Portrait of Archer Yang

Archer Yang

Associate Academic Member
Associate professor, McGill University, Department of Mathematics and Statistics
Research Topics
Deep Learning
Dimensionality Reduction Methods
Drug Discovery
High-Dimensional statistics
Learning on Graphs
Machine Learning in Genomics and Healthcare
Machine Learning Theory
Probabilistic Models
Website
Google Scholar

Biography

I am an Associate Professor in the Department of Mathematics and Statistics at McGill University, with affiliations as an Associate Member of the School of Computer Science and the Quantitative Life Science program.

I work on the theory and methods of statistical machine learning and uncertainty quantification, with a focus on biomedicine and drug discovery:

- Statistical machine learning

- High-dimensional inference

- Uncertainty quantification and reliable AI

- Computational statistics and scalable algorithms

- Biomedical, biochemical data science

- AI for drug discovery

Current Students

Daniel Bensimon
Master's Research - McGill University
Co-supervisor :
Eric Kolaczyk
Dylan Fang
Master's Research - McGill University
David Fleischer
PhD - McGill University
Github
ZIANG GAO GAO
PhD - McGill University
Ryan Jackson
Undergraduate - McGill University
Kent Lu
Master's Research - McGill University
Marshall Meng
Master's Research - McGill University
Co-supervisor :
Yue Li
Francois Rocheleau
Master's Research - McGill University
Weihua Shi
PhD - McGill University
Jack Song
Master's Research - McGill University
Principal supervisor :
Yue Li
Github
Harri Vanhems
Undergraduate - McGill University
Kunpeng Xu
Postdoctorate - McGill University
Principal supervisor :
Yue Li

