Publications

A Strong Node Classification Baseline for Temporal Graphs
Farimah Poursafaei
Željko Žilić
Reihaneh Rabbany
2022-04-20
Proceedings of the 2022 SIAM International Conference on Data Mining (SDM) (publié)
doi.org
Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data
Marie-Hélène Bourget
L. Kamentsky
Satrajit S. Ghosh
Giacomo Mazzamuto
Alberto Lazari
Christopher J. Markiewicz
Robert Oostenveld
Guiomar Niso
Yaroslav O. Halchenko
Ilona Lipp
Sylvain Takerkart
P. Toussaint
Ali Raza Khan
Gustav Nilsonne
Filippo Maria Castelli
Julien Cohen-Adad
The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data and metadata in a reusab… (voir plus)le way. First developed for magnetic resonance imaging (MRI) datasets, the community-led specification evolved rapidly to include other modalities such as magnetoencephalography, positron emission tomography, and quantitative MRI (qMRI). In this work, we present an extension to BIDS for microscopy imaging data, along with example datasets. Microscopy-BIDS supports common imaging methods, including 2D/3D, ex/in vivo, micro-CT, and optical and electron microscopy. Microscopy-BIDS also includes comprehensible metadata definitions for hardware, image acquisition, and sample properties. This extension will facilitate future harmonization efforts in the context of multi-modal, multi-scale imaging such as the characterization of tissue microstructure with qMRI.
2022-04-19
Frontiers in Neuroscience (published)
doi.org
Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data
Marie-Hélène Bourget
Lee Kamentsky
Satrajit S. Ghosh
Giacomo Mazzamuto
Alberto Lazari
Christopher J. Markiewicz
Robert Oostenveld
Guiomar Niso
Yaroslav O. Halchenko
Ilona Lipp
Sylvain Takerkart
Paule-Joanne Toussaint
Ali R. Khan
Gustav Nilsonne
Filippo Maria Castelli
Stefan Ross Eric Franklin Anthony Rémi Christopher J. Taylor Appelhoff
Julien Cohen-Adad
The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data and metadata in a reusab… (voir plus)le way. First developed for magnetic resonance imaging (MRI) datasets, the community-led specification evolved rapidly to include other modalities such as magnetoencephalography, positron emission tomography, and quantitative MRI (qMRI). In this work, we present an extension to BIDS for microscopy imaging data, along with example datasets. Microscopy-BIDS supports common imaging methods, including 2D/3D, ex/in vivo, micro-CT, and optical and electron microscopy. Microscopy-BIDS also includes comprehensible metadata definitions for hardware, image acquisition, and sample properties. This extension will facilitate future harmonization efforts in the context of multi-modal, multi-scale imaging such as the characterization of tissue microstructure with qMRI.
2022-04-19
Frontiers in Neuroscience (publié)
doi.org
On the Origin of Hallucinations in Conversational Models: Is it the Datasets or the Models?
Nouha Dziri
Sivan Milton
Mo Yu
Osmar R Zaiane
Siva Reddy
Knowledge-grounded conversational models are known to suffer from producing factually invalid statements, a phenomenon commonly called hallu… (voir plus)cination. In this work, we investigate the underlying causes of this phenomenon: is hallucination due to the training data, or to the models? We conduct a comprehensive human study on both existing knowledge-grounded conversational benchmarks and several state-of-the-art models. Our study reveals that the standard benchmarks consist of > 60% hallucinated responses, leading to models that not only hallucinate but even amplify hallucinations. Our findings raise important questions on the quality of existing datasets and models trained using them. We make our annotations publicly available for future research.
2022-04-17
ArXiv (preprint)
doi.org
arxiv.org
On the Origin of Hallucinations in Conversational Models: Is it the Datasets or the Models?
Nouha Dziri
Sivan Milton
Mo Yu
Osmar R Zaiane
Siva Reddy
Knowledge-grounded conversational models are known to suffer from producing factually invalid statements, a phenomenon commonly called hallu… (voir plus)cination. In this work, we investigate the underlying causes of this phenomenon: is hallucination due to the training data, or to the models? We conduct a comprehensive human study on both existing knowledge-grounded conversational benchmarks and several state-of-the-art models. Our study reveals that the standard benchmarks consist of > 60% hallucinated responses, leading to models that not only hallucinate but even amplify hallucinations. Our findings raise important questions on the quality of existing datasets and models trained using them. We make our annotations publicly available for future research.
