Teaching · Supervision

Supervised Theses

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.

7PhD theses supervised · 3 ongoing
25Master's theses supervised · 2 ongoing
8Bachelor's theses supervised
7doctoral researchers mentored
65%of Master's & Bachelor's students published their thesis as first author (20/31)
74%of Master's & Bachelor's students co-authored a paper from their thesis (23/31, any author position)
47 shown

PhD theses

YearStudentThesisHome institutionRole · co-supervisors
ongoing since May 2023David D. GaviriaFederated Learning in Medical Imaging (working title)University of BonnPrimary supervisor
ongoing since Oct 2025Jiajun ZengTowards a Robust and Generalizable Multimodal AI Framework for Medical Multimodal Understanding (working title)University of BonnPrimary supervisor
with Thomas Schultz
ongoing since Oct 2025Adea NesturiLifelong Federated Learning with Foundation Models (working title)University of BonnPrimary supervisor
2026Ario SadafiArtificial Intelligence for Hematological Diagnostics: From Single-Cell Analysis to Disease Classification · thesis ↗
submitted 18 Sep 2025 · defended 18 Mar 2026
In the student's words
I 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 MunichScientific mentor
supervisor of record: Nassir Navab
examiners: Nassir NavabPeter SchüfflerAndrea Loddo
2025Hasan SarhanLearning Transferable Descriptive Disentangled Representations · thesis ↗
with Carl Zeiss Meditec
submitted 22 May 2024 · defended 13 Feb 2025
In the student's words
My 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 MunichPrimary scientific supervisor
supervisor of record: Nassir Navab
examiners: Nassir NavabBernhard Kainz
2023Agnieszka TomczakDeep Learning for Blood Cell Image Analysis · thesis ↗
submitted 22 Feb 2023 · defended 18 Oct 2023
In the student's words
I'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 MunichPrimary scientific supervisor
supervisor of record: Nassir Navab
examiners: Nassir NavabNasir RajpootShadi Albarqouni
2023Tariq BdairAnnotation-Efficient Medical Imaging with Deep Learning · thesis ↗
submitted 6 Oct 2022 · defended 16 May 2023
In the student's words
A 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 MunichPrimary scientific supervisor
supervisor of record: Nassir Navab
examiners: Nassir NavabGeorg LangsShadi Albarqouni
2023Sai Gokul HariharanNovel 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 words
The 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 MunichScientific mentor
supervisor of record: Nassir Navab
examiners: Nassir NavabMathias Unberath
2023Duy M. H. Nguyen–
Mentored until the end of 2023
University of Stuttgart & IMPRS-ISExternal scientific mentor
2022Roger D. Soberanis-MukulHybrid Convolutional and Graph-Convolutional Framework for Segmentation Refinement · thesis ↗
submitted 27 Sep 2021 · defended 28 Feb 2022
In the student's words
To Prof. Nassir Navab and Prof. Shadi Albarqouni, for all the mentoring and support during the doctorate.
From the acknowledgements of the thesis.
TU MunichScientific mentor
supervisor of record: Nassir Navab
examiners: Nassir NavabBjörn Menze
2021Christoph BaurAnomaly Detection in Brain MRI: From Supervised to Unsupervised Deep Learning · thesis ↗
submitted 28 Oct 2020 · defended 13 Apr 2021
In the student's words
I'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 MunichScientific mentor
supervisor of record: Nassir Navab
examiners: Nassir NavabBen Glocker
2021Mai BuiRegression Optimization for Camera Localization · thesis ↗
with Siemens
submitted 13 Jul 2020 · defended 29 Jan 2021
In the student's words
A 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 MunichScientific mentor
supervisor of record: Nassir Navab
examiners: Nassir NavabAleš Leonardis
2021Anees KaziGraph Deep Learning for Healthcare Applications · thesis ↗
submitted 24 Nov 2020 · defended 18 May 2021
In the student's words
This 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 MunichScientific mentor
supervisor of record: Nassir Navab
examiners: Nassir NavabDaniel RueckertMichael Bronstein
2020Amal LahianiDeep Learning Solutions for Cancer Drug Development in Digital Pathology · thesis ↗
with Roche
submitted 18 Feb 2020 · defended 22 Oct 2020
In the student's words
Further, 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: Nassir Navab
examiners: Nassir NavabNasir RajpootWilko Weichert

