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20242026
most citedFrom Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics

1 citations · 1 across the 6 of their papers we have counts for

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7 papers

cs.SE2026

Why Are AI Agent Involved Pull Requests (Fix-Related) Remain Unmerged? An Empirical Study

Khairul Alam, Saikat Mondal, Banani Roy

Autonomous coding agents (e.g., OpenAI Codex, Devin, GitHub Copilot) are increasingly used to generate fix-related pull requests (PRs) in real world software repositories. However,…

cs.SE2026

What Drives Issue Resolution Speed? An Empirical Study of Scientific Workflow Systems on GitHub

Khairul Alam, Banani Roy

Scientific Workflow Systems (SWSs) play a vital role in enabling reproducible, scalable, and automated scientific analysis. Like other open-source software, these systems depend on…

cs.SE2025

Are Classical Clone Detectors Good Enough For the AI Era?

Ajmain Inqiad Alam, Palash Roy, Farouq Al-omari +3

The increasing adoption of AI-generated code has reshaped modern software development, introducing syntactic and semantic variations in cloned code. Unlike traditional human-writte…

cs.SE20251 cited

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics

Khairul Alam, Banani Roy

Scientific Workflow Systems such as Galaxy and Nextflow are essential for scalable, reproducible, and automated bioinformatics analyses. However, developing and understanding scien…

cs.SE2025

From Questions to Insights: Exploring XAI Challenges Reported on Stack Overflow Questions

Saumendu Roy, Saikat Mondal, Banani Roy +1

The lack of interpretability is a major barrier that limits the practical usage of AI models. Several eXplainable AI (XAI) techniques (e.g., SHAP, LIME) have been employed to inter…

cs.SE2024

Developer Challenges on Large Language Models: A Study of Stack Overflow and OpenAI Developer Forum Posts

Khairul Alam, Kartik Mittal, Banani Roy +1

Large Language Models (LLMs) have gained widespread popularity due to their exceptional capabilities across various domains, including chatbots, healthcare, education, content gene…