Publications

The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology
Erin E. Gill
Baofeng Jia
Carmen Lia Murall
Raphaël Poujol
Muhammad Zohaib Anwar
Nithu Sara John
Justin Richardsson
Ashley Hobb
Abayomi S. Olabode
Alexandru Lepsa
Ana T. Duggan
Andrea D. Tyler
Arnaud N'Guessan
Atul Kachru
Brandon Chan
Catherine Yoshida
Christina K. Yung
David Bujold
Dusan Andric
Edmund Su … (voir 46 de plus)
Emma J. Griffiths
Gary Van Domselaar
Gordon W. Jolly
Heather K. E. Ward
Henrich Feher
Jared Baker
Jared T. Simpson
Jaser Uddin
Jiannis Ragoussis
Jon Eubank
Jörg H. Fritz
José Héctor Gálvez
Karen Fang
Kim Cullion
Leonardo Rivera
Linda Xiang
Matthew A. Croxen
Mitchell Shiell
Natalie Prystajecky
Pierre-Olivier Quirion
Rosita Bajari
Samantha Rich
Samira Mubareka
Sandrine Moreira
Scott Cain
Steven G. Sutcliffe
Susanne A. Kraemer
Yelizar Alturmessov
Yann Joly
Marc Fiume
Terrance P. Snutch
Cindy Bell
Catalina López-Correa
Julie G. Hussin
Jeffrey B. Joy
Caroline Colijn
Paul M. K. Gordon
William W. L. Hsiao
Art F. Y. Poon
Natalie C. Knox
Mélanie Courtot
Lincoln Stein
Sarah P. Otto
Guillaume Bourque
B. Jesse Shapiro
Fiona S. L. Brinkman
The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform t… (voir plus)he public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN – VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). In addition, the portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. From inception to execution, the portal was developed with a conscientious focus on strong data governance principles and practices. Extensive efforts ensured a commitment to Canadian privacy laws, data security standards, and organizational processes. This portal has been coupled with other resources, such as Viral AI, and was further leveraged by the Coronavirus Variants Rapid Response Network (CoVaRR-Net) to produce a suite of continually updated analytical tools and notebooks. Here we highlight this portal (https://virusseq-dataportal.ca/), including its contextual data not available elsewhere, and the Duotang (https://covarr-net.github.io/duotang/duotang.html), a web platform that presents key genomic epidemiology and modelling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the portal (COVID-MVP, CoVizu), are all open source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses.
2024-09-30
Microbial Genomics (publié)
doi.org
The oneirogen hypothesis: modeling the hallucinatory effects of classical psychedelics in terms of replay-dependent plasticity mechanisms
Colin Bredenberg
Fabrice Normandin
Blake Richards
Guillaume Lajoie
Abstract Classical psychedelics induce complex visual hallucinations in humans, generating percepts that are co-herent at a … (voir plus)low level, but which have surreal, dream-like qualities at a high level. While there are many hypotheses as to how classical psychedelics could induce these effects, there are no concrete mechanistic models that capture the variety of observed effects in humans, while remaining consistent with the known pharmacological effects of classical psychedelics on neural circuits. In this work, we propose the “oneirogen hypothesis”, which posits that the perceptual effects of classical psychedelics are a result of their pharmacological actions inducing neural activity states that truly are more similar to dream-like states. We simulate classical psychedelics’ effects via manipulating neural network models trained on perceptual tasks with the Wake-Sleep algorithm. This established machine learning algorithm leverages two activity phases, a perceptual phase (wake) where sensory inputs are encoded, and a generative phase (dream) where the network internally generates activity consistent with stimulus-evoked responses. We simulate the action of psychedelics by partially shifting the model to the ‘Sleep’ state, which entails a greater influence of top-down connections, in line with the impact of psychedelics on apical dendrites. The effects resulting from this manipulation capture a number of experimentally observed phenomena including the emergence of hallucinations, increases in stimulus-conditioned variability, and large increases in synaptic plasticity. We further provide a number of testable predictions which could be used to validate or invalidate our oneirogen hypothesis.
