Reusing code can expedite software creation, analysis and exploration of data. Expediency can be particularly valuable for users of computational notebooks, where duplication allows them to quickly test hypotheses and iterate over data, without creating code from scratch. In this thesis, I’ll explore the topic of code duplication and the behaviour of code reuse for Jupyter notebooks; quantifying and describing snippets of code and explore potential barriers for reuse. As part of this thesis I conducted two studies into Jupyter notebooks use. In my first study, I mined GitHub repositories, quantifying and describing code duplicates contained within repositories that contained at least one Jupyter notebook. For my second study, I conducted an observational user study using a contextual inquiry, where my participants solved specific tasks using notebooks, while I observed and took notes. The work in this thesis can be categorized as exploratory, since both my studies were aimed at generating hypotheses for which further studies can build upon. My contributions with this thesis is two-fold: a thorough description of code duplicates contained within GitHub repositories and an exploration of the behaviour behind code reuse in Jupyter notebooks. It is my desire that others can build upon this work to provide new tools, addressing some of the issues outlined in this thesis. / Graduate

The use of AI tools for code generation is increasing in popularity, and two of these tools are ChatGPT and GitHub Copilot. These tools could potentially reduce development time and costs for developers and companies, however, ensuring the correctness and quality of AI-generated code is crucial for its adoption. This study conducted a quantitative controlled experiment to evaluate the code generation capabilities of Copilot and ChatGPT in terms of code correctness and quality. The experiment aimed to address research questions regarding the performance of these AI tools. The results indicate that both ChatGPT and Copilot can generate correct code from given instructions, though there is room for improvement. ChatGPT achieved a correctness rate of 87.33%, while Copilot performed slightly better at 89%. Statistical analysis revealed no significant difference in code correctness between the two tools. Regarding code quality, ChatGPT demonstrated impressive performance, with 98.52% of generated lines free from quality rule violations. Furthermore, 80.7% of ChatGPT-generated algorithms had no quality rule violations. Copilot generated correct lines for 94.07% of total lines but only achieved 64.7% of algorithms with no quality rule violations. The statistical analysis showed a statistically significant difference in code quality between ChatGPT and Copilot, indicating that ChatGPT generally produces higher quality code. This research contributes to understanding the capabilities of AI code generation tools and highlights their potential to produce correct and high-quality code.

No description available.

No description available.

Expander codes are sparse graph-based codes with good decoding algorithms. We present a linear-time decoding algorithm for (C,D, alpha, gamma) expander codes based on graphs with any expansion factor given that the minimum distances of the inner codes are bounded below. We also design graph-based codes with hierarchical locality. Such codes provide tiered recovery, depending on the number of erasures. A small number of erasures may be handled by only accessing a few other symbols, allowing for small locality, while larger number may involve a greater number of symbols. This provides an alternative to requiring disjoint repair groups. We also consider availability in this context, relying on the interplay between inner codes and the Tanner graph. We define new families of algebraic geometry codes for the purpose of code-based cryptography. In particular, we consider twisted Hermitian codes, twisted codes from a quotient of the Hermitian curve; and twisted norm-trace codes. These codes have Schur squares with large dimensions and hence could be considered as potential replacements for Goppa codes in the McEliece cryptosytem. However, we study the code-based cryptosystem based on twisted Hermitian codes and lay foundations for a potential attack on such a cryptosystem. / Doctor of Philosophy / Coding theory finds applications in various places such as data transmission, data storage, and even post-quantum cryptography. The goal of data transmission is to ensure fast and efficient information transfer. It is ideal to correct maximum number of errors introduced during transmission by noisy channels. We provide a new construction of expander codes (graph-based codes) and provide a linear-time decoding algorithm which corrects a constant-fraction of errors for these codes given any expansion factor. In this context, channel noise causes distortion of symbols, so that received symbols may be different than those originally sent. We are also interested in codes for erasure recovery, meaning those which restore missing symbols. A recent technique to recover the sent messages is by accesing a small subset of this received information, called locality. We analyze the locality properties of Tanner codes equipped with specific inner code. Code-based cryptography is a leading candidate in the post-quantum setting, meaning it is believed to be secure against quantum algorithms. The McEliece cryptosystem in which the underlying code is a Goppa code is popularly studied and is a top candidate in the NIST competition. However, the adoption of this system is not immediate due to its large key sizes. Code-based cryptosystems based on codes other than Goppa codes might provide a solution. We provide constructions of a new family of codes, called twisted algebraic geomtery codes which may provide alternatives of Goppa codes in the McEliece cryptosystem.

