Dr. Duygu Sarikaya

Profile

My research interests span defining the technologies of future, artificial intelligence powered, healthcare applications. More specifically, I work on surgical vision and perception and medical image computing.

 

• MIRAI Research Group (Medical Imaging and GeneRative AI)
• part of Artificial Intelligence Research theme. 
• collaborator of the Science and Technologies Of Robotics in Medicine (STORM) Lab.
• part of the executive board of Robotics at Leeds. (→ Check our Robotics at Leeds Seminars)
• part of the Association for Surgical Education (ASE) AI Task Force.
• PhD supervisor at UKRI Centre for Doctoral Training in Artificial Intelligence for Medical Diagnosis and Care.

I received my MS and PhD from Computer Science and Engineering, University at Buffalo, State University of New York. I am a Fulbright alumna.

Current Students:

• Lucy Fothergill,  6 DoF Pose Estimation in Surgical Videos (supervising with Dominic Jones and Pietro Valdastri)
• Yushi Guo, Surgical Video Understanding and Anticipation (supervising with Pietro Valdastri)
• Nanzhu Chen, Representation Learning for Human Action Recognition (supervising with Brandon Bennett and He Wang)
• George Baker, Medical Image Understanding through Vision-Language Models (supervising with Nishant Ravikumar, Marc De Kamps, and Kieran Zucker)
• Arpita Saggar, A Virtual Patient to Support Medical Training (supervising with David Hogg, Vania Dimitrova, and Jonathan Darling)
• Xin Ci Wong,  How much ‘Real Data’ do you need Really? (supervising with Nishant Ravikumar, Marc De Kamps, and Kieran Zucker)
• Sevde Kutuk, Surgical Video Captioning (MS, supervising with Tuba Caglikantar)
• Ali Coban, Summarization of Ultrasound Cardiac Videos (MS, supervising with Ceren Guzel Turhan)

* in order of supervision and starting date

MIRAI Research group

Formerly I was:

• Assistant Professor at the Computer Engineering department, Gazi University.
• Post-doctoral Researcher at MediCIS, INSERM, Universite de Rennes working on Connected Optimized Network & Data in Operating Rooms Project with multiple academic and industrial partners, funded by BPI France.
• Project Coordinator and Researcher at ATLAS Program, Roswell Park Comprehensive Cancer Center working in close collaboration with clinicians on Deep Blue Project, funded by the Roswell Park Alliance Foundation.
• Research Assistant at Vision and Perceptual Machines Lab at University at Buffalo, State University of New York on a National Institutes of Health (NIH) project in collaboration with Roswell Park Comprehensive Cancer Center.

 

• I like kpop, indie, alternative, modern rock, modern art, science fiction, fiction (soul swap, time travel, after life, past lives, supernatural, reincarnation, fantastical, magic realism), cities, architecture ...
• I am currently reading The Dark Forest by Liu Cixin, next on my list: The Creative Act: A Way of Being by Rick Rubin
• My current favorite artist is James Jean.
• DC > Marvel

 

Research interests

News:

• We are seeking PhD candidates to join an exciting project on Medical Vision-Language Models. This is a fully-funded offer open to all nationalities (App. due 31^st of October): Medical Vision-Language Models | Project Opportunities | PhD | University of Leeds
• We are looking for a Research Fellow for our SpectraSpace project. Applications are open now (App. due 20^th of October): https://jobs.leeds.ac.uk/Vacancy.aspx?ref=EPSCP1161 
• October 2024: We will present Tugberk’s work PlutoNet: An Efficient Polyp Segmentation Network with Modified Partial Decoder and Decoder Consistency Training at AECAI workshop, MICCAI.
• September 2024: Umit Mert Caglar, PhD candidate from the Graduate School of Informatics, METU visited us as part of an Erasmus traineeship.
• July 2024:  I delivered a lecture at the UCL Medical Image Computing Summer School (MedICSS) 2024.
• March 2024: I will start my Aurora Women’s Leadership Development Programme.
• March 2024: AE-CAI | CARE | OR 2.0 Joint MICCAI Workshop is accepted. See you in Morocco! 
• Feb 2023:  SpectraSpace is awarded by the CLIRPath-AI Network funded by EPSRC.
• Jan 2024:  I delivered a talk at Robotics at Leeds Workshop. 

