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Reproducibility is a cornerstone of scientific progress, yet its state in large language model (LLM)-based software engineering (SE) research remains poorly understood. This paper presents the first large-scale, empirical study of…

Software Engineering · Computer Science 2025-12-02 Mohammed Latif Siddiq , Arvin Islam-Gomes , Natalie Sekerak , Joanna C. S. Santos

Although a standard in natural science, reproducibility has been only episodically applied in experimental computer science. Scientific papers often present a large number of tables, plots and pictures that summarize the obtained results,…

Digital Libraries · Computer Science 2017-09-06 Fernando Chirigati , Rebecca Capone , Dennis Shasha , Remi Rampin , Juliana Freire

R has become a cornerstone of scientific and statistical computing due to its extensive package ecosystem, expressive syntax, and strong support for reproducible analysis. However, as data sizes and computational demands grow, native R…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-05-13 Xiran Zhang , Javier Conejero , Sameh Abdulah , Jorge Ejarque , Ying Sun , Rosa M. Badia , David E. Keyes , Marc G. Genton

The scarcity of high-quality training data presents a fundamental bottleneck to scaling machine learning models. This challenge is particularly acute in recommendation systems, where extreme sparsity in user interactions leads to rugged…

Information Retrieval · Computer Science 2026-05-12 Luankang Zhang , Hao Wang , Zhongzhou Liu , Mingjia Yin , Yonghao Huang , Jiaqi Li , Wei Guo , Yong Liu , Huifeng Guo , Defu Lian , Enhong Chen

Computational reproducibility refers to obtaining consistent results when rerunning an experiment. Jupyter Notebook, a web-based computational notebook application, facilitates running, publishing, and sharing computational experiments…

Software Engineering · Computer Science 2025-09-30 A S M Shahadat Hossain , Colin Brown , David Koop , Tanu Malik

Recent advances in retrieval-augmented generation (RAG) have initiated a new era in repository-level code completion. However, the invariable use of retrieval in existing methods exposes issues in both efficiency and robustness, with a…

Software Engineering · Computer Science 2024-06-05 Di Wu , Wasi Uddin Ahmad , Dejiao Zhang , Murali Krishna Ramanathan , Xiaofei Ma

Context: Retrieval-augmented code generation relies on cross-file repository context, but retrieved snippets may come from obsolete project states. Objectives: We study whether temporally stale repository snippets act as harmless noise or…

Software Engineering · Computer Science 2026-05-15 Haojun Weng , Qianqian Yang , Hao Fu , Haobin Pan , Xinwei Lv

Different software tools have been developed with the purpose of performing offline evaluations of recommender systems. However, the results obtained with these tools may be not directly comparable because of subtle differences in the…

Information Retrieval · Computer Science 2018-10-12 Diego Monti , Giuseppe Rizzo , Maurizio Morisio

The rapid growth of Retrieval-Augmented Generation (RAG) has created a proliferation of toolkits, yet a fundamental gap remains between experimental prototypes and robust, production-ready systems. We present SearchGym, a modular…

Information Retrieval · Computer Science 2026-03-06 Jerome Tze-Hou Hsu

In the computer vision and machine learning communities, as well as in many other research domains, rigorous evaluation of any new method, including classifiers, is essential. One key component of the evaluation process is the ability to…

Computer Vision and Pattern Recognition · Computer Science 2024-12-19 Sébastien Piérard , Anaïs Halin , Anthony Cioppa , Adrien Deliège , Marc Van Droogenbroeck

Scientific software is essential to scientific innovation and in many ways it is distinct from other types of software. Abandoned (or unmaintained), buggy, and hard to use software, a perception often associated with scientific software can…

Software Engineering · Computer Science 2025-06-23 Addi Malviya Thakur , Reed Milewicz , Mahmoud Jahanshahi , Lavínia Paganini , Bogdan Vasilescu , Audris Mockus

Modern LLM agents increasingly create their own tools at runtime -- from Python functions to API clients -- yet existing benchmarks evaluate them almost exclusively by downstream task completion. This is analogous to judging a software…

Software Engineering · Computer Science 2026-04-02 Alibek T. Kaliyev , Artem Maryanskyy

Multi-modal generative document parsing systems challenge traditional evaluation: unlike deterministic OCR or layout models, they often produce semantically correct yet structurally divergent outputs. Conventional metrics-CER, WER, IoU, or…

Computation and Language · Computer Science 2025-09-25 Renyu Li , Antonio Jimeno Yepes , Yao You , Kamil Pluciński , Maximilian Operlejn , Crag Wolfe

Reproducibility in research remains hindered by complex systems involving data, models, tools, and algorithms. Studies highlight a reproducibility crisis due to a lack of standardized reporting, code and data sharing, and rigorous…

Software Engineering · Computer Science 2024-11-05 Venkat S. Malladi , Maria Yazykova , Olesya Melnichenko , Yulia Dubinina

Open source software development, particularly within institutions such as universities and research laboratories, is often decentralized and difficult to track. Although academic teams produce many impactful scientific tools, their…

Software Engineering · Computer Science 2026-02-27 Juanita Gomez , Emily Lovell , Stephanie Lieggi , Alvaro A. Cardenas , James Davis

Objective: Reproducibility is a core tenet of scientific research. A reproducible study is one where the results can be recreated by different investigators in different circumstances using the same methodology and materials. Unfortunately,…

Quantitative Methods · Quantitative Biology 2019-07-17 Aaron Bowers , Shelby Rauh , Drayton Rorah , Daniel Tritz , Lance Frye , Matt Vassar

Open-Source Software (OSS) vulnerabilities bring great challenges to the software security and pose potential risks to our society. Enormous efforts have been devoted into automated vulnerability detection, among which deep learning…

Cryptography and Security · Computer Science 2024-02-09 Xinchen Wang , Ruida Hu , Cuiyun Gao , Xin-Cheng Wen , Yujia Chen , Qing Liao

Many applications in Reinforcement Learning (RL) usually have noise or stochasticity present in the environment. Beyond their impact on learning, these uncertainties lead the exact same policy to perform differently, i.e. yield different…

Machine Learning · Computer Science 2024-01-23 Manon Flageat , Bryan Lim , Antoine Cully

Deep learning has revolutionized computing in many real-world applications, arguably due to its remarkable performance and extreme convenience as an end-to-end solution. However, deep learning models can be costly to train and to use,…

Machine Learning · Computer Science 2024-11-19 Yao Lu , Peixin Zhang , Jingyi Wang , Lei Ma , Xiaoniu Yang , Qi Xuan

World models are central to building agents that can reason, plan, and generalize beyond their training data. However, research on world models is currently fragmented, with disparate codebases, data pipelines, and evaluation protocols…

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