2024-09-29
bioRxiv (accepté)
doi.org
Automating MedSAM by Learning Prompts with Weak Few-Shot Supervision
Melanie Gaillochet
Christian Desrosiers
Hervé Lombaert
2024-09-27
Lecture Notes in Computer Science (publié)
doi.org
arxiv.org
Genetic Interplay Between White Matter Hyperintensities and Alzheimer's Disease: A Brain-Body Perspective
Manpreet Singh
Kimia Shafighi
Flavie E. Detcheverry
Fanta Dabo
Ikrame Housni
Sridar Narayanan
Sarah A. Gagliano Taliun
Danilo Bzdok
AmanPreet Badhwar
MRI-detected white matter hyperintensities (WMH) are often recognized as markers of cerebrovascular abnormalities and an index of vascular b… (voir plus)rain injury, and are frequently present in individuals with Alzheimer’s disease (AD). Given the emerging bidirectional communication between the brain-body axis in both WMHs and AD, it is important to understand their genetic underpinnings across the whole body. However, literature on this is scarce. We investigated the brain-body axis by breaking down heritability estimates of these phenotypes across the whole body, – i.e., partitioning heritability. Our aims were to identify genetic underpinnings specific to WMHs, and common between WMHs and AD, by assessing (a) the partitioned heritability of WMHs and AD across the brain-body axis with tissue-specific annotations, (b) the partitioned heritability of WMHs and AD across the brain-body axis with cell-specific annotations, and (c) the genes associated with WMHs and AD, and verifying their expression levels across the whole body. Our tissue-specific analysis revealed that WMH-associated SNPs were significantly enriched in tissues beyond the brain, namely liver, cardiovascular, and kidney – with liver being a common tissue enriched for both WMHs and AD. Our cell-specific analysis showed enrichment of vascular endothelial cells across the tissue types enriched for WMHs, highlighting their central role in the development of WMHs. Additionally, our gene-level analysis highlighted overlapping patterns of tissue enrichment for both WMHs and AD, and showed interactions between WMH and AD associated genes. Our findings provide new insights into the systemic influences potentially contributing to WMH pathology, in particular, multi-system endothelial disorder. We hope that our multisystemic genetic findings will stimulate future WMH-research into specific pathways across the brain-body axis.
2024-09-27
medRxiv (prépublication)
doi.org
Refining SARS-CoV-2 intra-host variation by leveraging large-scale sequencing data
Fatima Mostefai
Jean-Christophe Grenier
Raphaël Poujol
Julie Hussin
Understanding viral genome evolution during host infection is crucial for grasping viral diversity and evolution. Analyzing intra-host singl… (voir plus)e nucleotide variants (iSNVs) offers insights into new lineage emergence, which is important for predicting and mitigating future viral threats. Despite next-generation sequencing’s potential, challenges persist, notably sequencing artifacts leading to false iSNVs. We developed a workflow to enhance iSNV detection in large NGS libraries, using over 130 000 SARS-CoV-2 libraries to distinguish mutations from errors. Our approach integrates bioinformatics protocols, stringent quality control, and dimensionality reduction to tackle batch effects and improve mutation detection reliability. Additionally, we pioneer the application of the PHATE visualization approach to genomic data and introduce a methodology that quantifies how related groups of data points are represented within a two-dimensional space, enhancing clustering structure explanation based on genetic similarities. This workflow advances accurate intra-host mutation detection, facilitating a deeper understanding of viral diversity and evolution.
