Teaching · Supervision
PhD, Master's and Bachelor's theses supervised or mentored by Shadi Albarqouni at the University of Bonn, the University Hospital Bonn, Helmholtz Munich and TU Munich, with the students' home institutions and co-supervisors. Open thesis topics are listed under Positions.
| Year | Student | Thesis | Home institution | Role · co-supervisors |
|---|---|---|---|---|
| ongoing since May 2023 | Federated Learning in Medical Imaging (working title) | University of Bonn | Primary supervisor | |
| ongoing since Oct 2025 | Towards a Robust and Generalizable Multimodal AI Framework for Medical Multimodal Understanding (working title) | University of Bonn | Primary supervisor with | |
| ongoing since Oct 2025 | Lifelong Federated Learning with Foundation Models (working title) | University of Bonn | Primary supervisor | |
| 2026 | Artificial Intelligence for Hematological Diagnostics: From Single-Cell Analysis to Disease Classification · thesis ↗ submitted 18 Sep 2025 · defended 18 Mar 2026 In the student's wordsI would like to thank Anna Bogdanova, Tingying Peng, and Shadi Albarqouni for their constructive input and support on various projects throughout my Ph.D. Your help has always been greatly appreciated.From the acknowledgements of the thesis. | TU Munich & Helmholtz Munich | Scientific mentor supervisor of record: examiners: | |
| 2025 | Learning Transferable Descriptive Disentangled Representations · thesis ↗ with Carl Zeiss Meditec submitted 22 May 2024 · defended 13 Feb 2025 In the student's wordsMy deepest gratitude goes to my mentors Dr. Abouzar Eslami and Dr. Shadi Albarqouni. […] Dr. Albarqouni has guided me scientifically and mentally. His belief in me and the work we did together is what kept me going and I am forever grateful for that.From the acknowledgements of the thesis. | TU Munich | Primary scientific supervisor supervisor of record: examiners: | |
| 2023 | Deep Learning for Blood Cell Image Analysis · thesis ↗ submitted 22 Feb 2023 · defended 18 Oct 2023 In the student's wordsI'd also like to thank Prof. Dr. Shadi Albarqouni for guiding and inspiring me through all these years, not letting my excitement about research fade and routinely motivating me with discussions and questions. Thank you very much for introducing me to deep learning for medical applications and supporting me through the process of becoming a scientist.From the acknowledgements of the thesis. | TU Munich | Primary scientific supervisor supervisor of record: examiners: | |
| 2023 | Annotation-Efficient Medical Imaging with Deep Learning · thesis ↗ submitted 6 Oct 2022 · defended 16 May 2023 In the student's wordsA full thank goes to Dr. Shadi Albarqoni for all the mentoring and support during the doctorate. He inspired me and was my leader and teacher on this journey.From the acknowledgements of the thesis. | TU Munich | Primary scientific supervisor supervisor of record: examiners: | |
| 2023 | Sai Gokul Hariharan | Novel Analytical and Learning-based Image Processing Techniques for Dose Reduction in Interventional X-ray Imaging · thesis ↗ with Siemens Healthineers submitted 13 Dec 2022 · defended 27 Jun 2023 In the student's wordsThe feedback and advice from my supervisors, advisors as well as colleagues, especially Prof. Dr. Shadi Albarqouni, at Technische Universität München […]From the acknowledgements of the thesis. | TU Munich | Scientific mentor supervisor of record: examiners: |
| 2023 | – Mentored until the end of 2023 | University of Stuttgart & IMPRS-IS | External scientific mentor | |
| 2022 | Hybrid Convolutional and Graph-Convolutional Framework for Segmentation Refinement · thesis ↗ submitted 27 Sep 2021 · defended 28 Feb 2022 In the student's wordsTo Prof. Nassir Navab and Prof. Shadi Albarqouni, for all the mentoring and support during the doctorate.From the acknowledgements of the thesis. | TU Munich | Scientific mentor supervisor of record: examiners: | |
