12 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…
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…
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…
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)…
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…
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…