2024-09-27
NAR Genomics and Bioinformatics (publié)
doi.org
Longitudinal bi-criteria framework for assessing national healthcare responses to pandemic outbreaks
Adel Guitouni
Nabil Belacel
Loubna Benabbou
Belaid Moa
Munire Erman
Halim Abdul
2024-09-26
Scientific Reports (publié)
doi.org
Replication of a GWAS signal near
<i>HLA-DQA2</i>
with acute myeloid leukemia using a disease-only cohort and external population-based controls
Rose Laflamme
Véronique Lisi
Josée Hébert
Guy Sauvageau
Sébastien Lemieux
Vincent-Philippe Lavallee
Guillaume Lettre
Acute myeloid leukemia (AML) is the most common type of acute leukemia in adults. Its risk factors include rare and highly penetrant somatic… (voir plus) mutations. Genome-wide association studies (GWAS) have also identified four common inherited variants associated with AML risk, but these findings have not yet been confirmed in many independent datasets. Here, we performed a replication study with 567 AML cases from the Leucegene cohort and 1,865 controls from the population-based cohort CARTaGENE (CaG). Because genotypes were generated using different technologies in the two datasets (e.g. low- vs. high-coverage whole-genome sequencing), we applied stringent quality-control filters to minimize type I errors. We showed using data reduction methods (e.g. principal component analysis [PCA] and uniform manifold approximation and projection [UMAP]) that our approach successfully integrated the Leucegene and CaG genetic data. We replicated the association between cytogenetically normal (CN)-AML and rs3916765, a variant located near HLA-DQA2 (odds ratio [95% confidence interval] = 1.88 [1.21-2.93], P- value=0.005). The effect size of this association was stronger when we restricted the analyses to AML patients with NPM1 mutations (odds ratios >2.35). We found HLA- DOB to be the most significantly upregulated gene in Leucegene participants with the CN-AML protective A-allele at rs3916765. We further found that several HLA class II genes are also differentially expressed albeit at lower statistical significance. Our results confirm that a common genetic variant at the HLA locus associates with AML risk, providing new opportunities to improve disease prognosis and treatment.
2024-09-26
medRxiv (prépublication)
doi.org
CALE: Continuous Arcade Learning Environment
Jesse Farebrother
Pablo Samuel Castro
We introduce the Continuous Arcade Learning Environment (CALE), an extension of the well-known Arcade Learning Environment (ALE) [Bellemare … (voir plus)et al., 2013]. The CALE uses the same underlying emulator of the Atari 2600 gaming system (Stella), but adds support for continuous actions. This enables the benchmarking and evaluation of continuous-control agents (such as PPO [Schulman et al., 2017] and SAC [Haarnoja et al., 2018]) and value-based agents (such as DQN [Mnih et al., 2015] and Rainbow [Hessel et al., 2018]) on the same environment suite. We provide a series of open questions and research directions that CALE enables, as well as initial baseline results using Soft Actor-Critic. CALE is available as part of the ALE athttps://github.com/Farama-Foundation/Arcade-Learning-Environment.
2024-09-25
NeurIPS.cc/2024/Datasets_and_Benchmarks_Track (poster)
doi.org
openreview.net
CVQA: Culturally-diverse Multilingual Visual Question Answering Benchmark
David LE MEUR
David Orlando Romero Mogrovejo
Chenyang Lyu
Haryo Akbarianto Wibowo
Teresa Lynn
Injy Hamed
Aditya Nanda Kishore Khandavally
Aishik Mandal
Alina Dragonetti
Artem Abzaliev
Atnafu Lambebo Tonja
Bontu Fufa Balcha
Chenxi Whitehouse
Christian Salamea-Palacios
Dan John Velasco
David Ifeoluwa Adelani
D. Meur
Emilio Villa Cueva
Fajri Koto
Fauzan Farooqui … (voir 57 de plus)
Frederico Belcavello
Ganzorig Batnasan
Gisela Vallejo
Gráinne Caulfield
Guido Ivetta
Haiyue Song
Henok Biadglign Ademtew
Hernán Maina
Holy Lovenia
Israel Abebe Azime
Jan Christian Blaise Cruz
Jay Gala
