Portrait of Yue Li

Yue Li

Associate Academic Member
Assistant Professor, McGill University, School of Computer Science
Research Topics
Computational Biology

Biography

I completed my PhD degree in computer science and computational biology at the University of Toronto in 2014. Prior to joining McGill University, I was a postdoctoral associate at the Computer Science and Artificial Intelligence Laboratory (CSAIL) at MIT (2015–2018).

In general, my research program covers three main research areas that involve applied machine learning in computational genomics and health. More specifically, it focuses on developing interpretable probabilistic learning models and deep learning models to model genetic, epigenetic, electronic health record and single-cell genomic data.

By systematically integrating multimodal and longitudinal data, I aim to have impactful applications in computational medicine, including building intelligent clinical recommender systems, forecasting patient health trajectories, making personalized polygenic risk predictions, characterizing multi-trait functional genetic mutations, and dissecting cell-type-specific regulatory elements that underpin complex traits and diseases in humans.

Current Students

PhD - McGill University
Master's Research - McGill University
Master's Research - McGill University
PhD - McGill University
Principal supervisor :
PhD - McGill University
Master's Research - McGill University
Principal supervisor :
PhD - McGill University
Master's Research - McGill University
Co-supervisor :
PhD - McGill University
Master's Research - McGill University
PhD - McGill University
Master's Research - McGill University
PhD - McGill University

Publications

FedWeight: mitigating covariate shift of federated learning on electronic health records data through patients re-weighting
Mike He Zhu
Jun Bai
Na Li
Xiaoxiao Li
Dianbo Liu
Harnessing agent-based frameworks in CellAgentChat to unravel cell-cell interactions from single-cell and spatial transcriptomics
Vishvak Raghavan
Yumin Zheng
Toward whole-genome inference of polygenic scores with fast and memory-efficient algorithms.
Shadi Zabad
Chirayu Anant Haryan
Simon Gravel
Sanchit Misra
ECLARE: multi-teacher contrastive learning via ensemble distillation for diagonal integration of single-cell multi-omic data
Dylan Mann-Krzisnik
Integrating multimodal single-cell data, such as scRNA-seq and scATAC-seq, is key for decoding gene regulatory networks but remains challeng… (see more)ing due to issues like feature harmonization and limited quantity of paired data. To address these challenges, we introduce ECLARE, a novel framework combining multi-teacher ensemble knowledge distillation with contrastive learning for diagonal integration of single-cell multi-omic data. ECLARE trains teacher models on paired datasets to guide a student model for unpaired data, leveraging a refined contrastive objective and transport-based loss for precise cross-modality alignment. Experiments demonstrate ECLARE’s competitive performance in cell pairing accuracy, multimodal integration and biological structure preservation, indicating that multi-teacher knowledge distillation provides an effective mean to improve a diagonal integration model beyond its zero-shot capabilities. Additionally, we validate ECLARE’s applicability through a case study on major depressive disorder (MDD) data, illustrating its capability to reveal gene regulatory insights from unpaired nuclei. While current results highlight the potential of ensemble distillation in multi-omic analyses, future work will focus on optimizing model complexity, dataset scalability, and exploring applications in diverse multi-omic contexts. ECLARE establishes a robust foundation for biologically informed single-cell data integration, facilitating advanced downstream analyses and scaling multi-omic data for training advanced machine learning models.
scGraphETM: Graph-Based Deep Learning Approach for Unraveling Cell Type-Specific Gene Regulatory Networks from Single-Cell Multi-Omics Data
Wenqi Dong
Manqi Zhou
Boyu Han
Yi Wang
SpaTM: Topic Models for Inferring Spatially Informed Transcriptional Programs
Adrien Osakwe
Wenqi Dong
Qihuang Zhang
Robert Sladek
Spatial transcriptomics has revolutionized our ability to characterize tissues and diseases by contextualizing gene expression with spatial … (see more)organization. Available methods require researchers to either train a model using histology-based annotations or use annotation-free clustering approaches to uncover spatial domains. However, few methods provide researchers with a way to jointly analyze spatial data from both annotation-free and annotation-guided perspectives using consistent inductive biases and levels of interpretability. A single framework with consistent inductive biases ensures coherence and transferability across tasks, reducing the risks of conflicting assumptions. To this end, we propose the Spatial Topic Model (SpaTM), a topic-modeling framework capable of annotation-guided and annotation-free analysis of spatial transcriptomics data. SpaTM can be used to learn gene programs that represent histology-based annotations while providing researchers with the ability to infer spatial domains with an annotation-free approach if manual annotations are limited or noisy. We demonstrate SpaTM’s interpretability with its use of topic mixtures to represent cell states and transcriptional programs and how its intuitive framework facilitates the integration of annotation-guided and annotation-free analyses of spatial data with downstream analyses such as cell type deconvolution. Finally, we demonstrate how both approaches can be used to extend the analysis of large-scale snRNA-seq atlases with the inference of cell proximity and spatial annotations in human brains with Major Depressive Disorder.
Towards whole-genome inference of polygenic scores with fast and memory-efficient algorithms
Shadi Zabad
Chirayu Anant Haryan
Simon Gravel
Sanchit Misra
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… (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.
scMoE: single-cell mixture of experts for learning hierarchical, cell-type-specific, and interpretable representations from heterogeneous scRNA-seq data
Michael Huang
MiRGraph: A hybrid deep learning approach to identify microRNA-target interactions by integrating heterogeneous regulatory network and genomic sequences
Pei Liu
Yong Liu
Jiawei Luo
Bidirectional Generative Pre-training for Improving Healthcare Time-series Representation Learning
Ziyang Song
Qincheng Lu
Mike He Zhu