Yue Li

Claris Gu

Maîtrise recherche - McGill

Eric Huang

Maîtrise recherche - McGill

Yixuan Li

Doctorat - McGill

Superviseur⋅e principal⋅e :

Archer Yang

Dylan Mann-Krzisnik

Doctorat - McGill

Marshall Meng

Maîtrise recherche - McGill

Superviseur⋅e principal⋅e :

Doctorat - McGill

Doctorat - McGill

Co-superviseur⋅e :

Jun Ding

Jack Song

Maîtrise recherche - McGill

Co-superviseur⋅e :

Archer Yang

Bo-Hong Wang

Maîtrise recherche - McGill

Kunpeng Xu

Postdoctorat - McGill

Co-superviseur⋅e :

Archer Yang

Publications

Supervised multi-specialist topic model with applications on large-scale electronic health record data

Ziyang Song

Xavier Sumba Toral

Yixin Xu

Aihua Liu

Liming Guo

Guido Powell

Aman Verma

David Buckeridge

Ariane Marelli

Motivation: Electronic health record (EHR) data provides a new venue to elucidate disease comorbidities and latent phenotypes for precision … (voir plus)medicine. To fully exploit its potential, a realistic data generative process of the EHR data needs to be modelled. We present MixEHR-S to jointly infer specialist-disease topics from the EHR data. As the key contribution, we model the specialist assignments and ICD-coded diagnoses as the latent topics based on patient's underlying disease topic mixture in a novel unified supervised hierarchical Bayesian topic model. For efficient inference, we developed a closed-form collapsed variational inference algorithm to learn the model distributions of MixEHR-S. We applied MixEHR-S to two independent large-scale EHR databases in Quebec with three targeted applications: (1) Congenital Heart Disease (CHD) diagnostic prediction among 154,775 patients; (2) Chronic obstructive pulmonary disease (COPD) diagnostic prediction among 73,791 patients; (3) future insulin treatment prediction among 78,712 patients diagnosed with diabetes as a mean to assess the disease exacerbation. In all three applications, MixEHR-S conferred clinically meaningful latent topics among the most predictive latent topics and achieved superior target prediction accuracy compared to the existing methods, providing opportunities for prioritizing high-risk patients for healthcare services. MixEHR-S source code and scripts of the experiments are freely available at https://github.com/li-lab-mcgill/mixehrS

2021-07-31

Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (publié)

arxiv.org

Publisher Correction: The default network of the human brain is associated with perceived social isolation

R. Nathan Spreng

Emile Dimas

Laetitia Mwilambwe-Tshilobo

Alain Dagher

Philipp Koellinger

Gideon Nave

Anthony Ong

Julius M. Kernbach

Thomas V. Wiecki

Tian Ge

Avram J. Holmes

B. T. Thomas Yeo

Gary R. Turner

Robin I. M. Dunbar

Danilo Bzdok

2021-05-20

Nature Communications (publié)

The default network of the human brain is associated with perceived social isolation

R. Nathan Spreng

Emile Dimas

Laetitia Mwilambwe-Tshilobo

Alain Dagher

Philipp Koellinger

Gideon Nave

Anthony Ong

Julius M. Kernbach

Thomas V. Wiecki

Tian Ge

Avram J. Holmes

B. T. Thomas Yeo

Gary R. Turner

Robin I. M. Dunbar

Danilo Bzdok

Humans survive and thrive through social exchange. Yet, social dependency also comes at a cost. Perceived social isolation, or loneliness, a… (voir plus)ffects physical and mental health, cognitive performance, overall life expectancy, and increases vulnerability to Alzheimer’s disease-related dementias. Despite severe consequences on behavior and health, the neural basis of loneliness remains elusive. Using the UK Biobank population imaging-genetics cohort (n = ~40,000, aged 40–69 years when recruited, mean age = 54.9), we test for signatures of loneliness in grey matter morphology, intrinsic functional coupling, and fiber tract microstructure. The loneliness-linked neurobiological profiles converge on a collection of brain regions known as the ‘default network’. This higher associative network shows more consistent loneliness associations in grey matter volume than other cortical brain networks. Lonely individuals display stronger functional communication in the default network, and greater microstructural integrity of its fornix pathway. The findings fit with the possibility that the up-regulation of these neural circuits supports mentalizing, reminiscence and imagination to fill the social void.

2020-11-30

Nature Communications (publié)

Global Surveillance of COVID-19 by mining news media using a multi-source dynamic embedded topic model.

Pratheeksha Nair

Zhi Wen

Imane Chafi

Anya Okhmatovskaia

Guido Powell

Yannan Shen

David L. Buckeridge

As the COVID-19 pandemic continues to unfold, understanding the global impact of non-pharmacological interventions (NPI) is important for fo… (voir plus)rmulating effective intervention strategies, particularly as many countries prepare for future waves. We used a machine learning approach to distill latent topics related to NPI from large-scale international news media. We hypothesize that these topics are informative about the timing and nature of implemented NPI, dependent on the source of the information (e.g., local news versus official government announcements) and the target countries. Given a set of latent topics associated with NPI (e.g., self-quarantine, social distancing, online education, etc), we assume that countries and media sources have different prior distributions over these topics, which are sampled to generate the news articles. To model the source-specific topic priors, we developed a semi-supervised, multi-source, dynamic, embedded topic model. Our model is able to simultaneously infer latent topics and learn a linear classifier to predict NPI labels using the topic mixtures as input for each news article. To learn these models, we developed an efficient end-to-end amortized variational inference algorithm. We applied our models to news data collected and labelled by the World Health Organization (WHO) and the Global Public Health Intelligence Network (GPHIN). Through comprehensive experiments, we observed superior topic quality and intervention prediction accuracy, compared to the baseline embedded topic models, which ignore information on media source and intervention labels. The inferred latent topics reveal distinct policies and media framing in different countries and media sources, and also characterize reaction to COVID-19 and NPI in a semantically meaningful manner. Our PyTorch code is available on Github (htps://github.com/li-lab-mcgill/covid19_media).

2020-11-09

Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (publié)