Portrait of Yannis Trakadis is unavailable

Yannis Trakadis

Affiliate Member
Assistant Professor, McGill University, Department of Medicine and Department of Human Genetics
Research Topics
Learning on Graphs
Medical Machine Learning
Molecular Modeling
Natural Language Processing

Biography

Dr. Trakadis is a physician who specializes in genetics (medical geneticist) and practices medicine at the McGill University Health Centre.

He is active in the Canadian College of Medical Genetics, serving as chair of their Metabolics Committee and member of their Canadian Clinical Practice Guideline Development Committee.

Dr. Trakadis is a Fonds de recherche du Québec - Santé (FRQS) Clinical Research Scholar (mid-career), which was awarded in recognition of his research on applying machine learning (ML) to the health domain. His lab has applied ML to the analysis of genomic and downstream functional data from thousands of individuals. More specifically, the lab has developed novel ML methods for the analysis of clinical, genomic, transcriptomic and metabolomic data to enable more personalized medical care.

His academic interests include the clinical integration of novel technologies and digital health models, with the primary focus being the application of AI to advance precision medicine.

Publications

Disease-Specific Prediction of Missense Variant Pathogenicity with DNA Language Models and Graph Neural Networks
Mohamed Ghadie
Sameer Sardaar
Yannis Trakadis
2025-10-13
Bioengineering (published)
doi.org
Disease-Specific Prediction of Missense Variant Pathogenicity with DNA Language Models and Graph Neural Networks
Mohamed Ghadie
Sameer Sardaar
Yannis Trakadis
2025-10-13
Bioengineering (published)
doi.org
Disease-Specific Prediction of Missense Variant Pathogenicity with DNA Language Models and Graph Neural Networks
Mohamed Ghadie
Sameer Sardaar
Yannis Trakadis
Accurate prediction of the impact of genetic variants on human health is of paramount importance to clinical genetics and precision medicine… (see more). Recent machine learning (ML) studies have tried to predict variant pathogenicity with different levels of success. However, most missense variants identified on a clinical basis are still classified as variants of uncertain significance (VUS). Our approach allows for the interpretation of a variant for a specific disease and, thus, for the integration of disease-specific domain knowledge. We utilize a comprehensive knowledge graph, with 11 types of interconnected biomedical entities at diverse biomolecular and clinical levels, to classify missense variants from ClinVar. We use BioBERT to generate embeddings of biomedical features for each node in the graph, as well as DNA language models to embed variant features directly from genomic sequence. Next, we train a two-stage architecture consisting of a graph convolutional neural network to encode biological relationships. A neural network is then used as the classifier to predict disease-specific pathogenicity of variants, essentially predicting edges between variant and disease nodes. We compare performance across different versions of our model, obtaining prediction-balanced accuracies as high as 85.6% (sensitivity: 90.5%; NPV: 89.8%) and discuss how our work can inform future studies in this area.
2025-10-13
Bioengineering (published)
doi.org
Current landscape of clinical genetics knowledge and attitudes among Non-Geneticist Physicians - the McGill genetics education survey (McGES).
Sarah Abdullah-Maklan
Yannis Trakadis
2025-10-01
Journal of Community Genetics (published)
doi.org
