Luigia Petre

Åbo Akademi University · Faculty of Science and Engineering

Methylation classification is an essential component for integrative diagnosis in glioma, however, the DNA methylation classification is not always available for all the samples. We hypothesized that Raman spectroscopy might be suitable to predict the glioma methylome, based upon its ability to create a molecular fingerprint of the tumor and would...

Constructing a large biological model is a difficult, error-prone process. Small errors in writing a part of the model cascade to the system level and their sources are difficult to trace back. In this paper we extend a recent approach based on Event-B, a state-based formal method with refinement as its central ingredient, allowing us to validate f...

BACKGROUND DNA methylation is an essential component for integrative diagnosis in glioma. Methylation subtype prediction of gliomas is currently done via sample extraction of high-quality of reasonable amount of DNA (~1ug), methylome profiling, followed by probe identification, curation and subsequent analysis via different random forest classifier...

We present a Software Quality course taught in a MSc program in Computer Science and Engineering. The course takes an overview (‘breadth’) approach, reviewing the most important topics that contribute to the quality of software. The course has been taught traditionally as well as online; we discuss the advantages and disadvantages of both styles an...

Constructing a large biological model is a difficult, error-prone process. Small errors in writing a part of the model cascade to the system level and their sources are difficult to trace back. In this paper we extend a recent approach based on Event-B, a state-based formal method with refinement as its central ingredient, allowing us to validate f...

Biology offers many examples of large-scale, complex, concurrent systems: many processes take place in parallel, compete on resources and influence each other's behavior. The scalable modeling of biological systems continues to be a very active field of research. In this paper we introduce a new approach based on Event-B, a state-based formal metho...

Biology offers many examples of large-scale, complex, concurrent systems: many processes take place in parallel, compete on resources and influence each other's behavior. The scalable modeling of biological systems continues to be a very active field of research. In this paper we introduce a new approach based on Event-B, a state-based formal metho...

As of this moment, 50 gravitational wave (GW) detections have been announced, thanks to the observational efforts of the LIGO-Virgo collaboration, working with the Advanced LIGO and the Advanced Virgo interferometers. The detection of signals is complicated by the noise-dominated nature of the data. Conventional approaches in GW detection procedure...

BACKGROUND DNA methylation is an essential component for integrative diagnosis of gliomas. Methylation subtype prediction of gliomas is currently done via sample extraction of high-quality DNA (~1ug), methylome profiling, followed by probe identification, curation and subsequent analysis via different random forest classifiers. However, the DNA met...

As of this moment, fifty gravitational waves (GW) detections have been announced, thanks to the observational efforts of the LIGO-Virgo Collaboration, working with the Advanced LIGO and the Advanced Virgo interferometers. The detection of signals is complicated by the noise-dominated nature of the data. Conventional approaches in GW detection proce...

This book constitutes the refereed proceedings of the Third International Workshop and Tutorial, FMTea 2019, Held as Part of the Third World Congress on Formal Methods, FM 2019, Porto, Portugal, October 2019. The 14 full papers presented together with 3 abstract papers were carefully reviewed and selected from 22 submissions. The papers are organiz...

There is a high interest in constructing large, detailed computational models for biological processes. This is often done by putting together existing submodels and adding to them extra details/knowledge. The result of such approaches is usually a model that can only answer questions on a very specific level of detail, and thus, ultimately, is of...

In this paper we compare models developed in two formal frameworks, Uppaal and Event-B, for the Optimised Link State Routing (OLSR) protocol. OLSR is one of the proactive routing protocols used in Mobile Ad-hoc Networks (MANETs) and Wireless Mesh Networks (WMNs). We also describe different aspects of the Uppaal and Event-B formalisms. This leads to...

Service composition has become commonplace nowadays, in large part due to the increased complexity of software and supporting networks. Composition can be of many types, for instance sequential, prioritising, non-deterministic. However, a fundamental feature of the services to be composed consists in their dependencies with respect to each other. I...

Formal methods traditionally address the question of transforming software engineering into a mature engineering discipline. This essentially refers to trusting that the software-intensive systems that form our society's infrastructures are behaving according to their specifications. More recently, formal methods are also used to understand propert...

