Le traitement du langage naturel à l'ère de l'IA générative
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Publications
Supervised multi-specialist topic model with applications on large-scale electronic health record data
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. Materials and Methods: 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. Results: 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. Availability and implementation: MixEHR-S source code and scripts of the experiments are freely available at https://github.com/li-lab-mcgill/mixehrS
2021-08-01
Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (publié)
Recent studies report that socioeconomic status (SES) correlates with brain structure. Yet, such findings are variable and little is known a… (voir plus)bout underlying causes. We present a well-powered voxel-based analysis of grey matter volume (GMV) across levels of SES, finding many small SES effects widely distributed across the brain, including cortical, subcortical and cerebellar regions. We also construct a polygenic index of SES to control for the additive effects of common genetic variation related to SES, which attenuates observed SES-GMV relations, to different degrees in different areas. Remaining variance, which may be attributable to environmental factors, is substantially accounted for by body mass index, a marker for lifestyle related to SES. In sum, SES affects multiple brain regions through measurable genetic and environmental effects. One-sentence Summary Socioeconomic status is linked with brain anatomy through a varying balance of genetic and environmental influences.
Local Structure Matters Most: Perturbation Study in NLU
Louis Clouâtre
Prasanna Parthasarathi
Amal Zouaq
Sarath Chandar
Recent research analyzing the sensitivity of natural language understanding models to word-order perturbations has shown that neural models … (voir plus)are surprisingly insensitive to the order of words.In this paper, we investigate this phenomenon by developing order-altering perturbations on the order of words, subwords, and characters to analyze their effect on neural models’ performance on language understanding tasks.We experiment with measuring the impact of perturbations to the local neighborhood of characters and global position of characters in the perturbed texts and observe that perturbation functions found in prior literature only affect the global ordering while the local ordering remains relatively unperturbed.We empirically show that neural models, invariant of their inductive biases, pretraining scheme, or the choice of tokenization, mostly rely on the local structure of text to build understanding and make limited use of the global structure.
Background: There is a growing recognition that strategies to reduce SARS-CoV-2 transmission should be responsive to local transmission dyna… (voir plus)mics. Studies have revealed inequalities along social determinants of health, but little investigation was conducted surrounding geographic concentration within cities. We quantified social determinants of geographic concentration of COVID-19 cases across sixteen census metropolitan areas (CMA) in four Canadian provinces. Methods: We used surveillance data on confirmed COVID-19 cases at the level of dissemination area. Gini (co-Gini) coefficients were calculated by CMA based on the proportion of the population in ranks of diagnosed cases and each social determinant using census data (income, education, visible minority, recent immigration, suitable housing, and essential workers) and the corresponding share of cases. Heterogeneity was visualized using Lorenz (concentration) curves. Results: Geographic concentration was observed in all CMAs (half of the cumulative cases were concentrated among 21-35% of each city's population): with the greatest geographic heterogeneity in Ontario CMAs (Gini coefficients, 0.32-0.47), followed by British Columbia (0.23-0.36), Manitoba (0.32), and Quebec (0.28-0.37). Cases were disproportionately concentrated in areas with lower income, education attainment, and suitable housing; and higher proportion of visible minorities, recent immigrants, and essential workers. Although a consistent feature across CMAs was concentration by proportion visible minorities, the magnitude of concentration by social determinants varied across CMAs. Interpretation: The feature of geographical concentration of COVID-19 cases was consistent across CMAs, but the pattern by social determinants varied. Geographically-prioritized allocation of resources and services should be tailored to the local drivers of inequalities in transmission in response to SARS-CoV-2's resurgence.