David Buckeridge

Daniala L Weir

Elizaveta Frolova

Rolan Alattar

Jessica Rogozinsky

Caroline Beauchamp

Rosalba Pupo

Susan J Bartlett

Emily McDonald

2024-11-24

BMJ Open (published)

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… (see more)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.

2024-10-17

ArXiv (preprint)

arxiv.org

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… (see more)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.

2024-10-10

NeurIPS.cc/2024/Workshop/TSALM (published)

openreview.net

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… (see more)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.

2024-10-10

NeurIPS.cc/2024/Workshop/TSALM (published)

openreview.net

TrajGPT: Irregular Time-Series Representation Learning for Health Trajectory Analysis

Ziyang Song

Qingcheng Lu

He Zhu

2024-10-03

ArXiv (preprint)

arxiv.org

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

2024-09-09

Harm Reduction Journal (published)

Development of a Framework for Establishing 'Gold Standard' Outbreak Data from Submitted SARS-CoV-2 Genome Samples

Yannan Shen

Russell Steele

Submitted genomic data for respiratory viruses reflect the emergence and spread of new variants. Although delays in submission limit the uti… (see more)lity of these data for prospective surveillance, they may be useful for evaluating other surveillance sources. However, few studies have investigated the use of these data for evaluating aberration detection in surveillance systems. Our study used a Bayesian online change point detection algorithm (BOCP) to detect increases in the number of submitted genome samples as a means of establishing 'gold standard' dates of outbreak onset in multiple countries. We compared models using different data transformations and parameter values. BOCP detected change points that were not sensitive to different parameter settings. We also found data transformations were essential prior to change point detection. Our study presents a framework for using global genomic submission data to develop 'gold standard' dates about the onset of outbreaks due to new viral variants.

2024-08-22

Medical Informatics Europe (published)

Canada's Provincial Covid-19 Pandemic Modelling Efforts: A Review of Mathematical Models and Their Impacts on the Responses

Yiqing Xia

Jorge Luis Flores Anato

Caroline Colijin

Naveed Janjua

Michael Otterstatter

Mike Irvine

Tyler Williamson

Marie B. Varughese

Michael Li

Nathaniel Osgood

David J. D. Earn

Beate Sander

Lauren E. Cipriano

Kumar Murty

Fanyu Xiu

Arnaud Godin

Amy Hurford

Sharmistha Mishra

Mathieu Maheu-Giroux

2024-07-25

Canadian Journal of Public Health (published)

Canada’s approach to SARS-CoV-2 sero-surveillance: Lessons learned for routine surveillance and future pandemics

Sheila F. O’Brien

Michael Asamoah-Boaheng

Brian Grunau

Mel Krajden

David M. Goldfarb

Maureen Anderson

Marc Germain

Patrick Brown

Derek R. Stein

Kami Kandola

Graham Tipples

Philip Awadalla

Amanda Lang

Lesley Behl

Tiffany Fitzpatrick

Steven J. Drews

2024-07-09

Canadian journal of public health (published)

A Bayesian Non-Stationary Heteroskedastic Time Series Model for Multivariate Critical Care Data

Zayd Omar

David A. Stephens

Alexandra M. Schmidt

2024-07-02

Statistics in Medicine (published)

arxiv.org

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

2024-06-28

Harm Reduction Journal (published)

Temporal trends in disparities in COVID-19 seropositivity among Canadian blood donors

Yuan Yu

Matthew J Knight

Diana Gibson

Sheila F O’Brien

W Alton Russell

Abstract Background In Canada’s largest COVID-19 serological study, SARS-CoV-2 antibodies in blood donors have been monitored since 2020. … (see more)No study has analysed changes in the association between anti-N seropositivity (a marker of recent infection) and geographic and sociodemographic characteristics over the pandemic. Methods Using Bayesian multi-level models with spatial effects at the census division level, we analysed changes in correlates of SARS-CoV-2 anti-N seropositivity across three periods in which different variants predominated (pre-Delta, Delta and Omicron). We analysed disparities by geographic area, individual traits (age, sex, race) and neighbourhood factors (urbanicity, material deprivation and social deprivation). Data were from 420 319 blood donations across four regions (Ontario, British Columbia [BC], the Prairies and the Atlantic region) from December 2020 to November 2022. Results Seropositivity was higher for racialized minorities, males and individuals in more materially deprived neighbourhoods in the pre-Delta and Delta waves. These subgroup differences dissipated in the Omicron wave as large swaths of the population became infected. Across all waves, seropositivity was higher in younger individuals and those with lower neighbourhood social deprivation. Rural residents had high seropositivity in the Prairies, but not other regions. Compared to generalized linear models, multi-level models with spatial effects had better fit and lower error when predicting SARS-CoV-2 anti-N seropositivity by geographic region. Conclusions Correlates of recent COVID-19 infection have evolved over the pandemic. Many disparities lessened during the Omicron wave, but public health intervention may be warranted to address persistently higher burden among young people and those with less social deprivation.

2024-06-05

International Journal of Epidemiology (published)