Portfolio
Amir Safavi-Naini
MD-MBA-MME physician-researcher, now based in Bern, building Agentic AI systems that curate, structure, and store biomedical data — and bake them for clinicians in their own taste. With 4+ years of hands-on experience across clinical datasets, medical imaging, and large language models, I focus on bridging the gap between computational power and bedside impact through interdisciplinary collaboration.
Languages: English (Proficient) · Persian (Native) · German (Beginner)
Education
Medical Doctorate (M.D.)
Shahid Beheshti University of Medical Sciences, Faculty of Medicine
GPA: 16.98/20
Thesis: Trend of Oropharyngeal and Oral Cavity Cancers in Iran from 2003 to 2017: Time Series Analysis of National Cancer Registry Database
Master of Science in Medical Education (M.Sc.)
Shahid Beheshti University of Medical Sciences, Virtual School of Medical Education and Management
GPA: 18.78/20
Thesis: Design, Implementation and Evaluation of "Digestive Diseases CyberPatient Bootcamp" using Virtual Patients
Thesis: EXAMINER: Developing Standard Medical Exams from Validated Source, Utilizing Large Language Models and Retrieval Augmented Generation
Master of Business Administration in Healthcare (non-degree)
Shahid Beheshti University of Medical Sciences, Virtual School of Medical Education and Management
GPA: 20/20
Master of Business Administration (non-degree)
University of Tehran, College of Engineering
GPA: 17/20
Academic Experience
Research Fellow (Remote)
Division of Data-Driven and Digital Medicine (D3M), Icahn School of Medicine at Mount Sinai
Benchmarking LLMs and VLMs in gastroenterology; Developing tools for LLM-based extraction and retrieval
USA
Research Fellow
Research Institute for Gastroenterology and Liver Diseases (RIGLD), SBMU
Founded PanCanAID — a not-for-profit data bank of abdominal CT scan and models for pancreas cancer early detection
Iran
Research Associate
Research Institute for Gastroenterology and Liver Diseases (RIGLD), SBMU
Lead coordinator of COVID-19 research in a multi-centric project involving 6 medical centers leading to dataset of 10,000 inpatients with 1,500 follow-ups
Iran
Research Associate
National Research Institute of Tuberculosis and Lung Disease, SBMU
Time series analysis of National Cancer Registry database for nasopharyngeal and oropharyngeal cancers
Iran
Instructor
Various Institutions
Participated as an invited instructor in 8 workshops: scientific research, scientific problems worth answering, machine learning as a medical designer, cross-discipline team
Iran
Peer-Mentorship
SBMU & RIGLD
Mentored 5 medical students as med-school peer, 23 (bio)medical students as research peer, and 6 startups as startup mentor
Iran
Publications(51)
Published
N Naderi et al. · Explainable, trustworthy, and responsible AI and multi-agent systems · 2026
DOI ↗SAA Safavi-Naini et al. · npj Digital Medicine · 2025
DOI ↗M Ghaffarzadeh-Esfahani et al. · Scientific Reports · 2025
DOI ↗MA Khalafi, SAA Safavi-Naini et al. · Scientific Reports · 2025
DOI ↗A Salahi-Niri et al. · Health Science Reports · 2025
DOI ↗Conceptualization, Supervision, Validation, Visualization, Methodology, Writing -- original draft
A Salahi-Niri et al. · Health Science Reports · 2025
DOI ↗T Savage et al. · Journal of the American Medical Informatics Association · 2025
DOI ↗Methodology, Editing the Original Draft
MT Norooz and SAA Safavi-Naini et al. · Health Science Reports · 2025
DOI ↗Conceptualization, Methodology, Formal analysis, Investigation, Software
A Ghaffari Jolfayi et al. · Navigating cardiology's future · 2025
DOI ↗SA Ahmad Safavi-Naini et al. · Gastrointestinal Endoscopy · 2025