With network-on-chip (NoC) as the fundamental communication paradigm for many core architectures, we need to be able to evaluate its correctness. In this paper we propose a proving methodology for this, based on the Event-B formal method. Our approach is fundamentally reusable, thus addressing the increasing complexity of manycore architectures as...

As (network) software is such an omnipresent component of contemporary mission-critical systems, formal analysis is required to provide the necessary certification or at least formal assurances for these systems. In this paper we focus on modelling and analysing the Optimised Link State Routing (OLSR) protocol, a distributed, proactive routing prot...

The refinement concept provides a formal tool for addressing the complexity of software-intensive systems, by verified stepwise development from an abstract specification towards an implementation. In this paper we propose a novel notion of refinement for a structured formalism dedicated to interactive systems, that combines a data-flow with a cont...

In the domain of environmental sciences, measurement is the process that maps some observed phenomenon to a formal measurement value, the latter being the result of a measurement process. The measurement process relies on data representing inherently informal physical quantities of possibly continuously changing phenomena. These measurement process...

Smart electrical grids refer to networked systems for distributing and transporting electricity from producers to consumers, by dynamically configuring the network through remotely controlled (dis)connectors. The consumers of the grid have typically distinct priorities, e.g., a hospital and an airport have the highest priority and the street lighti...

Wireless sensor–actor networks are a recent development of wireless networks where both ordinary sensor nodes and more sophisticated and powerful nodes, called actors, are present. In this paper we introduce several, increasingly more detailed, formal models for this type of wireless networks. These models formalise a recently introduced algorithm...

In this article we discuss how to improve the resilience of an existing control system. In recent years, our environment has become populated with numerous control systems due the to availability of low-cost technologies. For instance, modern home automation has become a cooperative network of multiple control systems, many of which communicate ove...

Location-awareness has become ubiquitous in today's lifestyles, with a significant role in enabling and disabling various computations. Thus, the location of a resource is an important instrument driving the execution and usage of the resource. For instance, reading a paper published online by a journal may work in a user's home network because the...

Characterising for contemporary systems is their dependence on constituent systems to provide information, functionality, and scalability. Moreover, as the tasks that systems perform are ever more intimate and critical in their nature, reliability and correctness are great concerns. On these matters, we outline a methodology for formal integration...

The increase in design complexity emphasises the relevance of formal verification techniques for both software and hardware. Formal methods with their mathematical-based modelling can provide proofs of various properties for the designs, thus ensuring a certain degree of complexity control and enhancing the system confidence. There are numerous for...

Multicore processing is quickly becoming ubiquitous, with more and more systems splitting the processing power between several processing cores instead of a single core. This approach is used not only to increase the total processing power and efficiency, but also to conserve energy. In this paper, we introduce a formal model created in Event-B of...

Smart devices have pervaded our society and encouraged lifestyles that depend on them. One of the fiundamental requirements for a successful dependency is that the general public be aware of the energy limitations of these devices and to stay in control of energy consumption. In this paper, the authors propose a formal specification method that tak...

Dependability (the degree of reliance that can be justifiably placed on software-intensive systems) is characterized by several attributes, including availability. In this chapter, we refer to network availability as the "network readiness for correct service" and model various network availability aspects such as resource accessibility, network no...

Peer-to-peer networks and other many-to-many relations have become popular especially for content transfer. To better understand and trust these types of networks, we need formally derived and verified models for them. Due to the large scale and heterogeneity of these networks, it may be difficult and cumbersome to create and analyse complete model...

The location of various network resources is of outmost interest when trying to model and analyze various computing and communicating contemporary platforms. Formal methods - fault-avoiding techniques for constructing robust software and systems - are instrumental in providing precise modeling formats and various analysis and development tools. In...

Smart devices have pervaded our society and encouraged lifestyles that depend on them. One of the fundamental requirements for a successful dependency is that the general public be aware of the energy limitations of these devices and to stay in control of energy consumption. In this paper, the authors propose a formal specification method that take...

