Shadi Albarqouni

Shadi Albarqouni

Visiting Scientist @ ETH Zürich | Senior Research Scientist and Team Lead @ TU Munich

Computer Vision Lab, ETH Zürich

Computer Aided Medical Procedures, TU Munich

Biography

Shadi Albarqouni is a Palestinian-German Computer Scientist. He received his B.Sc. and M.Sc. in Electrical Engineering from the IU Gaza, Palestine, in 2005, and 2010, respectively. In 2012, he received a prestigious DAAD research grant to pursue his PhD at the Chair for Computer Aided Medical Procedures (CAMP), Technical University of Munich (TUM), Germany. During his PhD, Albarqouni worked with Prof. Nassir Navab on developing machine learning algorithms to handle noisy labels, coming from crowdsourcing, in medical imaging. Albarqouni received his Ph.D. in Computer Science with summa cum laude in 2017.

Since then, Albarqouni has been working as a Senior Research Scientist & Team Lead at CAMP leading the Medical Image Analysis (MedIA) team with an emphasis on developing deep learning methods for medical applications. In 2019, he received the DAAD P.R.I.M.E. fellowship for one-year international mobility. Starting from Nov. 2019, Albarqouni is on sabbatical leave from TU Munich, and working as a Visiting Scientist at the Department of Information Technology and Electrical Engineering (D-ITET) at ETH Zürich, Switzerland. He is working with Prof. Ender Konukoglu on Modeling Uncertainty in Medical Imaging, in particular, the one associated with inter-/intra-raters variability.

Albarqouni has more than 60 peer-reviewd publications in both Medical Imaging Computing and Computer Vision published in high impacted journals, and top-tier conferences. He serves as a reviewer for many journals, e.g., IEEE TPAMI, MedIA, IEEE TMI, IEEE JBHI, IJCARS and Pattern Recognition, and top-tier conferences, e.g., ECCV, MICCAI, MIDL, BMVC, IPCAI, and ISBI among others. He is also a member at MICCAI, BMVA, IEEE EMBS, IEEE CS, and ATA society. Since 2015, he has been serving as a PC member for a couple of MICCAI workshops, e.g., COMPAY, and DART among others. Since 2019, Albarqouni has been serving as an Area Chair in Advance Machine Learning Theory at MICCAI.

His current research interests include Interpretable ML, Robustness, Uncertainty, and recently Federated Learning. He is also interested in Entrepreneurship and Startups for Innovative Medical Solutions.

Interests

  • Deep Learning with Medical Imaging
  • Representation Learning
  • Uncertainty
  • Federated Learning

Education

  • Ph.D. in Computer Science, 2017

    Technical University of Munich, Germany

  • M.Sc. in Electrical Engineering, 2010

    Islamic University of Gaza, Palestine

  • B.Sc. in Electrical Engineering, 2005

    Islamic University of Gaza, Palestine

Experience

Academic and Professional Experience

 
 
 
 
 

Visiting Scientist

Computer Vision Lab (CVL), ETH Zürich

Nov 2019 – Present Zürich, Switzerland
I am working together with Prof. Ender Konukoglu on Modeling Uncertainty in Medical Imaging, in particular, the one associated with inter-/intra-raters variability
 
 
 
 
 

Senior Research Scientist and Team Lead

Computer Aided Medical Procedures (CAMP), TU Munich

Jan 2017 – Present Munich, Germany

I am leading the Medical Image Analysis team and working toegther with a couple of PhD students on Deep Learning for Medical Applications.

Research: We have focused our research directions to develop fully-automated, high accurate solutions that save export labor and efforts, and mitigate the challenges in medical imaging, i.e. i) the availability of a few annotated data, ii) low inter-/intra-observers agreement, iii) high-class imbalance, iv) inter-/intra-scanners variability and v) domain shift. Our research portfolio can be categorized into Learn to Recognize, Adapt, Learn, Reason and Explain, incorporate prior knowledge, and collaborate with other AI agents

Teaching:

Fundraising:

  • Projects with Industry Partners (~1 MEUR)
  • Research Visits (~20 TEUR)
  • Individual Fellowships (~250 TEUR)

Supervision:

  • Mentoring of 10 on-going PhD candidates
  • Supervision of 27 successful and 3 on-going Master thesis
  • Supervision of 2 successful Bachelor thesis projects
 
 
 
 
 

Consultant and Expert in Telemedicine

German Corporation for International Cooperation GmbH (GIZ)

Nov 2014 – Nov 2014 Ramallah, Palestine
My tasks:

