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Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…

Adaptation and Self-Organizing Systems · Physics 2007-05-23 John F. McGowan , Ph. D

The software running in embedded or cyber-physical systems (CPS) is typically of proprietary nature, so users do not know precisely what the systems they own are (in)capable of doing. Most malfunctionings of such systems are not intended by…

Logic in Computer Science · Computer Science 2019-04-19 Sebastian Biewer , Pedro D'Argenio , Holger Hermanns

Background The theoretical requirements for a genetic code were well defined and modeled by George Gamow and Francis Crick in the 50-es. Their models failed. However the valid Genetic Code, provided by Nirenberg and Matthaei in 1961,…

Biomolecules · Quantitative Biology 2008-08-04 Jan C Biro

Many software developments projects fail due to quality problems. Software testing enables the creation of high quality software products. Since it is a cumbersome and expensive task, and often hard to manage, both its technical background…

Software Engineering · Computer Science 2015-03-17 Tim A. Majchrzak

As software development practices increasingly adopt AI-powered tools, ensuring that such tools can support secure coding has become critical. This study evaluates the effectiveness of GitHub Copilot's recently introduced code review…

Software Engineering · Computer Science 2025-09-18 Amena Amro , Manar H. Alalfi

Shaped by natural selection and other evolutionary forces, an organism's evolutionary history is reflected through its genome sequence, content of functional elements and organization. Consequently, organisms connected through phylogeny,…

Genomics · Quantitative Biology 2023-06-16 Serena Lam , Giorgio Gonnella

List recovery is a fundamental task for error-correcting codes, vastly generalizing unique decoding from worst-case errors and list decoding. Briefly, one is given ''soft information'' in the form of input lists S_1,...,S_n of bounded size,…

Information Theory · Computer Science 2025-10-10 Nicolas Resch , S. Venkitesh

Nowadays, software testing professionals are commonly required to develop coding skills to work on test automation. One essential skill required from those who code is the ability to implement code refactoring, a valued quality aspect of…

Software needs to be secure, in particular, when deployed to critical infrastructures. Secure coding guidelines capture practices in industrial software engineering to ensure the security of code. This study aims to assess the level of…

Software Engineering · Computer Science 2021-01-07 Tiago Espinha Gasiba , Ulrike Lechner , Maria Pinto-Albuquerque , Daniel Mendez Fernandez

This dissertation presents an evaluation of several language models on software defect datasets. A language Model (LM) "can provide word representation and probability indication of word sequences as the core component of an NLP system."…

Software Engineering · Computer Science 2019-09-24 Kailun Wang

Code review is an essential part to software development lifecycle since it aims at guaranteeing the quality of codes. Modern code review activities necessitate developers viewing, understanding and even running the programs to assess…

Software Engineering · Computer Science 2022-10-12 Zhiyu Li , Shuai Lu , Daya Guo , Nan Duan , Shailesh Jannu , Grant Jenks , Deep Majumder , Jared Green , Alexey Svyatkovskiy , Shengyu Fu , Neel Sundaresan

A crucial problem in genome assembly is the discovery and correction of misassembly errors in draft genomes. We develop a method that will enhance the quality of draft genomes by identifying and removing misassembly errors using paired…

Genomics · Quantitative Biology 2014-11-24 Martin D. Muggli , Simon J. Puglisi , Roy Ronen , Christina Boucher

Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…

Adaptation and Self-Organizing Systems · Physics 2007-05-23 H. Takagi , K. Kaneko , T. Yomo

The idea of computer vision as the Bayesian inverse problem to computer graphics has a long history and an appealing elegance, but it has proved difficult to directly implement. Instead, most vision tasks are approached via complex…

Artificial Intelligence · Computer Science 2013-07-02 Vikash K. Mansinghka , Tejas D. Kulkarni , Yura N. Perov , Joshua B. Tenenbaum

Software engineers spend a substantial amount of time using Web search to accomplish software engineering tasks. Such search tasks include finding code snippets, API documentation, seeking help with debugging, etc. While debugging a bug or…

Software Engineering · Computer Science 2020-06-02 Foyzul Hassan , Chetan Bansal , Nachiappan Nagappan , Thomas Zimmermann , Ahmed Hassan Awadallah

Conducting a randomization test is a common method for testing causal null hypotheses in randomized experiments. The popularity of randomization tests is largely because their statistical validity only depends on the randomization design,…

Methodology · Statistics 2025-01-15 Siyu Heng , Pamela A. Shaw

Stellar oscillation codes are software instruments that evaluate the normal-mode frequencies of an input stellar model. While inter-code comparisons are often used to confirm the correctness of calculations, they are not suitable for…

Solar and Stellar Astrophysics · Physics 2025-05-29 Richard H. D. Townsend , Rianna V. Kuenzi , Jørgen Christensen-Dalsgaard

The art of finding software vulnerabilities has been covered extensively in the literature and there is a huge body of work on this topic. In contrast, the intentional insertion of exploitable, security-critical bugs has received little…

Cryptography and Security · Computer Science 2020-07-07 Jannik Pewny , Thorsten Holz

The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific…

Other Quantitative Biology · Quantitative Biology 2009-11-13 Tidjani Negadi

Program errors can occur in any type of programming, and can manifest in a variety of ways, such as unexpected output, crashes, or performance issues. And program error diagnosis can often be too abstract or technical for developers to…

Software Engineering · Computer Science 2025-01-07 Zhenyu Xu , Victor S. Sheng