Best Practices for Machine Learning Experimentation in Scientific Applications

• URL: http://arxiv.org/abs/2511.21354v2
• Date: Thu, 27 Nov 2025 06:48:18 GMT
• Title: Best Practices for Machine Learning Experimentation in Scientific Applications
• Authors: Umberto Michelucci, Francesca Venturini,
• Abstract summary: This paper presents a practical and structured guide for conducting machine learning experiments in scientific applications.<n>We outline a step-by-step workflow, from dataset preparation to model selection and evaluation.<n>We propose metrics that account for overfitting and instability across folds, including the Logarithmic Overfitting Ratio (LOR) and the Composite Overfitting Score (COS)
• Score: 3.093890460224435
• License: http://creativecommons.org/licenses/by-nc-nd/4.0/
• Abstract: Machine learning (ML) is increasingly adopted in scientific research, yet the quality and reliability of results often depend on how experiments are designed and documented. Poor baselines, inconsistent preprocessing, or insufficient validation can lead to misleading conclusions about model performance. This paper presents a practical and structured guide for conducting ML experiments in scientific applications, focussing on reproducibility, fair comparison, and transparent reporting. We outline a step-by-step workflow, from dataset preparation to model selection and evaluation, and propose metrics that account for overfitting and instability across validation folds, including the Logarithmic Overfitting Ratio (LOR) and the Composite Overfitting Score (COS). Through recommended practices and example reporting formats, this work aims to support researchers in establishing robust baselines and drawing valid evidence-based insights from ML models applied to scientific problems.

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