Publications

Generalized Random Forests using Fixed-Point Trees
David L. Fleischer
David A. Stephens
Archer Yang
We propose a computationally efficient alternative to generalized random forests arXiv:1610.01271 (GRFs) for estimating heterogeneous effect… (see more)s in large dimensions. While GRFs rely on a gradient-based splitting criterion, which in large dimensions is computationally expensive and unstable, our method introduces a fixed-point approximation that eliminates the need for Jacobian estimation. This gradient-free approach preserves GRFs theoretical guarantees of consistency and asymptotic normality while significantly improving computational efficiency. We demonstrate that our method achieves multiple times the speed over standard GRFs without compromising statistical accuracy. Experiments on both simulated and real-world data, validate our approach. Our findings suggest that the proposed method is a scalable alternative for localized effect estimation in machine learning and causal inference applications.
2025-10-06
Proceedings of the 42nd International Conference on Machine Learning (published)
proceedings.mlr.press
arxiv.org
Multivariate Conformal Selection
Tian Bai
Yue Zhao
Xiang Yu
Archer Yang
Selecting high-quality candidates from large datasets is critical in applications such as drug discovery, precision medicine, and alignment … (see more)of large language models (LLMs). While Conformal Selection (CS) provides rigorous uncertainty quantification, it is limited to univariate responses and scalar criteria. To address this, we propose Multivariate Conformal Selection (mCS), a generalization of CS designed for multivariate response settings. Our method introduces regional monotonicity and employs multivariate nonconformity scores to construct conformal
2025-10-06
Proceedings of the 42nd International Conference on Machine Learning (published)
proceedings.mlr.press
A flexible machine learning Mendelian randomization estimator applied to predict the safety and efficacy of sclerostin inhibition
Marc-André Legault
Jason Hartford
Benoît J. Arsenault
Archer Yang
Joelle Pineau
2025-05-01
American Journal of Human Genetics (published)
doi.org
Abstract 4142894: Multimorbidity Trajectories Across the Lifespan in Patients with Congenital Heart Disease
Chao Li
Aihua Liu
Solomon Bendayan
Liming Guo
Judith Therrien
Archer Yang
Robyn Tamblyn
Jay Brophy
Yue Li
Ariane Marelli
Background: Befitted from advances in medical care, patients with congenital heart disease (CHD) now survive to adulthood but face elevated… (see more) risks of both cardiac and non-cardiac complications. Understanding the trajectories of comorbidity development over a patient's lifespan is cornerstone to optimize care expected to improve long-term health outcomes. Research Aim: This study aims to investigate the temporal sequences and evolution of comorbidities in CHD patients across their lifespan. We hypothesize that multimorbidity trajectories in CHD patients are linked to CHD lesion severity and age at onset of specific comorbidities. Methods: Using the Quebec CHD database which comprised data in outpatient visits, hospitalization records and vital status from 1983 to 2017, we designed a longitudinal cohort study evaluating the development of 39 comorbidities coded using ICD-9/10. Temporal sequences were mapped using median age of onset. Associations between disease pairs were quantified by hazard ratios from Cox proportional hazard models adjusting for age, sex, genetic syndrome, competing risks of death, and taking into account the time-varying nature of the predictor diseases. Results: The cohort included 9,764 individuals with severe and 127,729 with non-severe CHD lesions. In severe CHD patients, most comorbidities developed between ages 25 and 40. Comorbidity progression began with childhood cardiovascular diseases, followed by systemic diseases such as diabetes, liver and kidney diseases, and advanced to heart failure and dementia in middle adulthood. In addition, mental disorders emerged in early adulthood and were associated with subsequent development of kidney diseases and dementia. Different trajectories were observed in non-severe CHD patients with 2-3 decades later disease onsets and non-differential onsets between cardiovascular and systemic complications (Figure). Conclusions: Distinct multimorbidity trajectories were observed in CHD patients by CHD lesion severity. In patients with severe CHD lesions, early systemic diseases significantly influenced subsequent complications. These findings highlight the need for well-timed surveillance guidelines and interventions to improve health outcomes.
2024-11-12
Circulation (published)
doi.org
Structured Learning in Time-dependent Cox Models
Guanbo Wang
Yi Lian
Archer Yang
Robert W. Platt
Rui Wang
Sylvie Perreault
Marc Dorais
Mireille E. Schnitzer
2024-05-28
Statistics in Medicine (published)
doi.org
arxiv.org
MixEHR-SurG: a joint proportional hazard and guided topic model for inferring mortality-associated topics from electronic health records
Yixuan Li
Ariane Marelli
Archer Yang
Yue Li
Survival models can help medical practitioners to evaluate the prognostic importance of clinical variables to patient outcomes such as morta… (see more)lity or hospital readmission and subsequently design personalized treatment regimes. Electronic Health Records (EHRs) hold the promise for large-scale survival analysis based on systematically recorded clinical features for each patient. However, existing survival models either do not scale to high dimensional and multi-modal EHR data or are difficult to interpret. In this study, we present a supervised topic model called MixEHR-SurG to simultaneously integrate heterogeneous EHR data and model survival hazard. Our contributions are three-folds: (1) integrating EHR topic inference with Cox proportional hazards likelihood; (2) integrating patient-specific topic hyperparameters using the PheCode concepts such that each topic can be identified with exactly one PheCode-associated