Publications

Bayesian Imaging for Radio Interferometry with Score-Based Priors
No'e Dia
M. J. Yantovski-Barth
Alexandre Adam
Micah Bowles
Pablo Lemos
A. Scaife
Yashar Hezaveh
Laurence Perreault-Levasseur
U. Montŕeal
Ciela Institute
Flatiron Institute
2023-11-29
ArXiv (preprint)
doi.org
arxiv.org
Learning an Effective Evolution Equation for Particle-Mesh Simulations Across Cosmologies
Nicolas Payot
Pablo Lemos
Laurence Perreault-Levasseur
Carolina Cuesta-lazaro
C. Modi
Yashar Hezaveh
2023-11-29
ArXiv (preprint)
arxiv.org
arxiv.org
Silent bugs in deep learning frameworks: an empirical study of Keras and TensorFlow
Florian Tambon
Amin Nikanjam
Le An
Foutse Khomh
Giuliano Antoniol
2023-11-29
Empirical Software Engineering (published)
doi.org
arxiv.org
TimelyGPT: Extrapolatable Transformer Pre-training for Long-term Time-Series Forecasting in Healthcare
Ziyang Song
Qincheng Lu
Hao Xu
Mike He Zhu
David Buckeridge
Yue Li
2023-11-29
ArXiv (preprint)
doi.org
arxiv.org
TimelyGPT: Extrapolatable Transformer Pre-training for Long-term Time-Series Forecasting in Healthcare
Ziyang Song
Qincheng Lu
Hao Xu
Mike He Zhu
David Buckeridge
Yue Li
Motivation: Large-scale pre-trained models (PTMs) such as BERT and GPT have recently achieved great success in Natural Language Processing a… (see more)nd Computer Vision domains. However, the development of PTMs on healthcare time-series data is lagging behind. This underscores the limitations of the existing transformer-based architectures, particularly their scalability to handle large-scale time series and ability to capture long-term temporal dependencies. Methods: In this study, we present Timely Generative Pre-trained Transformer (TimelyGPT). TimelyGPT employs an extrapolatable position (xPos) embedding to encode trend and periodic patterns into time-series representations. It also integrates recurrent attention and temporal convolution modules to effectively capture global-local temporal dependencies. Materials: We evaluated TimelyGPT on two large-scale healthcare time series datasets corresponding to continuous biosignals and irregularly-sampled time series, respectively: (1) the Sleep EDF dataset consisting of over 1.2 billion timesteps; (2) the longitudinal healthcare administrative database PopHR, comprising 489,000 patients randomly sampled from the Montreal population. Results: In forecasting continuous biosignals, TimelyGPT achieves accurate extrapolation up to 6,000 timesteps of body temperature during the sleep stage transition, given a short look-up window (i.e., prompt) containing only 2,000 timesteps. For irregularly-sampled time series, TimelyGPT with a proposed time-specific inference demonstrates high top recall scores in predicting future diagnoses using early diagnostic records, effectively handling irregular intervals between clinical records. Together, we envision TimelyGPT to be useful in various health domains, including long-term patient health state forecasting and patient risk trajectory prediction. Availability: The open-sourced code is available at Github.
