Formalizing modularization and data hiding in synthetic biology

Biological systems employ compartmentalization and other co-localization strategies in order to orchestrate a multitude of biochemical processes by simultaneously enabling “data hiding” and modularization. This article presents recent research that embraces compartmentalization and co-location as an organizational programmatic principle in synthetic biological and biomimetic systems. In these systems, artificial vesicles and synthetic minimal cells are envisioned as nanoscale reactors for programmable biochemical synthesis and as chassis for molecular information processing. We present P systems, brane calculi, and the recently developed chemtainer calculus as formal frameworks providing data hiding and modularization and thus enabling the representation of highly complicated hierarchically organized compartmentalized reaction systems. We demonstrate how compartmentalization can greatly reduce the complexity required to implement computational functionality, and how addressable compartments permit the scaling-up of programmable chemical synthesis

Garbling Schemes and Applications

The topic of this thesis is garbling schemes and their applications. A garbling scheme is a set of algorithms for realizing secure two-party computation. A party called a client possesses a private algorithm as well as a private input and would like to compute the algorithm with this input. However, the client might not have enough computational resources to evaluate the function with the input on his own. The client outsources the computation to another party, called an evaluator. Since the client wants to protect the algorithm and the input, he cannot just send the algorithm and the input to the evaluator. With a garbling scheme, the client can protect the privacy of the algorithm, the input and possibly also the privacy of the output. The increase in network-based applications has arisen concerns about the privacy of user data. Therefore, privacy-preserving or privacy-enhancing techniques have gained interest in recent research. Garbling schemes seem to be an ideal solution for privacy-preserving applications. First of all, secure garbling schemes hide the algorithm and its input. Secondly, garbling schemes are known to have efficient implementations. In this thesis, we propose two applications utilizing garbling schemes. The first application provides privacy-preserving electronic surveillance. The second application extends electronic surveillance to more versatile monitoring, including also health telemetry. This kind of application would be ideal for assisted living services. In this work, we also present theoretical results related to garbling schemes. We present several new security definitions for garbling schemes which are of practical use. Traditionally, the same garbled algorithm can be evaluated once with garbled input. In applications, the same function is often evaluated several times with different inputs. Recently, a solution based on fully homomorphic encryption provides arbitrarily reusable garbling schemes. The disadvantage in this approach is that the arbitrary reuse cannot be efficiently implemented due to the inefficiency of fully homomorphic encryption. We propose an alternative approach. Instead of arbitrary reusability, the same garbled algorithm could be used a limited number of times. This gives us a set of new security classes for garbling schemes. We prove several relations between new and established security definitions. As a result, we obtain a complex hierarchy which can be represented as a product of three directed graphs. The three graphs in turn represent the different flavors of security: the security notion, the security model and the level of reusability. In addition to defining new security classes, we improve the definition of side-information function, which has a central role in defining the security of a garbling scheme. The information allowed to be leaked by the garbled algorithm and the garbled input depend on the representation of the algorithm. The established definition of side-information models the side-information of circuits perfectly but does not model side-information of Turing machines as well. The established model requires that the length of the argument, the length of the final result and the length of the function can be efficiently computable from the side-information function. Moreover, the