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The search for similar genetic sequences is one of the main bioinformatics tasks. The genetic sequences data banks are growing exponentially and the searching techniques that use linear time are not capable to do the search in the required…

Distributed, Parallel, and Cluster Computing · Computer Science 2015-07-13 Felipe Albrecht

With the advent of open source software, a veritable treasure trove of previously proprietary software development data was made available. This opened the field of empirical software engineering research to anyone in academia. Data that is…

Software Engineering · Computer Science 2022-04-19 Adam Tutko , Austin Z. Henley , Audris Mockus

Where can we find malware source code? This question is motivated by a real need: there is a dearth of malware source code, which impedes various types of security research. Our work is driven by the following insight: public archives, like…

Cryptography and Security · Computer Science 2020-06-01 Md Omar Faruk Rokon , Risul Islam , Ahmad Darki , Vagelis E. Papalexakis , Michalis Faloutsos

Researchers have made significant progress in automating the software development process in the past decades. Recent progress in Large Language Models (LLMs) has significantly impacted the development process, where developers can use…

Software Engineering · Computer Science 2024-07-26 Yuntong Zhang , Haifeng Ruan , Zhiyu Fan , Abhik Roychoudhury

The rapid evolution of software libraries poses a considerable hurdle for code generation, necessitating continuous adaptation to frequent version updates while preserving backward compatibility. While existing code evolution benchmarks…

Lessons learned (LL) records constitute the software organization memory of successes and failures. LL are recorded within the organization repository for future reference to optimize planning, gain experience, and elevate market…

Software Engineering · Computer Science 2021-10-12 Tamer Mohamed Abdellatif , Luiz Fernando Capretz , Danny Ho

Repository-level code generation remains challenging due to complex code dependencies and the limitations of large language models (LLMs) in processing long contexts. While retrieval-augmented generation (RAG) frameworks are widely adopted,…

Software Engineering · Computer Science 2025-03-27 Wenchao Gu , Juntao Chen , Yanlin Wang , Tianyue Jiang , Xingzhe Li , Mingwei Liu , Xilin Liu , Yuchi Ma , Zibin Zheng

Logging -- used for system events and security breaches to describe more informational yet essential aspects of software features -- is pervasive. Given the high transactionality of today's software, logging effectiveness can be reduced by…

Software Engineering · Computer Science 2022-07-20 Yiming Tang , Allan Spektor , Raffi Khatchadourian , Mehdi Bagherzadeh

Comments within code serve as a crucial foundation for software documentation, facilitating developers to communicate and understand the code effectively. However, code-comment inconsistency (CCI) can negatively affect software development,…

Software Engineering · Computer Science 2025-06-26 Renyi Zhong , Yintong Huo , Wenwei Gu , Jinxi Kuang , Zhihan Jiang , Guangba Yu , Yichen Li , David Lo , Michael R. Lyu

We have developed several autotuning benchmarks in CUDA that take into account performance-relevant source-code parameters and reach near peak-performance on various GPU architectures. We have used them during the development and evaluation…

Distributed, Parallel, and Cluster Computing · Computer Science 2021-02-11 Jiří Filipovič , Jana Hozzová , Amin Nezarat , Jaroslav Oľha , Filip Petrovič

With the increasing usage of JavaScript in web applications, there is a great demand to write JavaScript code that is reliable and maintainable. To achieve these goals, classes can be emulated in the current JavaScript standard version. In…

Software Engineering · Computer Science 2016-02-19 Leonardo Humberto Silva , Daniel Hovadick , Marco Tulio Valente , Alexandre Bergel , Nicolas Anquetil , Anne Etien

Peer code review locates common coding rule violations and simple logical errors in the early phases of software development, and thus reduces overall cost. However, in GitHub, identifying an appropriate code reviewer for a pull request is…

Software Engineering · Computer Science 2018-07-10 Mohammad Masudur Rahman , Chanchal K. Roy , Jason A. Collins

In many common scenarios, programmers need to implement functionality that is already provided by some third party library. This paper presents a tool called Hunter that facilitates code reuse by finding relevant methods in large code bases…

Software Engineering · Computer Science 2016-08-30 Yuepeng Wang , Yu Feng , Ruben Martins , Arati Kaushik , Isil Dillig , Steven P. Reiss

Beyond scratch coding, exploiting large-scale code repositories (e.g., GitHub) for practical tasks is vital in real-world software development, yet current benchmarks rarely evaluate code agents in such authentic, workflow-driven scenarios.…

Background: According to GitGuardian's monitoring of public GitHub repositories, secrets sprawl continued accelerating in 2022 by 67% compared to 2021, exposing over 10 million secrets (API keys and other credentials). Though many…

Cryptography and Security · Computer Science 2023-07-04 Setu Kumar Basak , Jamison Cox , Bradley Reaves , Laurie Williams

A source code difference (diff) indicates changes made by comparing new and old source codes, and it can be utilized in code reviews to help developers understand the changes made to the code. Although many diff generation methods have been…

Software Engineering · Computer Science 2024-09-27 Tsukasa Yagi , Shinpei Hayashi

Research is an incremental, iterative process, with new results relying and building upon previous ones. Scientists need to find, retrieve, understand, and verify results in order to confidently extend them, even when the results are their…

Computation · Statistics 2023-06-30 Gabriel Becker , Sara E. Moore , Michael Lawrence

To adapt to a constantly evolving landscape of cyber threats, organizations actively need to collect Indicators of Compromise (IOCs), i.e., forensic artifacts that signal that a host or network might have been compromised. IOCs can be…

Cryptography and Security · Computer Science 2023-03-09 Juan Caballero , Gibran Gomez , Srdjan Matic , Gustavo Sánchez , Silvia Sebastián , Arturo Villacañas

Dealing with merge conflicts in version control systems is a challenging task for software developers. Resolving merge conflicts is a time-consuming and error-prone process, which distracts developers from important tasks. Recent work shows…

Software Engineering · Computer Science 2022-08-11 Max Ellis , Sarah Nadi , Danny Dig

Current search techniques are limited to standard RAG query-document applications. In this paper, we propose a novel technique to expand the code and index for predicting the required APIs, directly enabling high-quality, end-to-end code…

Software Engineering · Computer Science 2025-10-01 Esakkivel Esakkiraja , Denis Akhiyarov , Aditya Shanmugham , Chitra Ganapathy