  • Discussing the importance of using telemedicine to provide comprehensive healthcare.
  • Giving examples of my experience in telemedicine in Palestine.
  • Participate in a panel discussion along with local speakers to discuss the different functions of telemedicine.
  • Give recommendations on how to continue with the telemedicine project
 
 
 
 
 

Research Scientist

Computer Aided Medical Procedures (CAMP), TU Munich

Oct 2013 – Dec 2016 Munich, Germany

I worked as a Research Scientist with Prof. Nassir Navab, Dr. Stefanie Demirci, and Dr. Tobias Lasser, on developing machine learning methods for biomedical imaging. My duties were:

Research:

Teaching:

Supervision:

  • Supervision of 6 successful Master thesis
  • Supervision of 2 successful Bachelor thesis projects
 
 
 
 
 

Visiting Research Scientist

German Center for Neurodegenerative Diseases (DZNE)

Apr 2013 – Dec 2016 Bonn, Germany
I worked with Dr. Ashraf Al-Amoudi and Dr. Ing. Weaam Al-Khaldi on developing image processing, i.e. 3D tomographic reconstruction and noise reduction techniques, for 3D cryo-electron tomographic data.
 
 
 
 
 

Lecturer

Electrical and Computer Engineering Department (ECE), IU Gaza

Feb 2011 – Jan 2012 Gaza, Palestine
I worked as Senior Project Advisor for the Computer Engineering Department, and as a Lecturer of the Robotics Course for the Electrical Engineering Department.
 
 
 
 
 

Instructor

University College of Applied Science (UCAS)

Sep 2007 – Jan 2012 Gaza, Palestine
I worked as an Instructor at the Information technology Department teaching a few courses like ICDL Course and Essentials of Information Technology; i.e. Search Engine Optimization (SEO), E-Commerce, E-Health, and Internet Security
 
 
 
 
 

Head of Information Technology Department

Nasser Pediatric Hospital

Nov 2006 – Oct 2012 Gaza, Palestine
I worked as a Networks Engineer for two years before being promoted to the head of the IT department at the hospital. My tasks were:

  • Build and maintain the network backbone infrastructure
  • Provide technical support for different departments at the hospital
  • Manage and integrate both Linux and Windows OS solutions
  • Implement and maintain the Health Information Management System (HIMS)
  • Contribute to the Bethlehem Aliance Project
  • Build and maintain the videoconference system for Educational/Teleconsultation purposes
  • An initiative of Establishing a Telemedicine Center in Palestine
 
 
 
 
 

Teaching Assistant

Electrical and Computer Engineering Department (ECE), IU Gaza

Feb 2006 – Jun 2007 Gaza, Palestine

Fellowships and Awards

Postdoctoral Researchers International Mobility Experience (PRIME) Fellowship

It is one of the prestigious fellowships for one year international mobility followed by half a year at German host institute. It is very comptetitvie as its acceptance rate around 12%.

Best Reviewer

I have been listed as one of the best reviewers among 600 reviewers at MICCAI 2018, Spain.

Highlighted on Leaderboard

Research Grants for Doctoral Candidates and Young Academics and Scientists

It is among the prestigious research grants offered for Palestinians. It is very comptetitvie as its acceptance rate less than 5%.

Latest News

Research Projects

Funded and Active Projects.

Deep Federated Learning in Healthcare

One of our recent and promising projects.

Learn from Crowds

Crowdsourcing, Gamification

Learn from Prior Knowledge

Manifold Learning, Graph Convolutional Networks

Learn to Adapt

Domain Adaptation, Style Transfer

Learn to Learn

Meta-Learning, Few-Shot Learning

Learn to Reason and Explain

Interpretable ML, Disentangled Representation, Fairness

Learn to Recognize

Detection, Classification, Segmentation, Anomaly Detection, Semi-/Weakly-Supervised Learning

Modelling Uncertainty in Deep Learning for Medical Applications

DAAD PRIME Fellowship at ETH Zürich and Imperial College London

Telemedicine in Palestine

Telemedicine in Palestine from Shadi Nabil Albarqouni Collaboration: Funding:

Community Engagement

Professional Services and Invited Talks in the last two years

Medium Blog: Journey through COVID-19 RSNA Papers

Disclaimer: I am neither a radiologist nor a clinician. I am a computer scientist who have been working on medical image computing for a while. I tried to summairze the key findings reported in almost 15 papers published in the Radiology Society in North America (RSNA) in the last two months.

Modelling Labels Uncertainty in Medical Imaging

Recent Publications

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Contact

  • Sternwartstr. 7, Zürich, 8006
  • Enter the ETF building and go to Office 104.2 on Floor B