2022-04-17
ArXiv (prépublication)
doi.org
arxiv.org
Improving Passage Retrieval with Zero-Shot Question Generation
Devendra Singh Sachan
Mike Lewis
Mandar S. Joshi
Armen Aghajanyan
Wen-292 Tau Yih
Joelle Pineau
Luke Zettlemoyer
We propose a simple and effective re-ranking method for improving passage retrieval in open question answering. The re-ranker re-scores retr… (voir plus)ieved passages with a zero-shot question generation model, which uses a pre-trained language model to compute the probability of the input question conditioned on a retrieved passage. This approach can be applied on top of any retrieval method (e.g. neural or keyword-based), does not require any domain- or task-specific training (and therefore is expected to generalize better to data distribution shifts), and provides rich cross-attention between query and passage (i.e. it must explain every token in the question). When evaluated on a number of open-domain retrieval datasets, our re-ranker improves strong unsupervised retrieval models by 6%-18% absolute and strong supervised models by up to 12% in terms of top-20 passage retrieval accuracy. We also obtain new state-of-the-art results on full open-domain question answering by simply adding the new re-ranker to existing models with no further changes.
2022-04-15
ArXiv (preprint)
doi.org
arxiv.org
Evolution of cell size control is canalized towards adders or sizers by cell cycle structure and selective pressures
Felix Proulx-Giraldeau
J. Skotheim
Paul François
Cell size is controlled to be within a specific range to support physiological function. To control their size, cells use diverse mechanisms… (voir plus) ranging from ‘sizers’, in which differences in cell size are compensated for in a single cell division cycle, to ‘adders’, in which a constant amount of cell growth occurs in each cell cycle. This diversity raises the question why a particular cell would implement one rather than another mechanism? To address this question, we performed a series of simulations evolving cell size control networks. The size control mechanism that evolved was influenced by both cell cycle structure and specific selection pressures. Moreover, evolved networks recapitulated known size control properties of naturally occurring networks. If the mechanism is based on a G1 size control and an S/G2/M timer, as found for budding yeast and some human cells, adders likely evolve. But, if the G1 phase is significantly longer than the S/G2/M phase, as is often the case in mammalian cells in vivo, sizers become more likely. Sizers also evolve when the cell cycle structure is inverted so that G1 is a timer, while S/G2/M performs size control, as is the case for the fission yeast S. pombe. For some size control networks, cell size consistently decreases in each cycle until a burst of cell cycle inhibitor drives an extended G1 phase much like the cell division cycle of the green algae Chlamydomonas. That these size control networks evolved such self-organized criticality shows how the evolution of complex systems can drive the emergence of critical processes.
2022-04-14
bioRxiv (preprint)
doi.org
Masked Siamese Networks for Label-Efficient Learning
Mahmoud Assran
Mathilde Caron
Ishan Misra
Piotr Bojanowski
Florian Bordes
Pascal Vincent
Armand Joulin
Michael Rabbat
Nicolas Ballas
We propose Masked Siamese Networks (MSN), a self-supervised learning framework for learning image representations. Our approach matches the … (voir plus)representation of an image view containing randomly masked patches to the representation of the original unmasked image. This self-supervised pre-training strategy is particularly scalable when applied to Vision Transformers since only the unmasked patches are processed by the network. As a result, MSNs improve the scalability of joint-embedding architectures, while producing representations of a high semantic level that perform competitively on low-shot image classification. For instance, on ImageNet-1K, with only 5,000 annotated images, our base MSN model achieves 72.4% top-1 accuracy, and with 1% of ImageNet-1K labels, we achieve 75.7% top-1 accuracy, setting a new state-of-the-art for self-supervised learning on this benchmark. Our code is publicly available.