side-information depends only on the function. In other words, the length of the argument, the length of the final result and the length of the function should only depend on the function. For circuits this is a natural requirement since the number of input wires tells the size of the argument, the number of output wires tells the size of the final result and the number of gates and wires tell the size of the function. On the other hand, the description of a Turing machine does not set any limitation to the size of the argument. Therefore, side-information that depends only on the function cannot provide information about the length of the argument. To tackle this problem, we extend the model of side-information so that side-information depends on both the function and the argument. The new model of side information allows us to define new security classes. We show that the old security classes are compatible with the new model of side-information. We also prove relations between the new security classes.Tämä väitöskirja käsittelee garblausskeemoja ja niiden sovelluksia. Garblausskeema on työkalu, jota käytetään turvallisen kahden osapuolen laskennan toteuttamiseen. Asiakas pitää hallussaan yksityistä algoritmia ja sen yksityistä syötettä, joilla hän haluaisi suorittaa tietyn laskennan. Asiakkaalla ei välttämättä ole riittävästi laskentatehoa, minkä vuoksi hän ei pysty suorittamaan laskentaa itse, vaan joutuu ulkoistamaan laskennan toiselle osapuolelle, palvelimelle. Koska asiakas tahtoo suojella algoritmiaan ja syötettään, hän ei voi vain lähettää niitä palvelimen laskettavaksi. Asiakas pystyy suojelemaan syötteensä ja algoritminsa yksityisyyttä käyttämällä garblausskeemaa. Verkkopohjaisten sovellusten kasvu on herättänyt huolta käyttäjien datan yksityisyyden turvasta. Siksi yksityisyyden säilyttävien tai yksityisyyden suojaa lisäävien tekniikoiden tutkimus on saanut huomiota. Garblaustekniikan avulla voidaan suojata sekä syöte että algoritmi. Lisäksi garblaukselle tiedetään olevan useita tehokkaita toteutuksia. Näiden syiden vuoksi garblausskeemat ovat houkutteleva tekniikka käytettäväksi yksityisyyden säilyttävien sovellusten toteutuksessa. Tässä työssä esittelemme kaksi sovellusta, jotka hyödyntävät garblaustekniikkaa. Näistä ensimmäinen on yksityisyyden säilyttävä sähköinen seuranta. Toinen sovellus laajentaa seurantaa monipuolisempaan monitorointiin, kuten terveyden kaukoseurantaan. Tästä voi olla hyötyä etenkin kotihoidon palveluille. Tässä työssä esitämme myös teoreettisia tuloksia garblausskeemoihin liittyen. Esitämme garblausskeemoille uusia turvallisuusmääritelmiä, joiden tarve kumpuaa käytännön sovelluksista. Perinteisen määritelmän mukaan samaa garblattua algoritmia voi käyttää vain yhdellä garblatulla syötteellä laskemiseen. Käytännössä kuitenkin samaa algoritmia käytetään usean eri syötteen evaluoimiseen. Hiljattain on esitetty tähän ongelmaan ratkaisu, joka perustuu täysin homomorfiseen salaukseen. Tämän ratkaisun ansiosta samaa garblattua algoritmia voi turvallisesti käyttää mielivaltaisen monta kertaa. Ratkaisun haittapuoli kuitenkin on, ettei sille ole tiedossa tehokasta toteutusta, sillä täysin homomorfiseen salaukseen ei ole vielä onnistuttu löytämään sellaista. Esitämme vaihtoehtoisen näkökulman: sen sijaan, että samaa garblattua algoritmia voisi käyttää mielivaltaisen monta kertaa, sitä voikin käyttää vain tietyn, ennalta rajatun määrän kertoja. Tämä näkökulman avulla voidaan määritellä lukuisia uusia turvallisuusluokkia. Todistamme useita relaatioita uusien ja vanhojen turvallisuusmääritelmien välillä. Relaatioiden avulla garblausskeemojen turvallisuusluokille saadaan muodostettua hierarkia, joka koostuu kolmesta komponentista. Tieto, joka paljastuu garblatusta algoritmista tai garblatusta syötteestä riippuu siitä, millaisessa muodossa algoritmi on esitetty, kutsutaan sivutiedoksi. Vakiintunut määritelmä mallintaa loogisen piiriin liittyvää sivutietoa täydellisesti, mutta ei yhtä hyvin Turingin koneeseen liittyvää sivutietoa. Tämä johtuu siitä, että jokainen yksittäinen looginen piiri asettaa syötteensä pituudelle rajan, mutta yksittäisellä Turingin koneella vastaavanlaista rajoitusta ei ole. Parannamme sivutiedon määritelmää, jolloin tämä ongelma poistuu. Uudenlaisen sivutiedon avulla voidaan määritellä uusia turvallisuusluokkia. Osoitamme, että vanhat turvallisuusluokat voidaan esittää uudenkin sivutiedon avulla. Todistamme myös relaatioita uusien luokkien välillä.Siirretty Doriast