DOI ↗E Arabpour, SA Ahmad Safavi-Naini et al. · Gastrointestinal Endoscopy · 2025
DOI ↗MA Khalafi, SAA Safavi-Naini et al. · Gastroenterology · 2025
DOI ↗SAA Safavi-Naini et al. · Gastroenterology · 2025
DOI ↗MA Pourhoseingholi et al. · Current Medicinal Chemistry · 2024
DOI ↗Methodology, Data Curation, Writing the Original Draft
MM Sajjadi et al. · Journal of Orthopedic and Spine Trauma · 2024
DOI ↗Data Analysis
M Raoufi et al. · Scientific Reports · 2024
DOI ↗Conceptualization, Methodology, Analysis, Writing the Original Draft
L Karout et al. · European Radiology · 2024
DOI ↗Data Collection
MA Pourhoseingholi et al. · Journal of Clinical Virology Plus · 2024
DOI ↗Data Curation, Writing the Original Draft
SAA Safavi-Naini et al. · Gastroenterology · 2024
DOI ↗A Allahgholipour, SAA Safavi-Naini et al. · Frontiers in Public Health · 2024
DOI ↗Data curation, Formal analysis, Writing -- original draft
S Khalili, SAA Safavi-Naini et al. · Scientific Reports · 2024
DOI ↗Conceptualization, Methodology, Programming and Analysis, Writing Original Draft, Visualization, Investigation
SAA Safavi-Naini et al. · Scientific Reports · 2024
DOI ↗Methodology, Writing Original Draft, Visualization, Investigation
SAA Safavi-Naini et al. · Medical Research Archives · 2024
DOI ↗SSM Tehrani et al. · BMC Medical Informatics and Decision Making · 2023
DOI ↗Data Preprocessing; Editing Manuscript Draft
MA Pourhoseingholi et al. · European Cytokine Network · 2023
DOI ↗Conceptualization, Data Curation, Supervision
SAA Safavi-Naini et al. · MedRxiv · 2023
DOI ↗Conceptualization, Project administration, Visualization, Investigation
Y Farsi and SAA Safavi-Naini et al. · 9th Annual Sessions of the American College of Surgeons (ACS) · 2023
DOI ↗Conceptualization, Project administration, Visualization, Investigation
N Azizi et al. · Cancers · 2023
DOI ↗Visualization, Methodology, Writing
F Siavoshi, SAA Safavi-Naini et al. · Scientific Reports · 2023
DOI ↗Conceptualization, Methodology, Programming, Data Curation, Formal analysis, Visualization, Project administration
H Hatami et al. · Biomedicines · 2023
DOI ↗Meta-Analysis, Visualization, Writing
S Barough, SAA Safavi-Naini et al. · Scientific Reports · 2023
DOI ↗Conceptualization; Administration; Data Curation; Writing; Algorithm Development
A Naini et al. · Iranian Journal of Otolaryngology · 2023
DOI ↗Data Analysis; Data Visualization; Writing; Planning; Methodology
M Azizmohammad Looha, SAA Safavi-Naini et al. · Student Research in Translational Medicine · 2023
DOI ↗AA Safavi-Naini, A Aghdaee · Student Research in Translational Medicine · 2023
H Majlesi et al. · Immunopathologia Persa · 2022
DOI ↗Administration; Conceptualization; Writing; Visualization
A Bashardoust and SAA Safavi-Naini · Canon Journal of Medicine · 2022
DOI ↗Conceptualization; Writing
T Sabaghian et al. · Iranian Journal of Kidney Disease · 2022
DOI ↗Data Analysis; Writing; Methodology
SAA Safavi-Naini and MA Pourhoseingholi · Gastroenterology and Hepatology From Bed to Bench · 2022
DOI ↗Data Analysis; Writing
H Hatamabadi et al. · BioMed Research International · 2022
DOI ↗Project Administration, Data Curation, Writing, Validation, Investigation
SAA Safavi-Naini et al. · BMC Research Notes · 2022
DOI ↗Conceptualization; Data Extraction; Methodology; Writing
Z Tajabadi et al. · Immunopathologia Persa · 2022
DOI ↗Investigation; Writing
M Farrokhi et al. · Kindle · 2021
Chapter on Otolaryngology
T Faghihi et al. · Iranian Journal of Radiology · 2021
DOI ↗Data Collection; Formal Analysis, Writing; Visualization
M Raoufi et al. · International Journal of Cancer Management · 2021
DOI ↗Writing; Data Gathering; Formal Analysis; Conceptualization