2022-04-14
ArXiv (prépublication)
doi.org
arxiv.org
Masked Siamese Networks for Label-Efficient Learning
Mahmoud Assran
Mathilde Caron
Ishan Misra
Piotr Bojanowski
Florian Bordes
Pascal Vincent
Armand Joulin
Michael Rabbat
Nicolas Ballas
We propose Masked Siamese Networks (MSN), a self-supervised learning framework for learning image representations. Our approach matches the … (voir plus)representation of an image view containing randomly masked patches to the representation of the original unmasked image. This self-supervised pre-training strategy is particularly scalable when applied to Vision Transformers since only the unmasked patches are processed by the network. As a result, MSNs improve the scalability of joint-embedding architectures, while producing representations of a high semantic level that perform competitively on low-shot image classification. For instance, on ImageNet-1K, with only 5,000 annotated images, our base MSN model achieves 72.4% top-1 accuracy, and with 1% of ImageNet-1K labels, we achieve 75.7% top-1 accuracy, setting a new state-of-the-art for self-supervised learning on this benchmark. Our code is publicly available.
2022-04-14
ArXiv (preprint)
doi.org
arxiv.org
Microscopy analysis neural network to solve detection, enumeration and segmentation from image-level annotations
Anthony Bilodeau
Constantin V.L. Delmas
Martin Parent
Paul De Koninck
Audrey Durand
Flavie Lavoie-Cardinal
2022-04-14
Nature Machine Intelligence (publié)
doi.org
Microscopy analysis neural network to solve detection, enumeration and segmentation from image-level annotations
Anthony Bilodeau
Constantin V. L. Delmas
M. Parent
Paul De Koninck
Audrey Durand
Flavie Lavoie-Cardinal
2022-04-14
Nature Machine Intelligence (published)
doi.org
User Experience of a Computer-Based Decision Aid for Prenatal Trisomy Screening: Mixed Methods Explanatory Study
Titilayo Tatiana Agbadje
Chantale Pilon
Pierre Bérubé
Jean‐claude Forest
François Rousseau
Samira Abbasgholizadeh-Rahimi
Yves Giguère
France Légaré
Background Mobile health tools can support shared decision-making. We developed a computer-based decision aid (DA) to help pregnant women an… (voir plus)d their partners make informed, value-congruent decisions regarding prenatal screening for trisomy. Objective This study aims to assess the usability and usefulness of computer-based DA among pregnant women, clinicians, and policy makers. Methods For this mixed methods sequential explanatory study, we planned to recruit a convenience sample of 45 pregnant women, 45 clinicians from 3 clinical sites, and 15 policy makers. Eligible women were aged >18 years and >16 weeks pregnant or had recently given birth. Eligible clinicians and policy makers were involved in prenatal care. We asked the participants to navigate a computer-based DA. We asked the women about the usefulness of the DA and their self-confidence in decision-making. We asked all participants about usability, quality, acceptability, satisfaction with the content of the DA, and collected sociodemographic data. We explored participants’ reactions to the computer-based DA and solicited suggestions. Our interview guide was based on the Mobile App Rating Scale. We performed descriptive analyses of the quantitative data and thematic deductive and inductive analyses of the qualitative data for each participant category. Results A total of 45 pregnant women, 14 clinicians, and 8 policy makers participated. Most pregnant women were aged between 25 and 34 years (34/45, 75%) and White (42/45, 94%). Most clinicians were aged between 35 and 44 years (5/14, 36%) and women (11/14, 79%), and all were White (14/14, 100%); the largest proportion of policy makers was aged between 45 and 54 years (4/8, 50%), women (5/8, 62%), and White (8/8, 100%). The mean usefulness score for preparing for decision-making for women was 80/100 (SD 13), and the mean self-efficacy score was 88/100 (SD 11). The mean usability score was 84/100 (SD 14) for pregnant women, 77/100 (SD 14) for clinicians, and 79/100 (SD 23) for policy makers. The mean global score for quality was 80/100 (SD 9) for pregnant women, 72/100 (SD 12) for clinicians, and 80/100 (SD 9) for policy makers. Regarding acceptability, participants found the amount of information just right (52/66, 79%), balanced (58/66, 88%), useful (38/66, 58%), and sufficient (50/66, 76%). The mean satisfaction score with the content was 84/100 (SD 13) for pregnant women, 73/100 (SD 16) for clinicians, and 73/100 (SD 20) for policy makers. Participants thought the DA could be more engaging (eg, more customizable) and suggested strategies for implementation, such as incorporating it into clinical guidelines. Conclusions Pregnant women, clinicians, and policy makers found the DA usable and useful. The next steps are to incorporate user suggestions for improving engagement and implementing the computer-based DA in clinical practice.
2022-04-14
JMIR Pediatrics and Parenting (published)
doi.org