A software classification scheme

Reusing code is one approach to software reusability. Code is the end product of the software lifecycle. It is delivered in a low level representation that is difficult to reuse unless an almost perfect match exists between available features and required specifications. There is a need to organize large inventories of software such that reusable code is easy to locate and exchange. The relative success in the reuse of code fragments reported by some software factories is due in part to their capacity to encapsulate domain specific functions and create specialized libraries of components classified by these locally standardized functions.A general software classification scheme that organizes reusability related attributes and common functions from different domains is proposed as a partial solution to the software reusability problem. For the problem of selecting from similar, potentially reusable. components, a partial solution based on evaluation of common characteristics is also proposed. A library system is presented that integrates the proposed classification scheme with an evaluation mechanism based on inherent component attributes, programming languages characteristics and reuser experience.The fundamental contribution of this dissertation is a formal treatment of a faceted scheme for software classification leading to better understanding of reusability at the code level. This approach has been prototyped in a library system for the semi-automatic classification of software components. Analysis were performed to evaluate the classification scheme. The results show the potential of the scheme in organizing collections of code fragments, in improving retrieval, and in simplifying the classification process. Tests of the evaluation mechanism showed positive correlation with evaluations conducted by potential reusers

Garbling Schemes and Applications

The topic of this thesis is garbling schemes and their applications. A garbling scheme is a set of algorithms for realizing secure two-party computation. A party called a client possesses a private algorithm as well as a private input and would like to compute the algorithm with this input. However, the client might not have enough computational resources to evaluate the function with the input on his own. The client outsources the computation to another party, called an evaluator. Since the client wants to protect the algorithm and the input, he cannot just send the algorithm and the input to the evaluator. With a garbling scheme, the client can protect the privacy of the algorithm, the input and possibly also the privacy of the output.  The increase in network-based applications has arisen concerns about the privacy of user data. Therefore, privacy-preserving or privacy-enhancing techniques have gained interest in recent research. Garbling schemes seem to be an ideal solution for privacy-preserving applications. First of all, secure garbling schemes hide the algorithm and its input. Secondly, garbling schemes are known to have efficient implementations.  In this thesis, we propose two applications utilizing garbling schemes. The first application provides privacy-preserving electronic surveillance. The second application extends electronic surveillance to more versatile monitoring, including also health telemetry. This kind of application would be ideal for assisted living services.  In this work, we also present theoretical results related to garbling schemes. We present several new security definitions for garbling schemes which are of practical use. Traditionally, the same garbled algorithm can be evaluated once with garbled input. In applications, the same function is often evaluated several times with different inputs. Recently, a solution based on fully homomorphic encryption provides arbitrarily reusable garbling schemes. The disadvantage in this approach is that the arbitrary reuse cannot be efficiently implemented due to the inefficiency of fully homomorphic encryption.  We propose an alternative approach. Instead of arbitrary reusability, the same garbled algorithm could be used a limited number of times. This gives us a set of new security classes for garbling schemes. We prove several relations between new and established security definitions. As a result, we obtain a complex hierarchy which can be represented as a product of three directed graphs. The three graphs in turn represent the different flavors of security: the security notion, the security model and the level of reusability.  In addition to defining new security classes, we improve the definition of side-information function, which has a central role in defining the security of a garbling scheme. The information allowed to be leaked by the garbled algorithm and the garbled input depend on the representation of the algorithm. The established definition of side-information models the side-information of circuits perfectly but does not model side-information of Turing machines as well. The established model requires that the length of the argument, the length of the final result and the length of the function can be efficiently computable from the side-information function. Moreover, the side-information depends only on the function. In other words, the length of the argument, the length of the final result and the length of the function should only depend on the function. For circuits this is a natural requirement since the number of input wires tells the size of the argument, the number of output wires tells the size of the final result and the number of gates and wires tell the size of the function. On the other hand, the description of a Turing machine does not set any limitation to the size of the argument. Therefore, side-information that depends only on the function cannot provide information about the length of the argument. To tackle this problem, we extend the model of side-information so that side-information depends on both the function and the argument. The new model of side information allows us to define new security classes. We show that the old security classes are compatible with the new model of side-information. We also prove relations between the new security classes.</p

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications

Cohesion Metrics for Improving Software Quality

Abstract Software product metrics aim at measuring the quality of software. Modu- larity is an essential factor in software quality. In this work, metrics related to modularity and especially cohesion of the modules, are considered. The existing metrics are evaluated, and several new alternatives are proposed. The idea of cohesion of modules is that a module or a class should consist of related parts. The closely related principle of coupling says that the relationships between modules should be minimized. First, internal cohesion metrics are considered. The relations that are internal to classes are shown to be useless for quality measurement. Second, we consider external relationships for cohesion. A detailed analysis using design patterns and refactorings confirms that external cohesion is a better quality indicator than internal. Third, motivated by the successes (and problems) of external cohesion metrics, another kind of metric is proposed that represents the quality of modularity of software. This metric can be applied to refactorings related to classes, resulting in a refactoring suggestion system. To describe the metrics formally, a notation for programs is developed. Because of the recursive nature of programming languages, the properties of programs are most compactly represented using grammars and formal lan- guages. Also the tools that were used for metrics calculation are described.Siirretty Doriast