S Nekoghadam et al. · The International Journal of Lower Extremity Wounds · 2021
DOI ↗Investigation; Writing
M Raoufi et al. · Archives of Academic Emergency Medicine · 2020
DOI ↗Writing; Planning; Data Gathering, Analysis
Preprint / Under Review
N Naderi, SAA Safavi-Naini et al. · · 2025
DOI ↗Z Atf, SAA Safavi-Naini et al. · · 2025
DOI ↗S Danaei et al. · · 2025
DOI ↗JS Samaan et al. · MedRxiv · 2024
DOI ↗SAA Safavi-Naini et al. · arXiv · 2024
DOI ↗Conferences
3rd Emirates International Colorectal Congress
Speaker
UAE
2nd National Conference on AI in Medical Imaging — Cardiac Imaging
Workshop Co-Director: Hands-on Generative AI for Cardiologists
Iran
2nd MedAI Summit
Speaker
Iran
Digestive Disease Week (DDW)
E-Posters Presentation
USA
Digestive Disease Week (DDW)
Distinguished Poster Award: GI-Copilot — RAG-based LLM for answering gastroenterology questions
Washington D.C., USA
Opportunities and Challenges of AI in Digital Health
Workshops Chair; Lecturer: Tutorial on AI Tools for Digital Health; Tutorial on LLMs for Digital Health
Tehran, Iran
3rd Iranian Endoscopy Conference
Workshop Director: Hands-on Data Pipelines for ML — ML for Medical Doctors
Iran
9th International Congress of Hepatitis and GI Endoscopy
Lecturer: MLasMD Workshop
Tehran, Iran
International Congress of AI in Medical Sciences
Prognostic Models in Image Processing
Kish, Iran
37th Congress of Iranian Society of Radiology
Tehran, Iran
15th Coloproctology Congress
3D Reconstruction of Perianal Fistula in MRI
Tehran, Iran
World Congress of Gastroenterology (WCOG)
Dubai, UAE
Iranian Congress of Gastroenterology and Hepatology (ICGH)
Executive Member of Scientific Committee
Tehran, Iran
USERN Congress
Best Junior Presentation: Excess Mortality and Reported Fatality in Iran
Synchronized (Iran, Turkey, Europe)
Leiden International Medical Students Conference (LIMSC)
7 Tesla MRI Workshop; Leiden Technology Park
Leiden, Netherlands
Antwerp International Medical Students Congress (AMSC)
DaVinci Robot Workshop
Antwerpen, Belgium
Awards & Honors
Distinguished Poster at Digestive Disease Week (DDW)
GI-Copilot: RAG-based LLM for answering gastroenterology questions
Best Junior Presenter at USERN
Excess Mortality and Reported Fatality in Iran
Bronze Medal in National Olympiad for Medical Science Students
Letter of Appreciation for Enhancing Medical Education During COVID-19
Utilizing virtual patients for medical education during the pandemic
Letter of Appreciation for Pediatrics Curriculum Enhancement
Creating a logbook and enhancing the pediatrics externship curriculum
Top 1% in University Entrance Exam
National university entrance examination (Konkur)
Teaching & Mentoring
Tutorial on AI Tools for Digital Health
Opportunities and Challenges of AI in Digital Health, Iran
Introduction to medical imaging tools in digital health
3-hour workshop
Tutorial on LLMs for Digital Health
Opportunities and Challenges of AI in Digital Health, Iran
Introduction to LLMs and RAG-based chatbots for QA and knowledge extraction
3-hour workshop
MLasMD Workshop
9th International Congress of Hepatitis and GI Endoscopy
Comprehensive, interactive workshop to prepare medical specialists to read AI papers, understand their challenges, and work in multidisciplinary teams
8-hour workshop
How to Prepare a Graphical Abstract
21-day research course, Student Research Committee of SBMU
2-hour session
Introduction to ML: Human Logic–Machine Logic
21-day research course, Student Research Committee of SBMU
4-hour workshop
Scientific Network and Role of Social Media
21-day research course, Student Research Committee of SBMU
ResearchGate, LinkedIn
2-hour session
