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Wen J, Hou J, Bonzel CL, Zhao Y, Castro VM, Gainer VS, Weisenfeld D, Cai T, Ho YL, Panickan VA, Costa L, Hong C, Gaziano JM, Liao KP, Lu J, Cho K, Cai T. LATTE: Label-efficient incident phenotyping from longitudinal electronic health records. PATTERNS (NEW YORK, N.Y.) 2024; 5:100906. [PMID: 38264714 PMCID: PMC10801250 DOI: 10.1016/j.patter.2023.100906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/06/2023] [Accepted: 12/01/2023] [Indexed: 01/25/2024]
Abstract
Electronic health record (EHR) data are increasingly used to support real-world evidence studies but are limited by the lack of precise timings of clinical events. Here, we propose a label-efficient incident phenotyping (LATTE) algorithm to accurately annotate the timing of clinical events from longitudinal EHR data. By leveraging the pre-trained semantic embeddings, LATTE selects predictive features and compresses their information into longitudinal visit embeddings through visit attention learning. LATTE models the sequential dependency between the target event and visit embeddings to derive the timings. To improve label efficiency, LATTE constructs longitudinal silver-standard labels from unlabeled patients to perform semi-supervised training. LATTE is evaluated on the onset of type 2 diabetes, heart failure, and relapses of multiple sclerosis. LATTE consistently achieves substantial improvements over benchmark methods while providing high prediction interpretability. The event timings are shown to help discover risk factors of heart failure among patients with rheumatoid arthritis.
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Affiliation(s)
- Jun Wen
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Jue Hou
- University of Minnesota, Minneapolis, MN, USA
| | - Clara-Lea Bonzel
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | | | | | | | - Tianrun Cai
- VA Boston Healthcare System, Boston, MA, USA
- Mass General Brigham, Boston, MA, USA
| | - Yuk-Lam Ho
- VA Boston Healthcare System, Boston, MA, USA
| | - Vidul A. Panickan
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | | | - J. Michael Gaziano
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Katherine P. Liao
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Junwei Lu
- VA Boston Healthcare System, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kelly Cho
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Tianxi Cai
- Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Hansford HJ, Cashin AG, Jones MD, Swanson SA, Islam N, Douglas SRG, Rizzo RRN, Devonshire JJ, Williams SA, Dahabreh IJ, Dickerman BA, Egger M, Garcia-Albeniz X, Golub RM, Lodi S, Moreno-Betancur M, Pearson SA, Schneeweiss S, Sterne JAC, Sharp MK, Stuart EA, Hernán MA, Lee H, McAuley JH. Reporting of Observational Studies Explicitly Aiming to Emulate Randomized Trials: A Systematic Review. JAMA Netw Open 2023; 6:e2336023. [PMID: 37755828 PMCID: PMC10534275 DOI: 10.1001/jamanetworkopen.2023.36023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/22/2023] [Indexed: 09/28/2023] Open
Abstract
Importance Observational (nonexperimental) studies that aim to emulate a randomized trial (ie, the target trial) are increasingly informing medical and policy decision-making, but it is unclear how these studies are reported in the literature. Consistent reporting is essential for quality appraisal, evidence synthesis, and translation of evidence to policy and practice. Objective To assess the reporting of observational studies that explicitly aimed to emulate a target trial. Evidence Review We searched Medline, Embase, PsycINFO, and Web of Science for observational studies published between March 2012 and October 2022 that explicitly aimed to emulate a target trial of a health or medical intervention. Two reviewers double-screened and -extracted data on study characteristics, key predefined components of the target trial protocol and its emulation (eligibility criteria, treatment strategies, treatment assignment, outcome[s], follow-up, causal contrast[s], and analysis plan), and other items related to the target trial emulation. Findings A total of 200 studies that explicitly aimed to emulate a target trial were included. These studies included 26 subfields of medicine, and 168 (84%) were published from January 2020 to October 2022. The aim to emulate a target trial was explicit in 70 study titles (35%). Forty-three studies (22%) reported use of a published reporting guideline (eg, Strengthening the Reporting of Observational Studies in Epidemiology). Eighty-five studies (43%) did not describe all key items of how the target trial was emulated and 113 (57%) did not describe the protocol of the target trial and its emulation. Conclusion and Relevance In this systematic review of 200 studies that explicitly aimed to emulate a target trial, reporting of how the target trial was emulated was inconsistent. A reporting guideline for studies explicitly aiming to emulate a target trial may improve the reporting of the target trial protocols and other aspects of these emulation attempts.
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Affiliation(s)
- Harrison J. Hansford
- School of Health Sciences, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Centre for Pain IMPACT, Neuroscience Research Australia, Sydney, Australia
| | - Aidan G. Cashin
- School of Health Sciences, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Centre for Pain IMPACT, Neuroscience Research Australia, Sydney, Australia
| | - Matthew D. Jones
- School of Health Sciences, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Centre for Pain IMPACT, Neuroscience Research Australia, Sydney, Australia
| | - Sonja A. Swanson
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- CAUSALab, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Nazrul Islam
- Oxford Population Health, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Susan R. G. Douglas
- School of Health Sciences, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
| | - Rodrigo R. N. Rizzo
- School of Health Sciences, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Centre for Pain IMPACT, Neuroscience Research Australia, Sydney, Australia
| | - Jack J. Devonshire
- Centre for Pain IMPACT, Neuroscience Research Australia, Sydney, Australia
| | - Sam A. Williams
- Centre for Pain IMPACT, Neuroscience Research Australia, Sydney, Australia
| | - Issa J. Dahabreh
- CAUSALab, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Barbra A. Dickerman
- CAUSALab, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Centre for Infectious Disease Epidemiology and Research, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Xabier Garcia-Albeniz
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- RTI Health Solutions, Barcelona, Spain
| | - Robert M. Golub
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Sara Lodi
- CAUSALab, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Margarita Moreno-Betancur
- Clinical Epidemiology & Biostatistics Unit, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Sallie-Anne Pearson
- School of Population Health, Faculty of Medicine and Health, UNSW Sydney, New South Wales, Australia
| | - Sebastian Schneeweiss
- Division of Pharmacoepidemiology, Department of Medicine, Brigham & Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan A. C. Sterne
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- NIHR Bristol Biomedical Research Centre, Bristol, United Kingdom
- Health Data Research UK South-West, Bristol, United Kingdom
| | - Melissa K. Sharp
- Department of Public Health and Epidemiology, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Elizabeth A. Stuart
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Miguel A. Hernán
- CAUSALab, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Hopin Lee
- University of Exeter Medical School, Exeter, United Kingdom
| | - James H. McAuley
- School of Health Sciences, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Centre for Pain IMPACT, Neuroscience Research Australia, Sydney, Australia
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