Current landscape of clinical genetics knowledge and attitudes among Non-Geneticist Physicians - the McGill genetics education survey (McGES)
Sarah Abdullah-Maklan
Yannis Trakadis
2025-10-01
Journal of Community Genetics (published)
doi.org
Current landscape of clinical genetics knowledge and attitudes among Non-Geneticist Physicians - the McGill genetics education survey (McGES).
Sarah Abdullah-Maklan
Yannis Trakadis
2025-10-01
Journal of Community Genetics (published)
doi.org
Metabolic Control and Frequency of Clinical Monitoring Among Canadian Children With Phenylalanine Hydroxylase Deficiency: A Retrospective Cohort Study
Nataliya Yuskiv
Ammar Saad
Beth K. Potter
Sylvia Stockler‐Ipsiroglu
John J. Mitchell
Steven Hawken
Kylie Tingley
Michael Pugliese
Monica Lamoureux
Andrea J. Chow
Jonathan B. Kronick
Kumanan Wilson
Annette Feigenbaum
Sharan Goobie
Michal Inbar-Feigenberg
Julian Little
Saadet Mercimek‐Andrews
Amy Pender
Chitra Prasad
Andreas Schulze … (see 9 more)
Yannis Trakadis
Gloria Ho
Hilary Vallance
Valerie Austin
Anthony Vandersteen
Andrea C. Yu
Cheryl Rockman‐Greenberg
Aizeddin Mhanni
Pranesh Chakraborty
2025-09-01
JIMD Reports (published)
doi.org
Graph Representation Learning for the Prediction of Medication Usage in the UK Biobank Based on Pharmacogenetic Variants
Bill Qi
Yannis Trakadis
2025-05-31
Bioengineering (published)
doi.org
Co-developing longitudinal patient registries for phenylketonuria and mucopolysaccharidoses in Canada
John Adams
Kim Angel
John J. Mitchell
Pranesh Chakraborty
Beth K. Potter
Michal Inbar-Feigenberg
Sylvia Stockler
Monica Lamoureux
Alison H. Howie
Alex Pace
Nancy J. Butcher
Cheryl Rockman-Greenberg
Robin Hayeems
Anne-Marie Laberge
Thierry Lacaze-Masmonteil
Jeff Round
Martin Offringa
Maryam Oksoui
Andreas Schulze
Kathy N. Speechley … (see 3 more)
Kednapa Thavorn
Yannis Trakadis
Kumanan Wilson
2024-04-01
Molecular Genetics and Metabolism (published)
doi.org
Co-developing longitudinal patient registries for phenylketonuria and mucopolysaccharidoses in Canada
John Adams
Kim Angel
John J. Mitchell
Pranesh Chakraborty
Beth K. Potter
Michal Inbar-Feigenberg
Sylvia Stockler
Monica Lamoureux
Alison H. Howie
Alex Pace
Nancy J. Butcher
Cheryl Rockman-Greenberg
Robin Hayeems
Anne-Marie Laberge
Thierry Lacaze-Masmonteil
Jeff Round
Martin Offringa
Maryam Oksoui
Andreas Schulze
Kathy N. Speechley … (see 3 more)
Kednapa Thavorn
Yannis Trakadis
Kumanan Wilson
2024-04-01
Molecular Genetics and Metabolism (published)
doi.org
Co-developing The Canadian MPS Registry: A longitudinal rare disease patient registry
John J. Mitchell
Michal Inbar-Feigenberg
Kim Angel
Pranesh Chakraborty
Monica Lamoureux
John Adams
Beth K. Potter
Sylvia Stockler-Ipsirolgu
Alison H. Howie
Alex Pace
Nancy J. Butcher
Cheryl Greenberg
Robin Hayeems
Anne-Marie Laberge
Jeff Round
Martin Offringa
Maryam Oskoui
Chelsea Ruth
Andreas Schulze
Kathy N. Speechley … (see 4 more)
Kednapa Thavorn
Yannis Trakadis
Kumanan Wilson
Thierry Lacaze
2024-02-01
Molecular Genetics and Metabolism (published)
doi.org
Co-developing The Canadian MPS Registry: A longitudinal rare disease patient registry
John J. Mitchell
Michal Inbar-Feigenberg
Kim Angel
Pranesh Chakraborty
Monica Lamoureux
John Adams
Beth K. Potter
Sylvia Stockler-Ipsirolgu
Alison H. Howie
Alex Pace
Nancy J. Butcher
Cheryl Greenberg
Robin Hayeems
Anne-Marie Laberge
Jeff Round
Martin Offringa
Maryam Oskoui
Chelsea Ruth
Andreas Schulze
Kathy N. Speechley … (see 4 more)
Kednapa Thavorn
Yannis Trakadis
Kumanan Wilson
Thierry Lacaze
2024-02-01
Molecular Genetics and Metabolism (published)
doi.org