| 2021 | Anomaly Detection in Brain MRI: From Supervised to Unsupervised Deep Learning · thesis ↗ submitted 28 Oct 2020 · defended 13 Apr 2021 In the student's wordsI'd also like to thank my mentor, Dr. Shadi Albarqouni, for his endless support, the countless fruitful, scientific discussions, his precious feedback and trust in my capabilities. Throughout the years, we have maintained a great, prosperous scientific relationship. I highly appreciate the ability to freely choose this research topic and follow my own instincts.From the acknowledgements of the thesis. | TU Munich | Scientific mentor supervisor of record: examiners: | |
| 2021 | Regression Optimization for Camera Localization · thesis ↗ with Siemens submitted 13 Jul 2020 · defended 29 Jan 2021 In the student's wordsA special acknowledgment is reserved for Shadi Albarqouni, who has played a major role in setting me on this path and has helped and guided me since my master studies.From the acknowledgements of the thesis. | TU Munich | Scientific mentor supervisor of record: examiners: | |
| 2021 | Graph Deep Learning for Healthcare Applications · thesis ↗ submitted 24 Nov 2020 · defended 18 May 2021 In the student's wordsThis cannot end without a proper thank you to Dr. Shadi Albarqouni and Prof. Diana Mateus for being patient with me during the early days of my Ph.D. and helping me get started in this wonderful journey I've been on for the past 4 years.From the acknowledgements of the thesis. | TU Munich | Scientific mentor supervisor of record: examiners: | |
| 2020 | Deep Learning Solutions for Cancer Drug Development in Digital Pathology · thesis ↗ with Roche submitted 18 Feb 2020 · defended 22 Oct 2020 In the student's wordsFurther, I wish to thank Dr. Shadi Albarqouni for his valuable supervision and his continuous advice and encouragement. I am grateful for all the fruitful discussions I had with him during the PhD and I appreciate his help and support.From the acknowledgements of the thesis. | TU Munich (external, with Roche) | Advisor / co-supervisor supervisor of record: examiners: |
| Year | Student | Thesis | Home institution | Role · co-supervisors |
|---|---|---|---|---|
| ongoing | – | TU Munich | Primary supervisor | |
| ongoing | – | German International University | Primary scientific supervisor with Nada Sharaf | |
| 2026 | Deep Learning for Lymph Node Metastasis Detection in Pancreatic Ductal Adenocarcinoma · paper 1 · paper 2 · paper 3 | University of Bonn | Primary supervisor with | |
| 2025 | Deep Learning for Image Quality Transfer: Ultra-Low-Field MRI · paper | TU Munich | Primary scientific supervisor supervisor of record: with | |
| 2025 | Development of a Machine Learning Algorithm for Histopathological Classification of Conjunctival Melanocytic Intraepithelial Lesions · paper | TU Munich | Primary scientific supervisor | |
| 2024 | – | University of Cassino (MAIA) | Primary scientific supervisor | |
| 2024 | Deep Learning for Giant Cell Arteritis Detection in Ultrasound Images: Classification of Arterial Wall Thickening · paper 1 · paper 2 · paper 3 · paper 4 | LMU Munich | Primary scientific supervisor supervisor of record: Eyke Hüllermeier with Timo Lohr | |
| 2022 | Michele Guerra | Full-Head CT Anomaly Detection · paper with deepc | TU Munich | Primary scientific supervisor supervisor of record: with Mehmet Yigitsoy |
| 2022 | Deep Learning Models for the Detection of Brain Anomalies in MR Images | TU Munich (with Helmholtz AI) | Primary scientific supervisor supervisor of record: Gordon Cheng with Nicolas Berberich | |
| 2021 | Multi-Modal Liver Segmentation with Federated Learning · paper | TU Munich | Primary scientific supervisor supervisor of record: with | |
| 2021 | Matthäus Heer | The Out-of-Distribution Blindspot of Unsupervised Lesion Detection using Variational Autoencoders · thesis ↗ · paper submitted 25 Feb 2021 In the student's wordsTremendous thank goes to my supervisors, Dr. Shadi Albarqouni, Xiaoran Chen and Janis Postels. Our weekly meetings gave me food for thought and were an essential part of my journey carrying out this thesis. Their unique competencies in a variety of fields made it possible to have fruitful, productive and fun discussions.From the acknowledgements of the thesis. | ETH Zurich & University of Zurich | Advisor / co-supervisor supervisor of record: with Jan UnkelbachXiaoran ChenJanis Postels |
