Portrait de David Buckeridge

David Buckeridge

Membre académique associé
Professeur titulaire, McGill University, Département d'épidémiologie, biostatistique et santé au travail
Sujets de recherche
Apprentissage automatique médical

Biographie

David Buckeridge est professeur titulaire à l'École de santé des populations et de santé mondiale de l'Université McGill, responsable de la santé numérique au Centre universitaire de santé McGill et directeur scientifique exécutif pour l'Agence de la santé publique du Canada. Titulaire d'une chaire de recherche du Canada (niveau 1) en informatique de la santé et en science des données, il a établi les projections concernant la demande dans le système de santé du Québec, dirigé la gestion des données et l'analyse pour le groupe de travail sur l'immunité canadienne et aidé l'Organisation mondiale de la santé à surveiller l'immunité mondiale contre le SRAS-CoV-2. Il est titulaire d'un doctorat en médecine (Université Queen's), d'une maîtrise en épidémiologie (Université de Toronto) et d'un doctorat en informatique biomédicale (Université Stanford), et est membre du Collège royal des médecins du Canada.

Étudiants actuels

Maîtrise recherche - McGill
Doctorat - McGill
Maîtrise recherche - McGill
Maîtrise recherche - McGill
Maîtrise recherche - McGill

Publications

A three-state coupled Markov switching model for COVID-19 outbreaks across Quebec based on hospital admissions
Dirk Douwes-Schultz
Alexandra M. Schmidt
Yannan Shen
Characterizing co-purchased food products with soda, fresh fruits, and fresh vegetables using loyalty card purchasing data in Montréal, Canada, 2015–2017
Hiroshi Mamiya
Kody Crowell
Catherine L. Mah
Amélie Quesnel-Vallée
Aman Verma
Extrapolatable Transformer Pre-training for Ultra Long Time-Series Forecasting
Ziyang Song
Qincheng Lu
Hao Xu
Mike He Zhu
MixEHR-Nest: Identifying Subphenotypes within Electronic Health Records through Hierarchical Guided-Topic Modeling
Ruohan Wang
Zilong Wang
Ziyang Song
Automatic subphenotyping from electronic health records (EHRs)provides numerous opportunities to understand diseases with unique subgroups a… (voir plus)nd enhance personalized medicine for patients. However, existing machine learning algorithms either focus on specific diseases for better interpretability or produce coarse-grained phenotype topics without considering nuanced disease patterns. In this study, we propose a guided topic model, MixEHR-Nest, to infer sub-phenotype topics from thousands of disease using multi-modal EHR data. Specifically, MixEHR-Nest detects multiple subtopics from each phenotype topic, whose prior is guided by the expert-curated phenotype concepts such as Phenotype Codes (PheCodes) or Clinical Classification Software (CCS) codes. We evaluated MixEHR-Nest on two EHR datasets: (1) the MIMIC-III dataset consisting of over 38 thousand patients from intensive care unit (ICU) from Beth Israel Deaconess Medical Center (BIDMC) in Boston, USA; (2) the healthcare administrative database PopHR, comprising 1.3 million patients from Montreal, Canada. Experimental results demonstrate that MixEHR-Nest can identify subphenotypes with distinct patterns within each phenotype, which are predictive for disease progression and severity. Consequently, MixEHR-Nest distinguishes between type 1 and type 2 diabetes by inferring subphenotypes using CCS codes, which do not differentiate these two subtype concepts. Additionally, MixEHR-Nest not only improved the prediction accuracy of short-term mortality of ICU patients and initial insulin treatment in diabetic patients but also revealed the contributions of subphenotypes. For longitudinal analysis, MixEHR-Nest identified subphenotypes of distinct age prevalence under the same phenotypes, such as asthma, leukemia, epilepsy, and depression. The MixEHR-Nest software is available at GitHub: https://github.com/li-lab-mcgill/MixEHR-Nest.
Bidirectional Generative Pre-training for Improving Healthcare Time-series Representation Learning
Ziyang Song
Qincheng Lu
He Zhu
Learning time-series representations for discriminative tasks, such as classification and regression, has been a long-standing challenge in … (voir plus)the healthcare domain. Current pre-training methods are limited in either unidirectional next-token prediction or randomly masked token prediction. We propose a novel architecture called Bidirectional Timely Generative Pre-trained Transformer (BiTimelyGPT), which pre-trains on biosignals and longitudinal clinical records by both next-token and previous-token prediction in alternating transformer layers. This pre-training task preserves original distribution and data shapes of the time-series. Additionally, the full-rank forward and backward attention matrices exhibit more expressive representation capabilities. Using biosignals and longitudinal clinical records, BiTimelyGPT demonstrates superior performance in predicting neurological functionality, disease diagnosis, and physiological signs. By visualizing the attention heatmap, we observe that the pre-trained BiTimelyGPT can identify discriminative segments from biosignal time-series sequences, even more so after fine-tuning on the task.
Bidirectional Generative Pre-training for Improving Healthcare Time-series Representation Learning
Ziyang Song
Qincheng Lu
Mike He Zhu
Evaluating the effectiveness of the Smart About Meds (SAM) mobile application among patients discharged from hospital: protocol of a randomised controlled trial
Robyn Tamblyn
Bettina Habib
Daniala L Weir
Elizaveta Frolova
Rolan Alattar
Jessica Rogozinsky
Caroline Beauchamp
Rosalba Pupo
Susan J Bartlett
Emily McDonald
Comparative evaluation of methodologies for estimating the effectiveness of non-pharmaceutical interventions in the context of COVID-19: a simulation study
Iris Ganser
Juliette Paireau
Simon Cauchemez
Rodolphe Thiébaut
M. Prague
TrajGPT: Healthcare Time-Series Representation Learning for Trajectory Prediction
Ziyang Song
Qincheng Lu
Mike He Zhu
In many domains, such as healthcare, time-series data is irregularly sampled with varying intervals between observations. This creates chall… (voir plus)enges for classical time-series models that require equally spaced data. To address this, we propose a novel time-series Transformer called **Trajectory Generative Pre-trained Transformer (TrajGPT)**. It introduces a data-dependent decay mechanism that adaptively forgets irrelevant information based on clinical context. By interpreting TrajGPT as ordinary differential equations (ODEs), our approach captures continuous dynamics from sparse and irregular time-series data. Experimental results show that TrajGPT, with its time-specific inference approach, accurately predicts trajectories without requiring task-specific fine-tuning.
TrajGPT: Healthcare Time-Series Representation Learning for Trajectory Prediction
Ziyang Song
Qincheng Lu
Mike He Zhu
In many domains, such as healthcare, time-series data is irregularly sampled with varying intervals between observations. This creates chall… (voir plus)enges for classical time-series models that require equally spaced data. To address this, we propose a novel time-series Transformer called **Trajectory Generative Pre-trained Transformer (TrajGPT)**. It introduces a data-dependent decay mechanism that adaptively forgets irrelevant information based on clinical context. By interpreting TrajGPT as ordinary differential equations (ODEs), our approach captures continuous dynamics from sparse and irregular time-series data. Experimental results show that TrajGPT, with its time-specific inference approach, accurately predicts trajectories without requiring task-specific fine-tuning.
TrajGPT: Irregular Time-Series Representation Learning for Health Trajectory Analysis
Ziyang Song
Qincheng Lu
Mike He Zhu
Correction: Economic evaluation of the effect of needle and syringe programs on skin, soft tissue, and vascular infections in people who inject drugs: a microsimulation modelling approach
Jihoon Lim
W Alton Russell
Mariam El-Sheikh
Dimitra Panagiotoglou