Artificial general intelligence: Proceedings of the Second Conference on Artificial General Intelligence, AGI 2009, Arlington, Virginia, USA, March 6-9, 2009

Artificial General Intelligence (AGI) research focuses on the original and ultimate goal of AI – to create broad human-like and transhuman intelligence, by exploring all available paths, including theoretical and experimental computer science, cognitive science, neuroscience, and innovative interdisciplinary methodologies. Due to the difficulty of this task, for the last few decades the majority of AI researchers have focused on what has been called narrow AI – the production of AI systems displaying intelligence regarding specific, highly constrained tasks. In recent years, however, more and more researchers have recognized the necessity – and feasibility – of returning to the original goals of the field. Increasingly, there is a call for a transition back to confronting the more difficult issues of human level intelligence and more broadly artificial general intelligence

Digital Forensics AI: on Practicality, Optimality, and Interpretability of Digital Evidence Mining Techniques

Digital forensics as a field has progressed alongside technological advancements over the years, just as digital devices have gotten more robust and sophisticated. However, criminals and attackers have devised means for exploiting the vulnerabilities or sophistication of these devices to carry out malicious activities in unprecedented ways. Their belief is that electronic crimes can be committed without identities being revealed or trails being established. Several applications of artificial intelligence (AI) have demonstrated interesting and promising solutions to seemingly intractable societal challenges. This thesis aims to advance the concept of applying AI techniques in digital forensic investigation. Our approach involves experimenting with a complex case scenario in which suspects corresponded by e-mail and deleted, suspiciously, certain communications, presumably to conceal evidence. The purpose is to demonstrate the efficacy of Artificial Neural Networks (ANN) in learning and detecting communication patterns over time, and then predicting the possibility of missing communication(s) along with potential topics of discussion. To do this, we developed a novel approach and included other existing models. The accuracy of our results is evaluated, and their performance on previously unseen data is measured. Second, we proposed conceptualizing the term “Digital Forensics AI” (DFAI) to formalize the application of AI in digital forensics. The objective is to highlight the instruments that facilitate the best evidential outcomes and presentation mechanisms that are adaptable to the probabilistic output of AI models. Finally, we enhanced our notion in support of the application of AI in digital forensics by recommending methodologies and approaches for bridging trust gaps through the development of interpretable models that facilitate the admissibility of digital evidence in legal proceedings

Digital Forensics AI: on Practicality, Optimality, and Interpretability of Digital Evidence Mining Techniques

Digital forensics as a field has progressed alongside technological advancements over the years, just as digital devices have gotten more robust and sophisticated. However, criminals and attackers have devised means for exploiting the vulnerabilities or sophistication of these devices to carry out malicious activities in unprecedented ways. Their belief is that electronic crimes can be committed without identities being revealed or trails being established. Several applications of artificial intelligence (AI) have demonstrated interesting and promising solutions to seemingly intractable societal challenges. This thesis aims to advance the concept of applying AI techniques in digital forensic investigation. Our approach involves experimenting with a complex case scenario in which suspects corresponded by e-mail and deleted, suspiciously, certain communications, presumably to conceal evidence. The purpose is to demonstrate the efficacy of Artificial Neural Networks (ANN) in learning and detecting communication patterns over time, and then predicting the possibility of missing communication(s) along with potential topics of discussion. To do this, we developed a novel approach and included other existing models. The accuracy of our results is evaluated, and their performance on previously unseen data is measured. Second, we proposed conceptualizing the term “Digital Forensics AI” (DFAI) to formalize the application of AI in digital forensics. The objective is to highlight the instruments that facilitate the best evidential outcomes and presentation mechanisms that are adaptable to the probabilistic output of AI models. Finally, we enhanced our notion in support of the application of AI in digital forensics by recommending methodologies and approaches for bridging trust gaps through the development of interpretable models that facilitate the admissibility of digital evidence in legal proceedings