This article presents the development of a modular software suite for automated analysis of scientific publications in PDF format. The system integrates vectorization, clustering, topic modelling, dimensionality reduction, and fuzzy logic to combine both formal (vector based) and semantic (topic-based) approaches. Interactive 3D visualization supports intuitive exploration of thematic clusters, allowing users to highlight relevant documents and adjust analytical parameters. Validation on a maritime safety case study confirmed Received: 7 October 2025 Revised: 4 November 2025 Accepted: 21 November 2025 Published: 24 November 2025 Citation: Nosov, P.; Melnyk, O.; Malaksiano, M.; Mamenko, P.; Onyshko, D.; Fomin, O.; Píštˇek, V.; Kuˇcera, P. Machine Learning-Based Semantic Analysis of Scientific Publications for Knowledge Extraction in Safety-Critical Domains. Mach. Learn. Knowl. Extr. 2025, 7, 150. https://doi.org/10.3390/ make7040150 Copyright: © 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/ licenses/by/4.0/). the system’s ability to process large publication collections, identify relevant sources, and reveal underlying knowledge structures. Compared to established frameworks such as PRISMAor Scopus/WoS Analytics, the proposed tool operates directly on full-text content, provides deeper thematic classification, and does not require subscription-based databases. The study also addresses the limitations arising from data bias and reproducibility issues in the semantic interpretability of safety-critical decision-making systems. The approach offers practical value for organizations in safety-critical domains—including transportation, energy, cybersecurity, and human–machine interaction—where rapid access to thematically related research is essential.