Smart devices have pervaded our society and encouraged lifestyles that depend on them. One of the fundamental requirements for a successful dependency is that the general public be aware of the energy limitations of these devices and to stay in control of energy consumption. In this paper, the authors propose a formal specification method that take...

Smart devices have pervaded our society and encouraged lifestyles that depend on them. One of the fundamental requirements for a successful dependency is that the general public be aware of the energy limitations of these devices and to stay in control of energy consumption. In this paper, the authors propose a formal specification method that take...

The number of communicating components has tremendously increased, both at the chip-level communication as well as in general networks. This leads to an increased complexity in the design of communication infrastructures. In order to rely on such complex communication designs, we need a correspondingly increased verification effort. In this paper w...

A reliable approach to designing systems is by applying formal methods, based on logics and set theory. In formal methods refinement based, we develop the system models stepwise, from an abstract level to a concrete one by gradually adding details. Each detail-adding level is proved to still validate the properties of the more abstract level. Due t...

Due to very fast and intensive development, the diameter of LAN deployment has increased to a bigger scale, advancing the concept of Campus Area Network. The huge modifications in network size have led to various concerns, some very crucial. One such example is the concern of proper design of network without which the aspects of quality, speed and...

Three-dimensional Networks-on-Chip (3D NoC) have recently emerged essentially via the stacking of multiple layers of two-dimensional NoCs. The resulting structures can support a very high level of parallelism for both communication and computation as well as higher speeds, at the cost of increased complexity. To address the potential problems due t...

Rapid development of digital technologies has led to the widespread use of software in all aspects of our life. The degree of reliance that can be justifiably placed on software-intensive systems is expressed by the notion of dependability. The complexity of modern software-intensive systems poses the greatest threat to dependability. Furthermore,...

Component-based development typically refers to assembling pre-existing pieces of software or hardware for integrating them into new systems. In this paper we introduce a formalism-based approach to verify the component boundaries, based on the component interdependencies. We base this synthesis method on B Action Systems and the animation techniqu...

Wireless sensor-actor networks are a recent development of wireless networks where both ordinary sensor nodes and more sophisticated and powerful nodes, called actors, are present. In this paper we formalize a recently introduced algorithm that recovers failed actor communication links via the existing sensor infrastructure. We prove via refinement...

Wireless sensor-actor networks are a recent development of wireless networks where both ordinary sensor nodes and more sophisticated and powerful nodes, called actors, are present. The role of the actors is to take various decisions relevant for the network based on the data retrieved and transmitted by the sensors. In order to fulfill their role,...

specification Safety requirements Elaborated safety analysis Safety analysis of implementation Refined specification Implementation Elaborated safety requirements Elaborated safety 9 3.3 Dependability impairment A safety-critical system is usually a control system with a computer-based controller managing a plant. There are two main entities involv...

Ethernet—a switched local area network—is the market leader for LAN Technologies today. From businesses to government organizations, home to shopping centers, and NGOs to universities, Ethernet is the sole shareholder of the local area networks. Due to such a wide-range, Ethernet has become an intensively addressed research area, with concerns rang...

Computer networks have become a critical part of our society as we, as users, need our networked world to function continually and at full capacity. One of the basic and often overlooked factors required for such qualities is that of energy. Energy consumption is a non-functional property that needs to be addressed by a network manager, at the more...

Abstract Computer networks have become ubiquitous in our society and thus, the various types of resources hosted by them are becoming,increasingly important. In this paper we study the resource availability in networks by defining a dedicated mid- dleware language. This language is a conservative extension of the action system formalism, a general...

trol system. Already the initial specification should ensure safety and be proved to be consistent. This can be achieved by translating the UML specification into B-action systems [BW96,WS98]. The translation is supported by the tool U2B [SB00]. The B-action systems is a formalism for supporting the development of complex distributed systems. The B...

In several state-based approaches to distributed computing, e.g., action systems, or UNITY, the computing nodes are commonly left unspecified or implicit. For instance, an action system comes with an informal description on how the system is supposed to be mapped into the network. The purpose of this paper is to make this mapping explicit so that,...

