Publications

Predicting Tactical Solutions to Operational Planning Problems under Imperfect Information
Eric Larsen
Sébastien Lachapelle
Yoshua Bengio
Emma Frejinger
Simon Lacoste-Julien
Andrea Lodi
This paper offers a methodological contribution at the intersection of machine learning and operations research. Namely, we propose a method… (voir plus)ology to quickly predict tactical solutions to a given operational problem. In this context, the tactical solution is less detailed than the operational one but it has to be computed in very short time and under imperfect information. The problem is of importance in various applications where tactical and operational planning problems are interrelated and information about the operational problem is revealed over time. This is for instance the case in certain capacity planning and demand management systems. We formulate the problem as a two-stage optimal prediction stochastic program whose solution we predict with a supervised machine learning algorithm. The training data set consists of a large number of deterministic (second stage) problems generated by controlled probabilistic sampling. The labels are computed based on solutions to the deterministic problems (solved independently and offline) employing appropriate aggregation and subselection methods to address uncertainty. Results on our motivating application in load planning for rail transportation show that deep learning algorithms produce highly accurate predictions in very short computing time (milliseconds or less). The prediction accuracy is comparable to solutions computed by sample average approximation of the stochastic program.
2021-09-20
INFORMS Journal on Computing (inconnu)
doi.org
arxiv.org
Stacked Hourglass Network with a Multi-level Attention Mechanism: Where to Look for Intervertebral Disc Labeling
Reza Azad
Lucas Rouhier
Julien Cohen-Adad
Labeling vertebral discs from MRI scans is important for the proper diagnosis of spinal related diseases, including multiple sclerosis, amyo… (voir plus)trophic lateral sclerosis, degenerative cervical myelopathy and cancer. Automatic labeling of the vertebral discs in MRI data is a difficult task because of the similarity between discs and bone area, the variability in the geometry of the spine and surrounding tissues across individuals, and the variability across scans (manufacturers, pulse sequence, image contrast, resolution and artefacts). In previous studies, vertebral disc labeling is often done after a disc detection step and mostly fails when the localization algorithm misses discs or has false positive detection. In this work, we aim to mitigate this problem by reformulating the semantic vertebral disc labeling using the pose estimation technique. To do so, we propose a stacked hourglass network with multi-level attention mechanism to jointly learn intervertebral disc position and their skeleton structure. The proposed deep learning model takes into account the strength of semantic segmentation and pose estimation technique to handle the missing area and false positive detection. To further improve the performance of the proposed method, we propose a skeleton-based search space to reduce false positive detection. The proposed method evaluated on spine generic public multi-center dataset and demonstrated better performance comparing to previous work, on both T1w and T2w contrasts. The method is implemented in ivadomed (https://ivadomed.org).
