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Reproducibility of the methods in medical imaging with deep learning
Umeå University, Faculty of Medicine, Department of Radiation Sciences.
Umeå University, Faculty of Medicine, Department of Radiation Sciences.ORCID iD: 0000-0002-0532-232X
Umeå University, Faculty of Medicine, Department of Radiation Sciences.
Umeå University, Faculty of Medicine, Department of Radiation Sciences.ORCID iD: 0000-0002-8971-9788
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2023 (English)In: Medical imaging with deep learning 2023 / [ed] Ipek Oguz; Jack Noble; Xiaoxiao Li; Martin Styner; Christian Baumgartner; Mirabela Rusu; Tobias Heinmann; Despina Kontos; Bennett Landman; Benoit Dawant, ML Research Press , 2023, p. 95-106Conference paper, Published paper (Refereed)
Abstract [en]

Concerns about the reproducibility of deep learning research are more prominent than ever, with no clear solution in sight. The Medical Imaging with Deep Learning (MIDL) conference has made advancements in employing empirical rigor with regards to reproducibility by advocating open access, and recently also recommending authors to make their code public—both aspects being adopted by the majority of the conference submissions. We have evaluated all accepted full paper submissions to MIDL between 2018 and 2022 using established, but adjusted guidelines addressing the reproducibility and quality of the public repositories. The evaluations show that publishing repositories and using public datasets are becoming more popular, which helps traceability, but the quality of the repositories shows room for improvement in every aspect. Merely 22% of all submissions contain a repository that was deemed repeatable using our evaluations. From the commonly encountered issues during the evaluations, we propose a set of guidelines for machine learning-related research for medical imaging applications, adjusted specifically for future submissions to MIDL. We presented our results to future MIDL authors who were eager to continue an open discussion on the topic of code reproducibility.

Place, publisher, year, edition, pages
ML Research Press , 2023. p. 95-106
Series
Proceedings of Machine Learning Research, ISSN 2640-3498 ; 227
Keywords [en]
Reproducibility, Reproducibility of the Methods, Deep Learning, Medical Imaging, Open Science, Transparent Research
National Category
Computer Sciences
Identifiers
URN: urn:nbn:se:umu:diva-215692Scopus ID: 2-s2.0-85189322413OAI: oai:DiVA.org:umu-215692DiVA, id: diva2:1807209
Conference
Medical Imaging with Deep Learning 2023, MIDL, Nashville, July 10-12, 2023
Note

Originally included in thesis in manuscript form. 

Available from: 2023-10-25 Created: 2023-10-25 Last updated: 2024-07-02Bibliographically approved
In thesis
1. Contributions to deep learning for imaging in radiotherapy
Open this publication in new window or tab >>Contributions to deep learning for imaging in radiotherapy
2023 (English)Doctoral thesis, comprehensive summary (Other academic)
Alternative title[sv]
Bidrag till djupinlärning för bildbehandling inom strålbehandling
Abstract [en]

Purpose: The increasing importance of medical imaging in cancer treatment, combined with the growing popularity of deep learning gave relevance to the presented contributions to deep learning solutions with applications in medical imaging.

Relevance: The projects aim to improve the efficiency of MRI for automated tasks related to radiotherapy, building on recent advancements in the field of deep learning.

Approach: Our implementations are built on recently developed deep learning methodologies, while introducing novel approaches in the main aspects of deep learning, with regards to physics-informed augmentations and network architectures, and implicit loss functions. To make future comparisons easier, we often evaluated our methods on public datasets, and made all solutions publicly available.

Results: The results of the collected projects include the development of robust models for MRI bias field correction, artefact removal, contrast transfer and sCT generation. Furthermore, the projects stress the importance of reproducibility in deep learning research and offer guidelines for creating transparent and usable code repositories.

Conclusions: Our results collectively build the position of deep learning in the field of medical imaging. The projects offer solutions that are both novel and aim to be highly applicable, while emphasizing generalization towards a wide variety of data and the transparency of the results.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2023. p. 100
Series
Umeå University medical dissertations, ISSN 0346-6612 ; 2264
Keywords
deep learning, medical imaging, radiotherapy, artefact correction, bias field correction, contrast transfer, synthetic CT, reproducibility
National Category
Radiology, Nuclear Medicine and Medical Imaging
Identifiers
urn:nbn:se:umu:diva-215693 (URN)9789180701945 (ISBN)9789180701952 (ISBN)
Public defence
2024-01-26, E04, Norrlands universitetssjukhus, Umeå, 13:00 (English)
Opponent
Supervisors
Available from: 2023-11-08 Created: 2023-10-25 Last updated: 2024-07-02Bibliographically approved

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Simkó, AttilaGarpebring, AndersJonsson, JoakimNyholm, TufveLöfstedt, Tommy

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