Publications

Towards a unified XAI-based framework for digital forensic investigations
Zainab Khalid
Farkhund Iqbal
Benjamin C. M. Fung
2024-09-30
Digital Investigation. The International Journal of Digital Forensics and Incident Response (publié)
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
Linear Weight Interpolation Leads to Transient Performance Gains
Gaurav Iyer
Gintare Karolina Dziugaite
David Rolnick
2024-09-27
TMLR (accepté)
openreview.net
openreview.net
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
Harnessing population diversity: in search of tools of the trade
Danilo Bzdok
Guy Wolf
Jakub Kopal
Big neuroscience datasets are not big small datasets when it comes to quantitative data analysis. Neuroscience has now witnessed the advent … (voir plus)of many population cohort studies that deep-profile participants, yielding hundreds of measures, capturing dimensions of each individual’s position in the broader society. Indeed, there is a rebalancing from small, strictly selected, and thus homogenized cohorts toward always larger, more representative, and thus diverse cohorts. This shift in cohort composition is prompting the revision of incumbent modeling practices. Major sources of population stratification increasingly overshadow the subtle effects that neuroscientists are typically studying. In our opinion, as we sample individuals from always wider diversity backgrounds, we will require a new stack of quantitative tools to realize diversity-aware modeling. We here take inventory of candidate analytical frameworks. Better incorporating driving factors behind population structure will allow refining our understanding of how brain–behavior relationships depend on human subgroups.
2024-09-26
GigaScience (publié)
doi.org
Harnessing population diversity: in search of tools of the trade
Danilo Bzdok
Guy Wolf
Jakub Kopal
Abstract Big neuroscience datasets are not big small datasets when it comes to quantitative data analysis. Neuroscience has now witnessed th… (voir plus)e advent of many population cohort studies that deep-profile participants, yielding hundreds of measures, capturing dimensions of each individual’s position in the broader society. Indeed, there is a rebalancing from small, strictly selected, and thus homogenized cohorts toward always larger, more representative, and thus diverse cohorts. This shift in cohort composition is prompting the revision of incumbent modeling practices. Major sources of population stratification increasingly overshadow the subtle effects that neuroscientists are typically studying. In our opinion, as we sample individuals from always wider diversity backgrounds, we will require a new stack of quantitative tools to realize diversity-aware modeling. We here take inventory of candidate analytical frameworks. Better incorporating driving factors behind population structure will allow refining our understanding of how brain–behavior relationships depend on human subgroups.
2024-09-26
GigaScience (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
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
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
Reconstructing Spatio-Temporal Trajectories of Visual Object Memories in the Human Brain
Julia Lifanov
Benjamin J. Griffiths
Juan Linde-Domingo
Catarina S. Ferreira
Martin Wilson
Stephen D. Mayhew
Ian Charest
Maria Wimber
2024-09-25
eNeuro (publié)
doi.org