The development of high integrity embedded systems remains an arduous and error-prone task, despite the efforts by researchers in inventing tools and techniques for design automation. Much of the problem arises from the fact that the semantics of the modeling languages for the various tools, are often distinct, and the semantics gaps are often filled manually through the engineer's understanding of one model or an abstraction. This provides an opportunity for bugs to creep in, other than standardizing software engineering errors germane to such complex system engineering. Since embedded systems applications such as avionics, automotive, or industrial automation are safety critical, it is very important to invent tools, and methodologies for safe and reliable system design. Much of the tools, and techniques deal with either the design of embedded platforms (hardware, networking, firmware etc), and software stack separately. The problem of the semantic gap between these two, as well as between models of computation used to capture semantics must be solved in order to design safer embedded systems. In this dissertation we propose a methodology for the end-to-end modeling and analysis of safety-critical embedded systems. Our approach consists of formal platform modeling, and analysis; formal application modeling; and 'correct-by-construction' code synthesis with the aim of bridging semantic gaps between the various abstractions and models required for the end-to-end system design. While the platform modeling language AADL has formal semantics, and analysis tools for real-time, and performance verification, the application behavior modeling in AADL is weak and part of an annex. In our work, we create the APECS (AADL and Polychrony based Embedded Computing Synthesis) methodology to allow an embedded system design specification all the way from platform architecture and platform components, the real-time behavior, non-functional properties, as well as the application software modeling. Our main contribution is to integrate a polychronous application software modeling language, and synthesis algorithms in order for synthesis of the embedded software running on the target platform, with the required constraints being met. We believe that a polychronous approach is particularly well suited for a multiprocessor/multi-controller distributed platform where different components often operate at independent rates and concurrently. Further, the use of a formal polychronous language will allow for formal validation of the software prior to code generation. We present a prototype framework that implements this approach, which we refer to as the AADL and Polychrony based Embedded Computing System (APECS). Our prototype utilizes an extended version of Ocarina to provide code generation for the AADL model. Our polychronous modeling language is MRICDF. Our prototype extends Ocarina to support software specification in MRICDF and generate multi-threaded software. Additionally, we implement an automated translation from Simulink to MRICDF, allowing designers to benefit from its formal semantics and exploit engineers' familiarity with Simulink tools, and legacy models. We present case studies utilizing APECS to implement safety critical systems both natively in MRICDF and in Simulink through automated translation. / Ph. D.

Consider a network which consists of noiseless point to point channels. In this network, the source node wants to send messages to a specific set of sink nodes. If an intermediate node v has just one input channel then the received symbol by that node can be replicated and sent to the outgoing channels from v. If v has at least two incoming channels then it has two options. It can either send the received symbols one-by-one, one symbol in each time unit, or v can transmit a combination of the received symbols. The former choice takes more time compared to the latter option, which is called network coding. In the literature, it has been shown that in a single source finite acyclic network the maximum throughput can be achieved by using linear network codes. Significant effort has been made to efficiently construct good network codes. In addition, a polynomial time algorithm for constructing a linear network code on a given network was introduced. Also an algorithm for constructing a linear multicast code on an acyclic network was introduced. Finally, a method for finding a representation matrix for the network matroid of a given network G was also introduced. This matrix can be used to construct a generic code. In this thesis we first provide a review of some known methods for constructing linear multicast, broadcast and dispersion codes for cyclic and acyclic networks. We then give a method for normalization of a non-normal code, and also give a new algorithm for constructing a linear multicast code on a cyclic network. The construction of generic network codes is also addressed. / Graduate / 0984 / 0544 / esmaeili@uvic.ca

This work deals with problems of the barcode applied to automatic identification. Description of their major part, creation of the bar code online generator, a web-page information system using the barcodes to identify the object, is presented.

Le code génétique est la table de correspondance entre codons (unité structurelle d'un gène) et acides aminés (brique élémentaire des protéines). Le code génétique est (1) universel, tous les êtres vivants ou presque partagent le même code; (2) univoque, chaque codon spécifie un seul acide aminé et (3) dégénéré, les acides aminés peuvent être codés par plusieurs codons. Ce code dégénéré est donc utilisé par l'ensemble du vivant mais pas de la même manière, certains codons synonymes étant utilisés préférentiellement chez des espèces et pas d'autres. Pour comprendre l'émergence des biais d'usage du code (BUC) génétique entre espèces, je me place dans un contexte évolutif.Dans ce manuscrit, je présente mes travaux de recherche en quatre parties. La première partie introductive décrit la mise en évidence et les propriétés du code génétique, son biais d'usage et les diverses caractéristiques de précédents modèles de codons. La deuxième partie présente le modèle d'évolution de codons SENCA pour Sites Evolution at the Nucleotides, Codons and Amino-acids layers que j'ai développé durant ma thèse. SENCA prend en compte la structure du code génétique. Je valide sa paramétrisation par des simulations numériques et une étude sur des espèces bactériennes ou archées. La partie suivante décrit deux extensions de SENCA qui modélisent plusieurs hypothèses d'origines évolutives du BUC et une application de SENCA sur les conséquences génomiques d'adaptations environnementales. La dernière partie étudie les origines de variations de BUC le long du génome humain par une approche de génomique comparative / In this manuscript, I introduce my doctoral research in four parts. The first introductive part highlights the properties of the genetic code and its usage bias but also the caracteristics of previous published codons models. The second part presents an evolutionary codons models named SENCA for Sites Evolution at the Nucleotides, Codons and Amino-acids layers that I developped. SENCA takes into account the genetic code structure. I perform simulations and study prokaryotes species to confirm its parametrization. The following part provides two extensions of SENCA to test the hypotheses concerning the evolutive origins of CUB and an application of SENCA to study the genomic consequences of an environmental adaptation. The last part studies the origins of CUB variation within the human genome using a comparative genomic strategy

Neste trabalho calculamos o peso e a dimensão de todos os códigos cíclicos de comprimento pn na álgebra de grupo FqCpn, onde p é um número primo e Fq é um corpo finito de característica q. Também calculamos o peso do código dado pela soma de dois códigos abelianos minimais em Fq(Cp × Cp), dessa forma foi possível fazer uma breve comparação entre códigos cíclicos e abelianos não cíclicos de comprimento p2. / In this work we compute the weight and the dimension of all cyclic codes of length pn in the group algebra FqCpn, where p is a prime number and Fq is a finite field of characteristic q. Furthermore, we compute the weight of codes which are given by the sum of two minimal abelian codes in Fq(Cp × Cp). In this way, it was possible to compare briefly cyclic codes and non-cyclic abelian codes of length p2.