2023-11-29
ArXiv (preprint)
doi.org
arxiv.org
Unraveling the Mysteries of Galaxy Clusters: Recurrent Inference Deconvolution of X-ray Spectra
C. L. Rhea
J. Hlavacek-Larrondo
Ralph P. Kraft
Ákos Bogdán
Alexandre Adam
Laurence Perreault-Levasseur
2023-11-29
ArXiv (preprint)
arxiv.org
arxiv.org
H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs
Brian Krug
Bo Hu
Haifen Chen
Adam Ptack
Xiao Chen
Kristjan H. Gretarsson
Shriya Deshmukh
Nisha Kabir
Augusto Faria Andrade
Elias Jabbour
Ashot S. Harutyunyan
John J. Y. Lee
Maud Hulswit
Damien Faury
Caterina Russo
Xinjing Xu
Michael Johnston
Audrey Baguette
Nathan A. Dahl
Alexander G. Weil … (see 12 more)
Benjamin Ellezam
Rola Dali
Mathieu Blanchette
Khadija Wilson
Benjamin A. Garcia
Rajesh Kumar Soni
Marco Gallo
Michael D. Taylor
Claudia Kleinman
Jacek Majewski
Nada Jabado
Chao Lu
2023-11-28
bioRxiv (preprint)
doi.org
Harnessing TCR/CAR Antagonism to Enhance Immunotherapeutic Precision
Taisuke Kondo
François X. P. Bourassa
Sooraj R. Achar
Justyn DuSold
Pablo Cespedes
Madison Wahlsten
Audun Kvalvaag
Guillaume Gaud
Paul E. Love
Michael Dustin
Grégoire Altan-Bonnet
Paul François
Naomi Taylor
2023-11-28
Blood (published)
doi.org
Identification of Acute Myeloid Leukemia Cell Surface Therapeutic Targets Using Single Cell RNA Sequencing Supported By Surface Proteomics
Véronique Lisi
Banafsheh Khakipoor
Azer Farah
Marie-Eve Bordeleau
Éric Audemard
Arnaud Metois
Louis Theret
Jean-Francois Spinella
Jalila Chagraoui
Ossama Moujaber
Laure Mallinger
Isabel Boivin
Nadine Mayotte
Azadeh Hajmirza
Eric Bonneil
Francois Béliveau
Albert Feghali
Geneviève Boucher
Patrick Gendron
Frederic Barabe … (see 6 more)
Sébastien Lemieux
Guillaume Richard-Carpentier
Josée Hébert
Philippe Roux
Guy Sauvageau
Vincent-Philippe Lavallee
Background: Acute myeloid leukemia (AML) comprises diverse genomic subgroups and remains hard to treat in most patients. Despite breakthrou… (see more)ghs in the therapeutic arsenal in recent years, clinical usage of therapeutic antibodies or chimeric antigen receptor T (CAR-T) cells has been lagging in contrast to other hematological malignancies. In fact, CD33 represents the only antibody-based strategy approved for this disease to date, highlighting the need to identify new promising targets. AML cells span a wide range of aberrant myeloid differentiation programs, complexifying the identification, by bulk genomics, of targets expressed in the most immature leukemic cells. Aims and Methods: To identify the expression landscape of surface proteins in immature leukemic cells, we performed single-cell RNA sequencing (scRNA-seq, 10x 3' Reagent Kits) of primary human AML cells from 20 specimens of the Leucegene cohort enriched in intermediate and adverse genetic backgrounds ( KMT2A-rearranged n=5, chromosome 5 and/or 7 deletions (abn5/7, n=5) complex karyotype (n=4), NPM1/DNMT3A/FLT3-ITD triple-mutant (n=3) and others (n=3)). A Random Forest classifier was developed to unbiasedly classify AML cells into distinct differentiation stages using normal bone marrow-derived scRNA-seq data from the Human Cell Atlas (HCA) consortium. Genes were scored based on their probability of coding for proteins expressed at the cell surface using the SPAT algorithm developed by our group (https://doi.org/10.1101/2023.07.07.547075), retaining high score ones. To validate surface expression, we concomitantly analyzed the surface proteome (hereafter named surfaceome) of 100 primary human AML samples from the Leucegene cohort, including all 20 samples profiled by scRNA-seq. Results: After quality control, we profiled and characterized 103 690 high quality cells (mean of 5185 cells/sample). We trained a Random Forest classifier to annotate cells in a two step process, first identifying plasma cells based on a restricted list of genes abundantly expressed in these cells and subsequently assigning the remaining cells to one of 33 cell types. We performed a five-fold cross validation of the model and subsequently determined