Jiahui Geng
Jesus-German Ortiz-Barajas
Jinheon Baek
Jocelyn Dunstan
Laura Alonso Alemany
Teresa Clifford
Kumaranage Ravindu Yasas Nagasinghe
Luciana Benotti
Luis Fernando D'Haro
Marcelo Viridiano
Marcos Estecha-Garitagoitia
Maria Camila Buitrago Cabrera
Mario Rodríguez-Cantelar
Mélanie Jouitteau
Mihail Minkov Mihaylov
Mohamed Fazli Mohamed Imam
Muhammad Farid Adilazuarda
Munkhjargal Gochoo
Munkh-Erdene Otgonbold
Naome Etori
Olivier NIYOMUGISHA
Paula Mónica Silva
Pranjal A Chitale
Raj Dabre
Rendi Chevi
Ruochen Zhang
Ryandito Diandaru
Samuel Cahyawijaya
Santiago Góngora
Soyeong Jeong
Sukannya Purkayastha
Tatsuki Kuribayashi
Thanmay Jayakumar
Tiago Timponi Torrent
Toqeer Ehsan
Vladimir Araujo
Yova Kementchedjhieva
Zara Burzo
Zheng Wei Lim
Zheng Xin Yong
Oana Ignat
Joan Nwatu
Rada Mihalcea
Thamar Solorio
Alham Fikri Aji
2024-09-25
NeurIPS.cc/2024/Datasets_and_Benchmarks_Track (présentation orale)
doi.org
openreview.net
Expecting The Unexpected: Towards Broad Out-Of-Distribution Detection
Charles Guille-escuret
Pierre-Andre Noel
Ioannis Mitliagkas
David Vázquez
Joao Monteiro
Improving the reliability of deployed machine learning systems often involves developing methods to detect out-of-distribution (OOD) inputs.… (voir plus) However, existing research often narrowly focuses on samples from classes that are absent from the training set, neglecting other types of plausible distribution shifts. This limitation reduces the applicability of these methods in real-world scenarios, where systems encounter a wide variety of anomalous inputs. In this study, we categorize five distinct types of distribution shifts and critically evaluate the performance of recent OOD detection methods on each of them. We publicly release our benchmark under the name BROAD (Benchmarking Resilience Over Anomaly Diversity). Our findings reveal that while these methods excel in detecting unknown classes, their performance is inconsistent when encountering other types of distribution shifts. In other words, they only reliably detect unexpected inputs that they have been specifically designed to expect. As a first step toward broad OOD detection, we learn a generative model of existing detection scores with a Gaussian mixture. By doing so, we present an ensemble approach that offers a more consistent and comprehensive solution for broad OOD detection, demonstrating superior performance compared to existing methods. Our code to download BROAD and reproduce our experiments is publicly available.
2024-09-25
NeurIPS.cc/2024/Datasets_and_Benchmarks_Track (poster)
doi.org
openreview.net
Learning Action and Reasoning-Centric Image Editing from Videos and Simulation
Benno Krojer
Dheeraj Vattikonda
Luis Lara
Varun Jampani
Eva Portelance
Christopher Pal
Siva Reddy
2024-09-25
NeurIPS.cc/2024/Datasets_and_Benchmarks_Track (spotlight)
openreview.net
openreview.net
LogiCity: Advancing Neuro-Symbolic AI with Abstract Urban Simulation
Bowen Li
Zhaoyu Li
Qiwei Du
Jinqi Luo
Wenshan Wang
Yaqi Xie
Simon Stepputtis
Chen Wang
Katia P. Sycara
Pradeep Kumar Ravikumar
Alexander G. Gray
Xujie Si
Sebastian Scherer
Recent years have witnessed the rapid development of Neuro-Symbolic (NeSy) AI systems, which integrate symbolic reasoning into deep neural n… (voir plus)etworks. However, most of the existing benchmarks for NeSy AI fail to provide long-horizon reasoning tasks with complex multi-agent interactions. Furthermore, they are usually constrained by fixed and simplistic logical rules over limited entities, making them far from real-world complexities. To address these crucial gaps, we introduce LogiCity, the first simulator based on customizable first-order logic (FOL) for an urban-like environment with multiple dynamic agents. LogiCity models diverse urban elements using semantic and spatial concepts, such as
2024-09-25
Datasets and Benchmarks Track @ Neural Information Processing Systems (poster)
doi.org
openreview.net