Action systems have been used successfully to describe discrete systems, i.e., systems with discrete control acting upon a discrete state space. In this paper we define continuous action systems that extend the action system approach to also model hybrid systems, i.e., systems with discrete control over a continuously evolving state. The semantics...

stem in terms of components and implementing it in terms of objects. In the analysis phase, we consider a software system as a set of services that have to be implemented. By conveniently grouping these services we can determine a set of components that are to provide them. These components have to be constructed, or, if they already exist, simply...

Component-based software engineering means constructing new systems from already existing, service-providing components. Object-based software engineering means constructing a new system in terms of interacting, distinct units of information and services called objects. Both components and objects have encapsulation properties and are accessed via...

In this paper we point out the potential of software engineering methods in developing control systems as well as in deriving the control software for them. The general strategy for such a development comprises two phases. An initial system-level specification models both the physical environment and its control software within the same state machi...

Action systems have been used successfully to describe discrete systems, i.e.,systems with discrete control acting upon a discrete state space. In this paper we extend the action system approach to hybrid systems by defining continuous action systems. These are systems with discrete control over a continuously evolving state, whose semantics is def...

The Unified Modeling Language (UML) consists in a set of diagrams that describe a system under development. A use case diagram specifies the required functionality of the system, showing the collaboration among a set of actors that are to perform certain tasks. We complement the use case diagrams by providing formal documents (like specifications o...

The Unified Modeling Language (UML) consists in a set of diagrams that describe a system under development. A use case diagram specifies the required functionality of the system, showing the collaboration among a set of actors that are to perform certain tasks. We complement the use case diagrams by providing formal documents (like specifications o...

The ambient calculus and the P-systems are models developed in different areas of computer science. Still, they are based on similar concepts and structures and are inspired from the same natural model of computation. On this basis, we point out how to transfer ideas and results from one framework to the other. We prove that any P-system can be sim...

The ambient calculus and the P-systems are models developed in di erent areas of computer science. Still, they are based on similar concepts and structures and are inspired from the same natural model of computation [BeBo92]. On this basis, we point out how to transfer ideas and results from one framework to the other. We prove that any P-system ca...

In several state-based approaches to distributed computing, e.g., action systems, or UNITY, the computing nodes are commonly left unspecified or implicit. For instance, an action system comes with an informal description on how the system is supposed to be mapped into the network. The purpose of this paper is to make this mapping explicit so that w...

The Unified Modeling Language (UML) consists of a set of diagrams that describe a system under development. A use case diagram specifies the required functionality of the system, showing the collaboration among a set of actors that are to perform certain tasks. We enhance use case diagrams by providing formal documents (like specifications or progr...

We show how to specify distributed control systems within the object-based OO-action systems framework by combining informal and formal specification methods in a novel way. UML diagrams serve partly as a starting point for the formal specification process as well as give direction for the refinement steps via which the control system stepwise evol...

When designing distributed object-based systems one is often faced with the problem of modelling the movement of objects from site to site in a distributed network. In order to model such an activity, some supervising or coordination mechanisms are needed, to insure correctness of both movement and communication in the network. In this paper we pro...

When designing distributed object-based systems one is often faced with the problem of modeling the movement of objects from site to site in a distributed network. In order to model such an activity, some supervising or coordination mechanisms are needed, to insure correctness of both movement and communication in the network. In this paper we prop...

We show how to specify distributed control systems within the object-based OO-action systems framework by combining informal and formal specification methods in a novel way. UML diagrams serve partly as a starting point for the formal specification process as well as give direction for the refinement steps via which the control system stepwise evol...

ChangeBlank(TRUE) || PlateLiquidRead || astate1:=areceive1 || awaited:=FALSEEND;RRemedy=PRE astate1=arsuspended1 & acmd=receive & plate=TRUETHEN ChangeBlank(TRUE) || MoveZ(zmid) || astate1:=areceive1 END;. . .ENDC.3 The actuators of the Analyser Actuator_Analyser.mchWe consider the calls on the global imported procedures from the Robot in R_proc.mc...