the accuracy of our classifier to be 92% on the test subset of the HCA data. Applied to our AML cell collection, a total of 35 053 cells (34%) were unbiasedly classified as Hematopoietic Stem Cell (HSC)-like, corresponding to the most phenotypically immature leukemic cells in each patient sample (ranging from 4 to 74 %). Accordingly, HSC-like AML cells preferentially express genes associated with normal HSCs, such as CD34, FAM30A, and SPINK2, and globally lack expression of mature lineages defining genes, further validating our classifier. The proportion of HSC-like cells varied among AML subgroups, and was lowest in KMT2A-r AML (median 19%) and highest in abn5/7 samples (46%). Integration of our AML atlas using Harmony algorithm preserved differentiation hierarchies across samples, with most cell types, including HSC-like cells, occupying a defined area in the low dimensional embedding. To identify new surface antigens specifically expressed in immature leukemic cells, we compared the high (≥8) SPAT score gene expression profile of AML HSC-like cells with that of normal HSC cells (HCA), and identified 60 genes significantly overexpressed in AML immature cells. Of those, 39 genes were also detected at the protein level by the surfaceome analysis, supporting their predicted expression at the cell surface in AML samples. 59% of these 39 genes (n=23) were detected in over 80% of the specimens analyzed by the surfaceome, and thus are nearly universally expressed in our AML cohort. To identify targets of therapies that could be repurposed, we next evaluated the relevance of our findings by querying the Thera-SAbDab database. Most interestingly, 8 of the 39 AML specific HSC markers are targeted by therapeutic antibodies FDA-approved or in clinical trials for the treatment of AML (n=4, IL3RA, FLT3, CD37 and TNFRSF10B) or other indications (n = 4). Conclusion Our genetically diverse AML single-cell atlas, supported by mass spectrometry, enables the identification of both subset-specific and pan-AML surface protein genes. These represent potential targets for antibody based strategy development or therapy repurposing in AML.
2023-11-28
Blood (published)
doi.org
Learning few-shot imitation as cultural transmission
Avishkar Bhoopchand
Bethanie Brownfield
Adrian Collister
Agustin Dal Lago
Ashley Edwards
Richard Everett
Alexandre Fréchette
Yanko Gitahy Oliveira
Edward Hughes
Kory Wallace Mathewson
Piermaria Mendolicchio
Julia Pawar
Miruna Pȋslar
Alex Platonov
Evan Senter
Sukhdeep Singh
Alexander Zacherl
Lei M Zhang
2023-11-28
Nature Communications (published)
doi.org
Room-temperature correlated states in twisted bilayer MoS$_2$
Fanfan Wu
Qiaoling Xu
Qinqin Wang
Yanbang Chu
Li Li
Jian Tang
Jieying Liu
Jinpeng Tian
Yiru Ji
Le Liu
Yalong Yuan
Zhiheng Huang
Jiaojiao Zhao
Xiaozhou Zan
Kenji Watanabe
Takashi Taniguchi
Dongxia Shi
Gangxu Gu
Yang Xu
Lede Xian … (see 3 more)
Wei Yang
Luojun Du
Guangyu Zhang
2023-11-28
ArXiv (preprint)
arxiv.org
arxiv.org
Symmetry Breaking and Equivariant Neural Networks
Sékou-Oumar Kaba
Siamak Ravanbakhsh
Using symmetry as an inductive bias in deep learning has been proven to be a principled approach for sample-efficient model design. However,… (see more) the relationship between symmetry and the imperative for equivariance in neural networks is not always obvious. Here, we analyze a key limitation that arises in equivariant functions: their incapacity to break symmetry at the level of individual data samples. In response, we introduce a novel notion of 'relaxed equivariance' that circumvents this limitation. We further demonstrate how to incorporate this relaxation into equivariant multilayer perceptrons (E-MLPs), offering an alternative to the noise-injection method. The relevance of symmetry breaking is then discussed in various application domains: physics, graph representation learning, combinatorial optimization and equivariant decoding.
2023-11-28
NeurIPS.cc/2023/Workshop/NeurReps (oral)
doi.org
openreview.net