionali \ue8 stata dimostrata per mezzo di due teoremi ed alcuni esperimenti al computer per il caso di studio del meccanismo regolativo del gene operone lac nella pathway glicolitica. Il secondo argomento di ricerca concerne nuovi approcci per la sintesi delle funzioni di regolazione di flusso. La regressione stepwise e le reti neurali sono state impiegate come approssimatori di funzioni, mentre algoritmi di ottimizzazione classici ed evolutivi (es. backpropagation, algoritmi genetici, particle swarm optimization ed algoritmi memetici) sono stati impiegati per l'addestramento dei modelli. Una completo workflow per l'analisi dei dati sperimentali \ue8 stato presentato. Esso gestisce ed indirizza l'intero processo di sintesi delle funzioni di regolazione, dalla preparazione dei dati alla selezione delle variabili, fino alla generazione dei modelli ed alla loro validazione. Le metodologie proposte sono state testate con successo tramite esperimenti al computer sui casi di studio dell'oscillatore mitotico negli embrioni anfibi e del non photochemical quenching (NPQ). L'ultimo tema di ricerca \ue8 infine piu' applicativo e riguarda la progettazione e lo sviluppo di una architettura Java basata su plugin e di una serie di plugin che consentono di automatizzare varie fasi del processo di modellazione con sistemi MP, come la simulazione di dinamiche, la determinazione dei flussi e la generazione delle funzioni di regolazione.Biological systems are groups of biological entities, (e.g., molecules and organisms), that interact together producing specific dynamics. These systems are usually characterized by a high complexity, since they involve a large number of components having many interconnections. Understanding biological system mechanisms, and predicting their behaviors in normal and pathological conditions is a crucial challenge in systems biology, which is a central research area on the border among biology, medicine, mathematics and computer science. In this thesis metabolic P systems, also called MP systems, have been employed as discrete modeling framework for the analysis of biological system dynamics. They are a deterministic class of P systems employing rewriting rules to represent chemical reactions and "flux regulation functions" to tune reactions reactivity according to the amount of substances present in the system. After an excursus on the literature about some conventional (i.e., differential equations, Gillespie's models) and unconventional (i.e., P systems and metabolic P systems) modeling frameworks, the results of my research are presented. They concern three research topics: i) equivalences between MP systems and hybrid functional Petri nets, ii) statistical and optimization perspectives in the generation of MP models from experimental data, iii) development of the virtual laboratory MetaPlab, a Java software based on MP systems. The equivalence between MP systems and hybrid functional Petri nets is proved by two theorems and some in silico experiments for the case study of the lac operon gene regulatory mechanism and glycolytic pathway. The second topic concerns new approaches to the synthesis of flux regulation functions. Stepwise linear regression and neural networks are employed as function approximators, and classical/evolutionary optimization algorithms (e.g., backpropagation, genetic algorithms, particle swarm optimization, memetic algorithms) as learning techniques. A complete pipeline for data analysis is also presented, which addresses the entire process of flux regulation function synthesis, from data preparation to feature selection, model generation and statistical validation. The proposed methodologies have been successfully tested by means of in silico experiments on the mitotic oscillator in early amphibian embryos and the non photochemical quenching (NPQ). The last research topic is more applicative, and pertains the design and development of a Java plugin architecture and several plugins which enable to automatize many tasks related to MP modeling, such as, dynamics computation, flux discovery, and regulation function synthesis