arXiv subjects
Publications and source records attributed to Peter Dawyndt.
NORI performs probabilistic inference to resolve ambiguous mappings between experimental observations and biological entities orders of magnitude faster than state-of-the-art methods. This makes large-scale analysis and extensive hyperparameter optimization possible, and supports a broader range of bioinformatics applications, including protein inference, taxonomic and functional analysis in omics-fields.
The rapid emergence of Large Language Models (LLMs) presents both opportunities and challenges for programming education. While students increasingly use generative AI tools, direct access often hinders the learning process by providing complete solutions rather than pedagogical hints. Concurrently, educators face significant workload and scalability challenges when providing timely, personalized feedback. This study investigates the capabilities of LLMs to safely and effectively assist educators in answering student questions within a CS1 programming course. To achieve this, we established a rigorous, reproducible evaluation process by curating a benchmark dataset of 170 authentic student questions from a learning management system, paired with ground-truth responses authored by subject matter experts. Because traditional text-matching metrics are insufficient for evaluating open-ended educational responses, we developed and validated a custom LLM-as-a-Judge metric optimized for assessing pedagogical accuracy. Our findings demonstrate that models, such as Gemini 3 flash, can surpass the quality baseline of typical educator responses, achieving high alignment with expert pedagogical standards. To mitigate persistent risks like hallucination and ensure alignment with course-specific context, we advocate for a "teacher-in-the-loop" implementation. Finally, we abstract our methodology into a task-agnostic evaluation framework, advocating for a shift in the development of educational LLM tools from ad-hoc, post-deployment testing to a quantifiable, pre-deployment validation process.
In programming education, providing manual feedback is essential but labour-intensive, posing challenges in consistency and timeliness. We introduce ECHO, a machine learning method to automate the reuse of feedback in educational code reviews by analysing patterns in abstract syntax trees. This study investigates two primary questions: whether ECHO can predict feedback annotations to specific lines of student code based on previously added annotations by human reviewers (RQ1), and whether its training and prediction speeds are suitable for using ECHO for real-time feedback during live code reviews by human reviewers (RQ2). Our results, based on annotations from both automated linting tools and human reviewers, show that ECHO can accurately and quickly predict appropriate feedback annotations. Its efficiency in processing and its flexibility in adapting to feedback patterns can significantly reduce the time and effort required for manual feedback provisioning in educational settings.
Source code plagiarism is a significant issue in educational practice, and educators need user-friendly tools to cope with such academic dishonesty. This article introduces the latest version of Dolos, a state-of-the-art ecosystem of tools for detecting and preventing plagiarism in educational source code. In this new version, the primary focus has been on enhancing the user experience. Educators can now run the entire plagiarism detection pipeline from a new web app in their browser, eliminating the need for any installation or configuration. Completely redesigned analytics dashboards provide an instant assessment of whether a collection of source files contains suspected cases of plagiarism and how widespread plagiarism is within the collection. The dashboards support hierarchically structured navigation to facilitate zooming in and out of suspect cases. Clusters are an essential new component of the dashboard design, reflecting the observation that plagiarism can occur among larger groups of students. To meet various user needs, the Dolos software stack for source code plagiarism detections now includes a web interface, a JSON application programming interface (API), a command line interface (CLI), a JavaScript library and a preconfigured Docker container. Clear documentation and a free-to-use instance of the web app can be found at https://dolos.ugent.be. The source code is also available on GitHub.
Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be, has emerged as an invaluable resource for analyzing metaproteomic data. It offers in-depth insights into both taxonomic distributions and functional characteristics of complex ecosystems. This tutorial explains essential concepts like Lowest Common Ancestor (LCA) determination and the handling of peptides with missed cleavages. It also provides a detailed, step-by-step guide on using the Unipept Web application and Unipept Desktop for thorough metaproteomics analyses. By integrating theoretical principles with practical methodologies, this tutorial empowers researchers with the essential knowledge and tools needed to fully utilize metaproteomics in their microbiome studies.
Dodona (dodona.ugent.be) is an intelligent tutoring system for computer programming. It bridges the gap between assessment and learning by providing real-time data and feedback to help students learn better, teachers teach better and educational technology become more effective. We demonstrate how Dodona can be used as a virtual co-teacher to stimulate active learning and support challenge-based education in open and collaborative learning environments. We also highlight some of the opportunities (automated feedback, learning analytics, educational data mining) and challenges (scalable feedback, open internet exams, plagiarism) we faced in practice. Dodona is free for use and has more than 36 thousand registered users across many educational and research institutes, of which 15 thousand new users registered last year. Lowering the barriers for such a broad adoption was achieved by following best practices and extensible approaches for software development, authentication, content management, assessment, security and interoperability, and by adopting a holistic view on computer-assisted learning and teaching that spans all aspects of managing courses that involve programming assignments. The source code of Dodona is available on GitHub under the permissive MIT open-source license.