phenotype; (3) multi-modal survival topic inference. This leads to a highly interpretable survival topic model that can infer PheCode-specific phenotype topics associated with patient mortality. We evaluated MixEHR-SurG using a simulated dataset and two real-world EHR datasets: the Quebec Congenital Heart Disease (CHD) data consisting of 8211 subjects with 75,187 outpatient claim records of 1767 unique ICD codes; the MIMIC-III consisting of 1458 subjects with multi-modal EHR records. Compared to the baselines, MixEHR-SurG achieved a superior dynamic AUROC for mortality prediction, with a mean AUROC score of 0.89 in the simulation dataset and a mean AUROC of 0.645 on the CHD dataset. Qualitatively, MixEHR-SurG associates severe cardiac conditions with high mortality risk among the CHD patients after the first heart failure hospitalization and critical brain injuries with increased mortality among the MIMIC-III patients after their ICU discharge. Together, the integration of the Cox proportional hazards model and EHR topic inference in MixEHR-SurG not only leads to competitive mortality prediction but also meaningful phenotype topics for in-depth survival analysis. The software is available at GitHub: https://github.com/li-lab-mcgill/MixEHR-SurG.
2024-05-01
Journal of Biomedical Informatics (published)
doi.org
arxiv.org
Machine Learning Informed Diagnosis for Congenital Heart Disease in Large Claims Data Source
Ariane Marelli
Chao Li
Aihua Liu
Hanh Nguyen
Harry Moroz
James M. Brophy
Liming Guo
David Buckeridge
Jian Tang
Archer Yang
Yue Li
2024-02-01
JACC: Advances (published)
doi.org
MixEHR-SurG: a joint proportional hazard and guided topic model for inferring mortality-associated topics from electronic health records
Yixuan Li
Ariane Marelli
Archer Yang
Yue Li
Survival models can help medical practitioners to evaluate the prognostic importance of clinical variables to patient outcomes such as morta… (see more)lity or hospital readmission and subsequently design personalized treatment regimes. Electronic Health Records (EHRs) hold the promise for large-scale survival analysis based on systematically recorded clinical features for each patient. However, existing survival models either do not scale to high dimensional and multi-modal EHR data or are difficult to interpret. In this study, we present a supervised topic model called MixEHR-SurG to simultaneously integrate heterogeneous EHR data and model survival hazard. Our contributions are three-folds: (1) integrating EHR topic inference with Cox proportional hazards likelihood; (2) integrating patient-specific topic hyperparameters using the PheCode concepts such that each topic can be identified with exactly one PheCode-associated phenotype; (3) multi-modal survival topic inference. This leads to a highly interpretable survival topic model that can infer PheCode-specific phenotype topics associated with patient mortality. We evaluated MixEHR-SurG using a simulated dataset and two real-world EHR datasets: the Quebec Congenital Heart Disease (CHD) data consisting of 8211 subjects with 75,187 outpatient claim records of 1767 unique ICD codes; the MIMIC-III consisting of 1458 subjects with multi-modal EHR records. Compared to the baselines, MixEHR-SurG achieved a superior dynamic AUROC for mortality prediction, with a mean AUROC score of 0.89 in the simulation dataset and a mean AUROC of 0.645 on the CHD dataset. Qualitatively, MixEHR-SurG associates severe cardiac conditions with high mortality risk among the CHD patients after the first heart failure hospitalization and critical brain injuries with increased mortality among the MIMIC-III patients after their ICU discharge. Together, the integration of the Cox proportional hazards model and EHR topic inference in MixEHR-SurG not only leads to competitive mortality prediction but also meaningful phenotype topics for in-depth survival analysis. The software is available at GitHub: https://github.com/li-lab-mcgill/MixEHR-SurG.
2023-12-20
ArXiv (preprint)
doi.org
arxiv.org
Privacy-preserving analysis of time-to-event data under nested case-control sampling
Lamin Juwara
Archer Yang
Ana M Velly
Paramita Saha-Chaudhuri
2023-12-13
Statistical Methods in Medical Research (published)
doi.org
Accelerating Generalized Random Forests with Fixed-Point Trees
David L. Fleischer
David A. Stephens
Archer Yang
2023-06-20
ArXiv (preprint)
doi.org
arxiv.org
A Tweedie Compound Poisson Model in Reproducing Kernel Hilbert Space
Yi Lian
Archer Yang
Boxiang Wang
Peng Shi
Robert William Platt
Abstract Tweedie models can be used to analyze nonnegative continuous data with a probability mass at zero. There have been wide application… (see more)s in natural science, healthcare research, actuarial science, and other fields. The performance of existing Tweedie models can be limited on today’s complex data problems with challenging characteristics such as nonlinear effects, high-order interactions, high-dimensionality and sparsity. In this article, we propose a kernel Tweedie model, Ktweedie, and its sparse variant, SKtweedie, that can simultaneously address the above challenges. Specifically, nonlinear effects and high-order interactions can be flexibly represented through a wide range of kernel functions, which is fully learned from the data; In addition, while the Ktweedie can handle high-dimensional data, the SKtweedie with integrated variable selection can further improve the interpretability. We perform extensive simulation studies to justify the prediction and variable selection accuracy of our method, and demonstrate the applications in ratemaking and loss-reserving in general insurance. Overall, the Ktweedie and SKtweedie outperform existing Tweedie models when there exist nonlinear effects and high-order interactions, particularly when the dimensionality is high relative to the sample size. The model is implemented in an efficient and user-friendly R package ktweedie (https://cran.r-project.org/package=ktweedie).
2022-12-13
Technometrics (published)
doi.org