25 papers · ranked by Valyu relevance
Diego Darriba, Tomáš Flouri, Alexandros Stamatakis
With Next Generation Sequencing Data (NGS) coming off age and being routinely used, evolutionary biology is transforming into a data-driven science. As a consequence, researchers have to rely on a growing number of increasingly complex software. All widely used tools in our field have grown considerably, in terms of…
Gábor Horváth, Réka Kovács, Richárd Szalay, Zoltán Porkoláb + 2 more
Static analysis is the analysis of a program without executing it that is carried out by an automated tool. It is a widely used approach for several problems. It is used for optimising code, large-scale refactoring, code metrics, code visualisation and several other purposes. Unfortunately, there are some strong…
W. F. Mader, Shangqing Liu, Wenhan Wang, Qiang Hu + 4 more
'Cen Zhang' 'Liming Nie' 'Yang Liu'] Large language models (LLMs) demonstrate significant potential to revolutionize software engineering (SE) by exhibiting outstanding performance in SE tasks such as code and document generation. However, the high reliability and risk control requirements in software engineering raise…
Fitzroy Nembhard, Marco Carvalho
The area of software development and secure coding can benefit significantly from advancements in virtual assistants. Research has shown that many coders neglect security in favor of meeting deadlines. This shortcoming leaves systems vulnerable to attackers. While a plethora of tools are available for programmers to…
Kajetan Kuszczyński, Michał Walkowski, Alessandra Rizzardi
The increasing complexity of web applications and systems, driven by ongoing digitalization, has made software security testing a necessary and critical activity in the software development lifecycle. This article compares the performance of open-source tools for conducting static code analysis for security purposes.…
Chen Tsfaty, Michael Fire
Title: Summary Modern software development often relies on open-source code sharing. Open-source code reuse, however, allows hackers to access wide developer communities, thereby potentially affecting many products. An increasing number of such “supply chain attacks” have occurred in recent years, taking advantage of…
Melih Peker, Ozcan Ozturk
Selecting a good set of optimization flags requires extensive effort and expert input. While most of the prior research considers using static, spatial, or dynamic features, some of the latest research directly applied deep neural networks to source code. We combined the static features, spatial features, and deep…
Tushar Sharma, Maria Kechagia, Stefanos Georgiou, Rohit Tiwari + 3 more
'Indira Vats' 'Hadi Moazen' 'Federica Sarro'] The advancements in machine learning techniques have encouraged researchers to apply these techniques to a myriad of software engineering tasks that use source code analysis, such as testing and vulnerability detection. Such a large number of studies hinders the community…
Aakanshi Gupta, Bharti Suri, Deepanshu Sharma, Sanjay Misra + 1 more
'Luis Fernandez-Sanz'] In the digitization era, the battery consumption factor plays a vital role for the devices that operate Android software, expecting them to deliver high performance and good maintainability.The study aims to analyze the Android-specific code smells, their impact on battery consumption, and the…
Gao Hao, Haytham Hijazi, João Durães, Júlio Medeiros + 7 more
'Ricardo Couceiro' 'Chan Tong Lam' 'César Teixeira' 'João Castelhano' 'Miguel Castelo Branco' 'Paulo Carvalho' 'Henrique Madeira'] Complexity is the key element of software quality. This article investigates the problem of measuring code complexity and discusses the results of a controlled experiment to compare…
Lisa Nguyen Quang, Stefan Krüger, Patrick L. Hill, Karim Ali + 1 more
'Eric Bodden'] To detect and x bugs and security vulnerabilities, software companies use static analysis as part of the development process. However, static analysis code itself is also prone to bugs. To ensure a consistent level of precision, as analyzed programs grow more complex, a static analysis has to handle more…
Florian Obermüller, Lena Bloch, Luisa Greifenstein, Ute Heuer + 1 more
'Gordon Fraser'] Block-based programming languages like Scratch enable children to be creative while learning to program. Even though the blockbased approach simplifies the creation of programs, learning to program can nevertheless be challenging. Automated tools such as linters therefore support learners by providing…