 

• Dec 2023:  Lucy attended the Hamlyn Winter School on Surgical Imaging and Vision in London. 
• Nov 2023:  I attended CLIRPath-AI Sandpit Event in Bristol. 
• Oct 2023: We organized the Joint 17th AE-CAI, 9th CARE and 5th OR 2.0 workshop at the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2023  in Vancouver.
• Oct 2023:  I delivered a talk at the AI^2 Forum organized by our CDT in Artificial Intelligence for Medical Diagnosis and Care.
• July 2023: I was a panelist at PGR conference by the School of Electronic and Electrical Engineering, UoL.
• June 2023: I delivered a talk as an invited Keynote Speaker at Robotic Awareness and Autonomy in Robotic Surgery workshop at the Hamlyn Symposium on Medical Robotics 2024 in London.
• June 2023: I was an Expert Panelist at the Mixed Reality – Computer Assisted Interventions (MR-CAI) workshop at the Hamlyn Symposium on Medical Robotics 2024 in London.
• June 2023: I delivered a talk as an invited Keynote Speaker at the Workshop on Medical Computer Vision at the Conference on Computer Vision and Pattern Recognition (CVPR) 2023 in Vancouver (online).
• June 2023: I delivered an invited talk at A Pint of Robotics.
• May 2023: I delivered an invited talk at the Terabotics terahertz robotics for surgery and medicine project meeting at the University of Exeter.
• Feb 2023: I joined the School of Computing at University of Leeds.

 

• Sept 2022: We organized the Joint 16th AE-CAI, 9th CARE and 5th OR 2.0 workshop at the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2022  in Singapore.
• June 2022: I delivered a talk as an invited Keynote Speaker at Recent Advances in Autonomous Surgery workshop at the Hamlyn Symposium on Medical Robotics 2023 in London.
• April 2022: I delivered a talk as an invited Plenary Speaker at the Conference on New Technologies for Computer and Robot Assisted Surgery (CRAS) 2022 in Naples.

 

I organized the First and Second International Workshops on Context-Aware Operating Theaters in conjunction with MICCAI, the second International Surgical Data Science Workshop in conjunction with CARS, MIcro-Surgical Anastomose Workflow Recognition on Training Sessions (MISAW) Challenge, part of the Endovis Grand Challenge in conjunction with MICCAI, Computer Vision and Augmented Reality in Surgery Workshop  in conjunction with Hamlyn Symposium on Medical Robotics, and a series of the Joint AE-CAI, CARE and OR 2.0 Workshops in conjunction with MICCAI.

I am Vice President of University at Buffalo, State University of New York Turkey Network – Alumni. I served as a board member of Women in MICCAI, and formerly was a member of the Student Board and the Educational Initiative at MICCAI.

 

Public Datasets:

ATLAS Dione Dataset for Robot-Assisted Surgery Video Understanding
ATLAS Dione dataset provides video data (86 full subject study videos (~910 action clips)) of ten surgeons from Roswell Park Cancer Institute (RPCI) (Buffalo, NY) performing six different surgical tasks on the daVinci Surgical System® (dVSS) with annotations of robotic tools per frame (for a subset of 99 action clips), actions taking place and their timestamps. It also provides information on the surgeon expertise levels based on the Dreyfus model.

MISAW (MIcro-Surgical Anastomose Workflow recognition on training sessions)
The MISAW data set is composed of 27 sequences of micro-surgical anastomosis on artificial blood vessels performed by 3 surgeons and 3 engineering students. The dataset contained video, kinematic, and procedural descriptions synchronized at 30Hz. The procedural descriptions contained phases, steps, and activities performed by the participants.

