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Although reproducibility is a core tenet of the scientific method, it remains challenging to reproduce many results. Surprisingly, this also holds true for computational results in domains such as systems biology where there have been…

Quantitative Methods · Quantitative Biology 2021-04-13 Michael L. Blinov , John H. Gennari , Jonathan R. Karr , Ion I. Moraru , David P. Nickerson , Herbert M. Sauro

Many research directions in machine learning, particularly in deep learning, involve complex, multi-stage experiments, commonly involving state-mutating operations acting on models along multiple paths of execution. Although machine…

Software Engineering · Computer Science 2020-06-16 Michela Paganini , Jessica Zosa Forde

In recent years, machine learning technologies have gained immense popularity and are being used in a wide range of domains. However, due to the complexity associated with machine learning algorithms, it is a challenge to make it…

Software Engineering · Computer Science 2024-10-15 Natalie Sinani , Sahil Salma , Paul Boutot , Sadaf Mustafiz

Recent advances in Multimodal Large Language Models (MLLMs) have enhanced their versatility as they integrate a growing number of modalities. Considering the heavy cost of training MLLMs, it is efficient to reuse the existing ones and…

Machine Learning · Computer Science 2025-10-23 Dingkun Zhang , Shuhan Qi , Xinyu Xiao , Kehai Chen , Xuan Wang

Existing prompt-optimization techniques rely on local signals to update behavior, often neglecting broader and recurring patterns across tasks, leading to poor generalization; they further rely on full-prompt rewrites or unstructured…

Software Engineering · Computer Science 2026-03-24 Balaji Dinesh Gangireddi , Aniketh Garikaparthi , Manasi Patwardhan , Arman Cohan

With the decline of Moore's law, optimizing program performance has become a major focus of software research. However, high-level optimizations such as API and algorithm changes remain elusive due to the difficulty of understanding the…

Machine learning (ML) reproducibility is often framed as a problem of incomplete artifact recording. This framing leads to systems that prioritize capturing datasets, code, configurations, and execution environments. However, in…

Human-Computer Interaction · Computer Science 2026-04-13 Zhiwei Li , Carl Kesselman

Embedded systems have proliferated in various consumer and industrial applications with the evolution of Cyber-Physical Systems and the Internet of Things. These systems are subjected to stringent constraints so that embedded software must…

Open science initiatives seek to make research outputs more transparent, accessible, and reusable, but ensuring that published findings can be independently reproduced remains a persistent challenge. In this paper we describe an AI-driven…

Artificial Intelligence · Computer Science 2025-12-16 Adrien Bibal , Steven N. Minton , Deborah Khider , Yolanda Gil

The quality of scientific code is a critical concern for the research community. Poorly written code can result in irreproducible results, incorrect findings, and slower scientific progress. In this study, we evaluate scientific code…

Software Engineering · Computer Science 2026-03-25 Shun Kashiwa , Ayla Kurdak , Savitha Ravi , Ridhi Srikanth , Angel Thakur , Sonia Chandra , Jonathan Truong , Michael Coblenz

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

Grounded Multimodal Named Entity Recognition (GMNER) extends traditional NER by jointly detecting textual mentions and grounding them to visual regions. While existing supervised methods achieve strong performance, they rely on costly…

Information Retrieval · Computer Science 2025-11-13 Jielong Tang , Shuang Wang , Zhenxing Wang , Jianxing Yu , Jian Yin

Reconstructing numerical simulations from control systems research papers is often hindered by underspecified parameters and ambiguous implementation details. We define the task of Paper to Simulation Recoverability, the ability of an…

Artificial Intelligence · Computer Science 2026-04-07 Vineet Bhat , Shiqing Wei , Ali Umut Kaypak , Prashanth Krishnamurthy , Ramesh Karri , Farshad Khorrami

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

The integration of machine learning techniques in materials discovery has become prominent in materials science research and has been accompanied by an increasing trend towards open-source data and tools to propel the field. Despite the…

Materials Science · Physics 2026-05-27 Daniel Persaud , Logan Ward , Jason Hattrick-Simpers

Autonomous language-model agents are increasingly evaluated on long-horizon tool-use tasks, but existing benchmarks rarely capture the complexity and nuance of real scientific work. To address this gap, we introduce Collider-Bench, a…

Machine Learning · Computer Science 2026-05-15 Darius A. Faroughy , Sofia Palacios Schweitzer , Ian Pang , Siddharth Mishra-Sharma , David Shih

Modern language agents must operate over long-horizon, multi-turn interactions, where they retrieve external information, adapt to observations, and answer interdependent queries. Yet, most LLM systems rely on full-context prompting,…

Computation and Language · Computer Science 2025-07-18 Zijian Zhou , Ao Qu , Zhaoxuan Wu , Sunghwan Kim , Alok Prakash , Daniela Rus , Jinhua Zhao , Bryan Kian Hsiang Low , Paul Pu Liang

Machine learning (ML) has been widely used in the literature to automate software engineering tasks. However, ML outcomes may be sensitive to randomization in data sampling mechanisms and learning procedures. To understand whether and how…

Software Engineering · Computer Science 2020-12-16 Cynthia C. S. Liem , Annibale Panichella

The explosive growth of multimodal data has driven the rapid development of multimodal entity linking (MEL) models. However, existing studies have not systematically investigated the impact of visual adversarial attacks on MEL models. We…

Information Retrieval · Computer Science 2025-08-22 Fang Wang , Yongjie Wang , Zonghao Yang , Minghao Hu , Xiaoying Bai

By bringing together code, text, and examples, Jupyter notebooks have become one of the most popular means to produce scientific results in a productive and reproducible way. As many of the notebook authors are experts in their scientific…

Software Engineering · Computer Science 2019-06-13 Jiawei Wang , Li Li , Andreas Zeller