Master's theses

YearStudentThesisHome institutionRole · co-supervisors
ongoingAmine Ben Dhiab–TU MunichPrimary supervisor
ongoingMayar Abdeldayem–German International UniversityPrimary scientific supervisor
with Nada Sharaf
2026Parinishtha BhallaDeep Learning for Lymph Node Metastasis Detection in Pancreatic Ductal Adenocarcinoma · paper 1 · paper 2 · paper 3University of BonnPrimary supervisor
with Thomas Schultz
2025Malek Al AbedDeep Learning for Image Quality Transfer: Ultra-Low-Field MRI · paperTU MunichPrimary scientific supervisor
supervisor of record: Nassir Navab
with Shahrooz Faghihroohi
2025Mert IkinciDevelopment of a Machine Learning Algorithm for Histopathological Classification of Conjunctival Melanocytic Intraepithelial Lesions · paperTU MunichPrimary scientific supervisor
2024Aya ELGebaly–University of Cassino (MAIA)Primary scientific supervisor
2024Sarah SchaabDeep Learning for Giant Cell Arteritis Detection in Ultrasound Images: Classification of Arterial Wall Thickening · paper 1 · paper 2 · paper 3 · paper 4LMU MunichPrimary scientific supervisor
supervisor of record: Eyke Hüllermeier
with Timo Lohr
2022Michele GuerraFull-Head CT Anomaly Detection · paper
with deepc
TU MunichPrimary scientific supervisor
supervisor of record: Daniel Rueckert
with Mehmet YigitsoyAbhijeet Parida
2022Simone LöhleinDeep Learning Models for the Detection of Brain Anomalies in MR ImagesTU Munich (with Helmholtz AI)Primary scientific supervisor
supervisor of record: Gordon Cheng
with Nicolas Berberich
2021Tobias BerneckerMulti-Modal Liver Segmentation with Federated Learning · paperTU MunichPrimary scientific supervisor
supervisor of record: Daniel Rueckert
with Jakob Weiß
2021Matthäus HeerThe Out-of-Distribution Blindspot of Unsupervised Lesion Detection using Variational Autoencoders · thesis ↗ · paper
submitted 25 Feb 2021
In the student's words
Tremendous 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 ZurichAdvisor / co-supervisor
supervisor of record: Ender Konukoglu
with Jan UnkelbachXiaoran ChenJanis Postels
2020/21Cagri YildizRobust Training of Neural Networks under Noisy LabelsTU MunichAdvisor / co-supervisor
supervisor of record: Nassir Navab
with Seong Tae Kim
2020Yousef YeganehFederated Learning with Non-IID Data · paperTU MunichPrimary supervisor
supervisor of record: Nassir Navab
with Azade Farshad
2020Tetiana KlymenkoDevelopment of a Spatio-Temporal Segmentation Model for Tumor Volume Calculation in Micro-CT · paperTU MunichPrimary supervisor
supervisor of record: Nassir Navab
with Seong Tae KimGuillaume Landry
2019Abhijeet ParidaFew-Shot Segmentation in Medical Imaging · paper
with Allianz
TU MunichPrimary supervisor
supervisor of record: Nassir Navab
with Arianne Tran
2019Agnieszka TomczakUncertainty in Deep Learning for Medical Applications · paperTU MunichPrimary supervisor
supervisor of record: Nassir Navab
c. 2018/19M. Tarek ShabanStainGAN: Stain Style Transfer for Digital Histological Images · paperTU MunichPrimary supervisor
supervisor of record: Nassir Navab
with Christoph Baur
2019Ghazal GhazeiPhase Recognition in Surgical WorkflowTU MunichPrimary supervisor
supervisor of record: Nassir Navab
c. 2017/18Markus DegelLeft Atrium Segmentation in 3D Ultrasound Using Volumetric Convolutional Neural Networks · paperTU MunichPrimary supervisor
supervisor of record: Nassir Navab
c. 2018Julia FokuhlWeakly-Supervised Liver Lesion Localisation and Classification with Spectral CT Data · paperTU MunichPrimary supervisor
supervisor of record: Nassir Navab
with Peter B. Noël
c. 2018Ahmed ElGazzarUncertainty-Driven Active Learning in Deep Hybrid ModelsTU MunichPrimary supervisor
supervisor of record: Nassir Navab
2017Christoph BaurDeep Feature Representation with Auxiliary Embedding · paper
with Rohde & Schwarz
TU MunichPrimary supervisor
supervisor of record: Nassir Navab
with Athanasios Karamalis
c. 2017Amelia Jiménez-SánchezWeakly-Supervised Anomaly Detection Assisted by Attention Models · paper 1 · paper 2TU MunichPrimary supervisor
supervisor of record: Nassir Navab
with Diana Mateus
2016Ulrich KonradDepth Recovery from Single-View Interventional X-ray Imaging · paperTU MunichPrimary supervisor
supervisor of record: Nassir Navab
with Stefanie DemirciLichao Wang
2016Mai BuiX-ray PoseNet: Recovering the Poses of Portable X-Ray Devices with Deep Learning · paper
with Siemens AG
TU MunichPrimary supervisor
supervisor of record: Nassir Navab
with Slobodan Ilic

Bachelor's theses

YearStudentThesisHome institutionRole · co-supervisors
2025Mohammad TahaDevelopmental Dysplasia of the Hip (DDH) Detection Using Deep LearningLMU MunichPrimary scientific supervisor
supervisor of record: Eyke Hüllermeier
with Alireza Javanmardi
2024Elyes FarjallahAffordable Deep Learning for Diagnosing Inherited and Common Retinal Diseases · paperKITPrimary scientific supervisor
2024Niklas KerkfeldInvestigating Transformer-based U-Nets for Clinically Significant Prostate Lesion Segmentation in BP-MRI · paper 1 · paper 2
May 2023 – Jan 2024
University of BonnPrimary supervisor
2019Mayar MostafaUncertainty in Deep Learning Model of Proximal Femur Fractures · paper 2
Mar 2019 – Sep 2019
TU MunichPrimary supervisor
supervisor of record: Nassir Navab
2019Maxime KayserAddressing Artefact-Related Image Challenges in Automated Polyp Detection · paper 1 · paper 2TU MunichPrimary supervisor
supervisor of record: Nassir Navab
with Roger D. Soberanis-Mukul
2017Stefan HaningerMeta-Learning of Regularization Parameters in X-ray Computed Tomography
15 May 2017 – 15 Sep 2017
TU MunichPrimary supervisor
supervisor of record: Tobias Lasser
2016Stefan MatlGamification in the Medical Context · paperTU MunichPrimary supervisor
supervisor of record: Nassir Navab
with Stefanie DemirciMaximilian Baust
2015/16Michael WenglerComparative Study on CNN InitializationTU MunichPrimary supervisor
supervisor of record: Nassir Navab