The increasing adoption of Jupyter notebooks in data science and machine learning workflows has created a gap between exploratory code development and production-ready software systems. While notebooks excel at iterative development and visualization, they often lack proper software engineering principles, making their transition to production environments challenging. This paper presents Codelevate, a novel multi-agent system that automatically transforms Jupyter notebooks into well-structured, maintainable Python code repositories. Our system employs three specialized agents - Architect, Developer, and Structure - working in concert through a shared dependency tree to ensure architectural coherence and code quality. Our experimental results validate Codelevate's capability to bridge the prototype-to-production gap through autonomous code transformation, yielding quantifiable improvements in code quality metrics while preserving computational semantics.

Machine Learning (ML) code, particularly within notebooks, often exhibits lower quality compared to traditional software. Bad practices arise at three distinct levels: general Python coding conventions, the organizational structure of the notebook itself, and ML-specific aspects such as reproducibility and correct API usage. However, existing analysis tools typically focus on only one of these levels and struggle to capture ML-specific semantics, limiting their ability to detect issues. This paper introduces Vespucci Linter, a static analysis tool with multi-level capabilities, built on Moose and designed to address this challenge. Leveraging a metamodeling approach that unifies the notebook's structural elements with Python code entities, our linter enables a more contextualized analysis to identify issues across all three levels. We implemented 22 linting rules derived from the literature and applied our tool to a corpus of 5,000 notebooks from the Kaggle platform. The results reveal violations at all levels, validating the relevance of our multi-level approach and demonstrating Vespucci Linter's potential to improve the quality and reliability of ML development in notebook environments.

As machine learning systems are increasingly deployed in high-stakes domains such as criminal justice, finance, and healthcare, the demand for interpretable and trustworthy models has intensified. Despite the proliferation of local explanation techniques, including SHAP, LIME, and counterfactual methods, there exists no standardized, reproducible framework for their comparative evaluation, particularly in fairness-sensitive settings. We introduce ExplainBench, an open-source benchmarking suite for systematic evaluation of local model explanations across ethically consequential datasets. ExplainBench provides unified wrappers for popular explanation algorithms, integrates end-to-end pipelines for model training and explanation generation, and supports evaluation via fidelity, sparsity, and robustness metrics. The framework includes a Streamlit-based graphical interface for interactive exploration and is packaged as a Python module for seamless integration into research workflows. We demonstrate ExplainBench on datasets commonly used in fairness research, such as COMPAS, UCI Adult Income, and LendingClub, and showcase how different explanation methods behave under a shared experimental protocol. By enabling reproducible, comparative analysis of local explanations, ExplainBench advances the methodological foundations of interpretable machine learning and facilitates accountability in real-world AI systems.

A BSTRACT In this work, we present a benchmark that consists of Jupyter notebooks development trajectories and allows measuring how large language models (LLMs) can leverage runtime information for predicting code output and code generation. We demonstrate that the current generation of LLMs performs poorly on these tasks and argue that there exists a significantly understudied domain in the development of code-based models, which involves incorporating the runtime context. 1 I NTRODUCTION Recent developments in code completion and generation have been significant. Over the past several years, the field has progressed from generating relatively simple programs (Chen et al., 2021) to solving real-world issues within software repositories (Jimenez et al., 2023). However, most studies in this area are based on static snapshots of code (Jiang et al., 2024), with only a small body of research exploring the potential of leveraging dynamic code properties, such as runtime information and memory state, for code generation (Chen et al., 2024). A key reason for this limitation is that common programming environments rarely allow code generation during execution, which is when runtime information can be gathered.

Grading student assignments in STEM courses is a laborious and repetitive task for tutors, often requiring a week to assess an entire class. For students, this delay of feedback prevents iterating on incorrect solutions, hampers learning, and increases stress when exercise scores determine admission to the final exam. Recent advances in AI-assisted education, such as automated grading and tutoring systems, aim to address these challenges by providing immediate feedback and reducing grading workload. However, existing solutions often fall short due to privacy concerns, reliance on proprietary closed-source models, lack of support for combining Markdown, LaTeX and Python code, or excluding course tutors from the grading process. To overcome these limitations, we introduce PyEvalAI, an AI-assisted evaluation system, which automatically scores Jupyter notebooks using a combination of unit tests and a locally hosted language model to preserve privacy. Our approach is free, open-source, and ensures tutors maintain full control over the grading process. A case study demonstrates its effectiveness in improving feedback speed and grading efficiency for exercises in a university-level course on numerics.

By connecting disparate sources of scientific literature, literature\-/based discovery (LBD) methods help to uncover new knowledge and generate new research hypotheses that cannot be found from domain-specific documents alone. Our work focuses on bisociative LBD methods that combine bisociative reasoning with LBD techniques. The paper presents LBD through the lens of reproducible science to ensure the reproducibility of LBD experiments, overcome the inconsistent use of benchmark datasets and methods, trigger collaboration, and advance the LBD field toward more robust and impactful scientific discoveries. The main novelty of this study is a collection of Jupyter Notebooks that illustrate the steps of the bisociative LBD process, including data acquisition, text preprocessing, hypothesis formulation, and evaluation. The contributed notebooks implement a selection of traditional LBD approaches, as well as our own ensemble-based, outlier-based, and link prediction-based approaches. The reader can benefit from hands-on experience with LBD through open access to benchmark datasets, code reuse, and a ready-to-run Docker recipe that ensures reproducibility of the selected LBD methods.

Epithelial cells form diverse structures from squamous spherical organoids to densely packed pseudostratified folded tissues. Quantification of cellular properties in these contexts requires high-resolution deep imaging and computational techniques to achieve truthful threedimensional (3D) structural features. Here, we describe a detailed step-by-step protocol for sample preparation, imaging and deep-learning-assisted cell segmentation to achieve accurate quantification of fluorescently labelled individual cells in 3D within live tissues. We share the "lessons learned" through troubleshooting 3D imaging of Drosophila wing discs, including considerations on the choice of microscopy modality and settings (objective, sample mounting) and available segmentation methods. In addition, we include a computational pipeline alongside custom code to assist replication of the protocol. While we focus on the segmentation of cell outlines from membrane labelling, this protocol applies to a wide variety of samples, and we believe it will be valuable for studying other tissues that demand complex analysis in 3D.