| 2020/21 | Cagri Yildiz | Robust Training of Neural Networks under Noisy Labels | TU Munich | Advisor / co-supervisor supervisor of record: with |
| 2020 | Federated Learning with Non-IID Data · paper | TU Munich | Primary supervisor supervisor of record: with Azade Farshad | |
| 2020 | Tetiana Klymenko | Development of a Spatio-Temporal Segmentation Model for Tumor Volume Calculation in Micro-CT · paper | TU Munich | Primary supervisor supervisor of record: with |
| 2019 | Few-Shot Segmentation in Medical Imaging · paper with Allianz | TU Munich | Primary supervisor supervisor of record: with Arianne Tran | |
| 2019 | Uncertainty in Deep Learning for Medical Applications · paper | TU Munich | Primary supervisor supervisor of record: | |
| c. 2018/19 | StainGAN: Stain Style Transfer for Digital Histological Images · paper | TU Munich | Primary supervisor supervisor of record: with | |
| 2019 | Ghazal Ghazei | Phase Recognition in Surgical Workflow | TU Munich | Primary supervisor supervisor of record: |
| c. 2017/18 | Markus Degel | Left Atrium Segmentation in 3D Ultrasound Using Volumetric Convolutional Neural Networks · paper | TU Munich | Primary supervisor supervisor of record: |
| c. 2018 | Julia Fokuhl | Weakly-Supervised Liver Lesion Localisation and Classification with Spectral CT Data · paper | TU Munich | Primary supervisor supervisor of record: with Peter B. Noël |
| c. 2018 | Ahmed ElGazzar | Uncertainty-Driven Active Learning in Deep Hybrid Models | TU Munich | Primary supervisor supervisor of record: |
| 2017 | Deep Feature Representation with Auxiliary Embedding · paper with Rohde & Schwarz | TU Munich | Primary supervisor supervisor of record: with Athanasios Karamalis | |
| c. 2017 | Weakly-Supervised Anomaly Detection Assisted by Attention Models · paper 1 · paper 2 | TU Munich | Primary supervisor supervisor of record: with Diana Mateus | |
| 2016 | Ulrich Konrad | Depth Recovery from Single-View Interventional X-ray Imaging · paper | TU Munich | Primary supervisor supervisor of record: with Stefanie DemirciLichao Wang |
| 2016 | X-ray PoseNet: Recovering the Poses of Portable X-Ray Devices with Deep Learning · paper with Siemens AG | TU Munich | Primary supervisor supervisor of record: with |
| Year | Student | Thesis | Home institution | Role · co-supervisors |
|---|---|---|---|---|
| 2025 | Developmental Dysplasia of the Hip (DDH) Detection Using Deep Learning | LMU Munich | Primary scientific supervisor supervisor of record: Eyke Hüllermeier with Alireza Javanmardi | |
| 2024 | Affordable Deep Learning for Diagnosing Inherited and Common Retinal Diseases · paper | KIT | Primary scientific supervisor | |
| 2024 | Niklas Kerkfeld | Investigating Transformer-based U-Nets for Clinically Significant Prostate Lesion Segmentation in BP-MRI · paper 1 · paper 2 May 2023 – Jan 2024 | University of Bonn | Primary supervisor |
| 2019 | Mayar Mostafa | Uncertainty in Deep Learning Model of Proximal Femur Fractures · paper 2 Mar 2019 – Sep 2019 | TU Munich | Primary supervisor supervisor of record: |
| 2019 | Maxime Kayser | Addressing Artefact-Related Image Challenges in Automated Polyp Detection · paper 1 · paper 2 | TU Munich | Primary supervisor supervisor of record: with |
| 2017 | Stefan Haninger | Meta-Learning of Regularization Parameters in X-ray Computed Tomography 15 May 2017 – 15 Sep 2017 | TU Munich | Primary supervisor supervisor of record: Tobias Lasser |
| 2016 | Stefan Matl | Gamification in the Medical Context · paper | TU Munich | Primary supervisor supervisor of record: with Stefanie DemirciMaximilian Baust |
| 2015/16 | Michael Wengler | Comparative Study on CNN Initialization | TU Munich | Primary supervisor supervisor of record: |
No theses match these filters.