Introduction to ML: Human Logic–Machine Logic
Invited by Student Research Committee of SBMU
2-hour session
Shape Your Vision
Invited by Student Research Committee of SBMU
From vision to long-term goals, from short-term goals to daily tasks
3-hour session
Introduction to ML: Human Logic–Machine Logic
21-day research course, Student Research Committee of SBMU
2-hour session
Role of Debriefing in Case-Based Learning
During MSEd (Dr. Soleiman Ahmadi)
Using Adobe Captivate to create cases and format post-session debriefing
2 hours of 8-hour workshop
Case-Based Learning in Medicine: CyberPatient
During MSEd (Dr. Soleiman Ahmadi; Dr. Karim Qayumi)
Using real cases to create standard virtual patients
8 hours of 6-day workshop
TA of Surgery Ward
Medical Internship, Emam Hossein Hospital, SBMU
Presentations for externs: Appendicitis, Fistula Management
1 month
Peer Mentor of Young Medical Students
Faculty of Medicine, SBMU
Helped first-year students form their vision, long-term goals, and strategies
4 years (4 mentees)
Research Mentor
Med school → Postdoc at RIGLD → D3M
Helping biomedical students start their research journey
16+ mentees
Clinical Experience
General Practitioner
Working at a private clinic and taking on part-time ED night shifts.
Medical Internship
Various Hospitals, SBMU
Twenty-month extensive clinical internship:
Industry & Startup
Founder and CEO
Phili.ai
Startup providing a unified interface for healthcare — a local device with LLM and EHR integration to augment patients, clinicians, and providers.
Digital Transformation Consultant
Saman Insurance
Developing an automated pipeline based on LLMs for organizing data (freelancing).
Project Consultant
Sakoo (Intelligent Platform)
Trained, deployed, and maintained AI for healthcare professionals involving the integration of LLM and MLOps (6 months, freelancing).
Project Consultant
Atie Hospital
Integrated a voice assistant into hospital systems (3 months).
Co-Founder
EZzy
Startup offering a platform for AI-driven annotation and labeling (4 months).
Co-founder & Strategy Officer
AI-MEIDIC
AI-based diagnosis of chest X-ray, providing risk stratification for COVID-19.
R&D Associate
MEDIAI
Worked on an AI-based alarming system for 15 emergency conditions of brain CT scans (9 months, paid part-time).
Journal Reviews(39+ reviews)
Skills & Tools
Software & Coding
Medical Imaging Tools
Research Skills
Cognitive & Meta-Cognitive
Laboratory Techniques
Other
References
Ali Soroush, MD, MS
Assistant Professor of Gastroenterology
Division of Data-Driven Decision Making (D3M), Icahn School of Medicine at Mount Sinai
Mentor and supervisor at D3M
Girish N. Nadkarni, MD, MPH
Chair, Windreich Department of AI and Human Health
Director, Hasso Plattner Institute for Digital Health, Icahn School of Medicine at Mount Sinai
Chair of D3M
Hamid R. Rabiee, Ph.D.
Distinguished Professor of Computer Science
Sharif University of Technology
Supervisor
Mohamad Amin Pourhoseingholi, Ph.D.
Associate Professor of Biostatistics
RIGLD & NIHR Nottingham Biomedical Research Centre
Mentor and supervisor at RIGLD
Hamid Asadzadeh Aghdaei, MD-Ph.D.
Associate Professor of Gastroenterology
Research Institute for Gastroenterology and Liver Diseases (RIGLD)
Supervisor at RIGLD
Alireza Vafaei Sadr, Ph.D.
Senior Data Scientist
Pennsylvania State University
Supervisor at MEDIAI
Mohammad Reza Zali, MD, FACG
Distinguished Professor of Gastroenterology
Research Institute for Gastroenterology and Liver Diseases (RIGLD)
President of RIGLD
Isaac Shiri, Ph.D.
Head of Artificial Intelligence in Cardiovascular Medicine
Bern University Hospital
Supervisor of research-focused PhD at Bern
Contact information available upon request.