Fabiano Pecorelli, Savanna Lujan, Valentina Lenarduzzi, Fabio Palomba + 1 more
Code smells are poor implementation choices that developers apply while evolving source code and that affect program maintainability. Multiple automated code smell detectors have been proposed: while most of them relied on heuristics applied over software metrics, a recent trend concerns the definition of machine…
K. A. S. Mislan, Jeffrey M. Heer, Ethan P. White
Code is increasingly central to research in ecology. From running statistical analyses for field and lab projects to developing software intended to be used broadly for modeling and data analysis, most ecologists now commonly write code as part of their research. It is important that the communication of research…
Nitesh Kumar Sharma, Ram Ayyala, Dhrithi Deshpande, Yesha M Patel + 11 more
Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are…
Jacqueline A Jansen, Artür Manukyan, Nour Al Khoury, Altuna Akalin
Data analysis is constrained by a shortage of skilled experts, particularly in biology, where detailed data interpretation is vital for understanding complex biological processes and developing new treatments and diagnostics. To address this, we developed mergen, an R package that leverages Large Language Models (LLMs)…
Delano Oliveira, Reydne Santos, Benedito de Oliveira, Martin Monperrus + 2 more
'Martin Monperrus' 'Fernando Castor' 'Fernanda Madeiral'] Abstract—Context: Code understandability plays a crucial role in software development, as developers spend between 58% and 70% of their time reading source code. Improving code understandability can lead to enhanced productivity and save maintenance costs.…
Marc-Antoine Jacques, Maciej Dobrzyński, Paolo Armando Gagliardi, Raphael Sznitman + 1 more
Fluorescent biosensors routinely yield thousands of single-cell, heterogeneous, multi-dimensional signaling trajectories that are difficult to mine for relevant information. We present CODEX, an approach based on artificial neural networks to guide exploration of time-series datasets and to identify motifs in dynamic…
Miloje Rakočević
In some previous works (2018a,b; 2019, 2021a,b, 2022) we presented a new type of mirror symmetry, expressed in the set of protein amino acids; such a symmetry, that it simultaneously represents the semiotic essence of the genetic code. In this paper we provide new evidences that the genetic code represents the unity of…
Pieter Floris Jacobs, Robert Pollice
Scientists across domains are often challenged to master domain-specific languages (DSLs) for their research, which are merely a means to an end but are pervasive in fields like computational chemistry. Automated code generation promises to overcome this barrier, allowing researchers to focus on their core expertise.…
Griffin Chure, Jonas Cremer
High-Performance Liquid Chromatography (HPLC) and Gas Chromatography are analytical techniques which allow for the quantitative characterization of the chemical components of mixtures . Technological advancements in sample preparation and mechanical automation have allowed HPLC to become a high-throughput tool which…
Babu Bassa
In this communication the author describes a software tool named "ChameleonSort". The software program, developed by the present author is useful in the sorting of biological sequence variants like those accumulating mutations while diverging from the common ancestors. Examples include viral protein variants, protein…
Pablo Quijano Velasco, Kedar Hippalgaonkar, Balamurugan Ramalingam
The discovery of optimal conditions of chemical reactions is a labor-intensive, time-consuming task that requires exploring a high-dimensional parametric space. Historically the optimization of chemical reactions has been performed by manual experimentation guided by human intuition and Design of Experiments where one…
Jeremy Li, Alex Rubinsteyn, Sergey Feldman, Timothy O’Donnell + 18 more
Scientific computing has become a central component of modern scientific discovery. Yet many computational tools are developed by small, specialized teams under incentives that encourage the release of rapidly prototyped tooling without commensurate attention to engineering concerns, including performance and…
Shirin Faraji, Johannes Ehrmaier, Maximilian Menger
Here, PySurf is introduced as an innovative code framework, which is specifically designed for rapid prototyping and development tasks for data-science applications in computational chemistry. To illustrate the potential of the framework, a code for nonadiabatic surface-hopping simulations based on the Landau-Zener…