I am a reviewer for Proceedings of IEEE, IEEE Transactions on Medical Imaging, Medical Image Analysis, Artifi€cial Intelligence in Medicine, The International Journal of Computer Assisted Radiology and Surgery, Computer Methods and Programs in Biomedicine, Computer Assisted Surgery, Medical Image Computing and Computer Assisted Interventions Conference (MICCAI), Computer Assisted Radiology and Surgery Conference (IJCARS), International Conference on Information Processing in Computer-Assisted Interventions (IPCAI). 

Current Opportunities:

1. We are seeking PhD candidates with a strong interest in computer vision, machine learning, and deep learning to join an exciting project on Medical Vision-Language Models.

This is a fully-funded offer open to all nationalities. You will have a chance to become part of the MIRAI Research Group (Medical Imaging and GeneRative AI).
You can find more information about the project, the team, and how to apply here: Medical Vision-Language Models | Project Opportunities | PhD | University of Leeds 

Application Deadline: Thursday, 31 October 2024
Start Date: Saturday, 1 February 2025

2. We are looking for a Research Fellow for our SpectraSpace project. Applications will be on an ongoing basis and are open now, fist round is due 20^th of October!: https://jobs.leeds.ac.uk/Vacancy.aspx?ref=EPSCP1161

Potential projects I am advertising:

• Learning to Automate Surgical Tasks from Demonstration 
• Modelling Surgical Motion and Activities 
• Medical Vision-Language Models for Visual Question Answering 
• Effectively Using Hyperspectral Imaging for Tissue Characterisation 

I am always looking for students with a good knowledge of fundamental topics in computer vision, machine learning and deep learning, along with strong coding skills. Experience with advanced deep learning topics such as generative learning, deep reinforcement learning will be preferred. 

<h4>Research projects</h4> <p>Some research projects I'm currently working on, or have worked on, will be listed below. Our list of all <a href="https://eps.leeds.ac.uk/dir/research-projects">research projects</a> allows you to view and search the full list of projects in the faculty.</p>

Qualifications

• PhD in Computer Science and Engineering, University at Buffalo, State University of New York
• MS in Computer Science and Engineering, University at Buffalo, State University of New York
• BS in Computer Engineering, TOBB University of Economics and Technology

Professional memberships

• AFHEA
• MICCAI Society
• IEEE
• IEEE Robotics and Automation Society

Student education

Data Science (Fall 2023), Intelligent Systems and Robotics (Spring 2024)

Past: Data Science, Deep Learning, Computer Vision, Image Processing, Machine Learning, Artificial Intelligence in Medicine, Expert Systems

Data Science Module 2023-2024 Cohort

Current postgraduate researchers

• Yushi Guo

<h4>Postgraduate research opportunities</h4> <p>We welcome enquiries from motivated and qualified applicants from all around the world who are interested in PhD study. Our <a href="https://phd.leeds.ac.uk">research opportunities</a> allow you to search for projects and scholarships.</p>

Projects

<li><a href="//phd.leeds.ac.uk/project/1858-effectively-using-hyperspectral-imaging-for-tissue-characterisation">Effectively Using Hyperspectral Imaging for Tissue Characterisation</a></li> <li><a href="//phd.leeds.ac.uk/project/1859-learning-to-automate-surgical-tasks-from-demonstration">Learning to Automate Surgical Tasks from Demonstration</a></li> <li><a href="//phd.leeds.ac.uk/project/1857-medical-vision-language-models-for-visual-question-answering">Medical Vision-Language Models for Visual Question Answering</a></li> <li><a href="//phd.leeds.ac.uk/project/1651-modelling-surgical-motion-and-activities">Modelling Surgical Motion and Activities</a></li>