2021-09-20
Machine Learning in Medical Imaging (publié)
doi.org
arxiv.org
An Autonomous Probing System for Collecting Measurements at Depth from Small Surface Vehicles
Yuying Huang
Yiming Yao
Johanna Hansen
Jeremy Mallette
Sandeep Manjanna
Gregory Dudek
David Meger
This paper presents the portable autonomous probing system (APS), a low-cost robotic design for collecting water quality measurements at tar… (voir plus)geted depths from an autonomous surface vehicle (ASV). This system fills an important but often overlooked niche in marine sampling by enabling mobile sensor observations throughout the near-surface water column without the need for advanced underwater equipment. We present a probe delivery mechanism built with commercially available components and describe the corresponding open-source simulator and winch controller. Finally, we demonstrate the system in a field deployment and discuss design trade-offs and areas for future improvement. Project details are available on https://johannah.github.io/publication/sample-at-depth our website
2021-09-19
OCEANS 2021: San Diego – Porto (publié)
doi.org
arxiv.org
Propagating Uncertainty Across Cascaded Medical Imaging Tasks for Improved Deep Learning Inference
Raghav Mehta
Thomas Christinck
Tanya Nair
Aurélie Bussy
Paul Lemaitre
Swapna Premasiri
Manuela Costantino
Mallar Chakravarty
Douglas Arnold
Yarin Gal
Tal Arbel
2021-09-19
IEEE Transactions on Medical Imaging (inconnu)
doi.org
Connectivity alterations in autism reflect functional idiosyncrasy
Oualid Benkarim
Casey Paquola
Bo-yong Park
Seok-Jun Hong
Jessica Royer
Reinder Vos de Wael
Sara Larivière
Sofie Valk
Danilo Bzdok
Laurent Mottron
Boris C. Bernhardt
Autism spectrum disorder (ASD) is commonly understood as an alteration of brain networks, yet case-control analyses against typically-develo… (voir plus)ping controls (TD) have yielded inconsistent results. Here, we devised a novel approach to profile the inter-individual variability in functional network organization and tested whether such idiosyncrasy contributes to connectivity alterations in ASD. Studying a multi-centric dataset with 157 ASD and 172 TD, we obtained robust evidence for increased idiosyncrasy in ASD relative to TD in default mode, somatomotor and attention networks, but also reduced idiosyncrasy in lateral temporal cortices. Idiosyncrasy increased with age and significantly correlated with symptom severity in ASD. Furthermore, while patterns of functional idiosyncrasy were not correlated with ASD-related cortical thickness alterations, they co-localized with the expression patterns of ASD risk genes. Notably, we could demonstrate that patterns of atypical idiosyncrasy in ASD closely overlapped with connectivity alterations that are measurable with conventional case-control designs and may, thus, be a principal driver of inconsistency in the autism connectomics literature. These findings support important interactions between inter-individual heterogeneity in autism and functional signatures. Our findings provide novel biomarkers to study atypical brain development and may consolidate prior research findings on the variable nature of connectome level anomalies in autism. Benkarim et al devise an approach to profile inter-individual variability in functional network organization and test whether such idiosyncrasy contributes to the connectivity alterations found in Autism Spectrum Disorder. Their approach provides potential biomarkers to study atypical brain development and may be used to consolidate prior research findings on the variable nature of connectome level anomalies in autism.
2021-09-14
Communications Biology (publié)
doi.org
Is Heterophily A Real Nightmare For Graph Neural Networks To Do Node Classification?
Sitao Luan
Chenqing Hua
Qincheng Lu
Jiaqi Zhu
Mingde Zhao
Shuyuan Zhang
Xiao-Wen Chang
Doina Precup
2021-09-11
ArXiv (prépublication)
arxiv.org
arxiv.org
Team NeuroPoly: Description of the Pipelines for the MICCAI 2021 MS New Lesions Segmentation Challenge
Uzay Macar
Enamundram Naga Karthik
Charley Gros
Andréanne Lemay
Julien Cohen-Adad
This paper gives a detailed description of the pipelines used for the 2nd edition of the MICCAI 2021 Challenge on Multiple Sclerosis Lesion … (voir plus)Segmentation. An overview of the data preprocessing steps applied is provided along with a brief description of the pipelines used, in terms of the architecture and the hyperparameters. Our code for this work can be found at: https://github.com/ivadomed/ms-challenge-2021.
2021-09-11
ArXiv (prépublication)
arxiv.org
arxiv.org
Routine Bandits: Minimizing Regret on Recurring Problems
Hassan Saber
L'eo Saci
Odalric-Ambrym Maillard
Audrey Durand
2021-09-09
Machine Learning and Knowledge Discovery in Databases. Research Track (publié)
doi.org
Decision Models and Technology Can Help Psychiatry Develop Biomarkers
Daniel S. Barron
Justin T. Baker
Kristin S. Budde
Danilo Bzdok
Simon B. Eickhoff
Karl J. Friston
Peter T. Fox
Paul Geha
Stephen Heisig
Avram J. Holmes
Jukka-Pekka Onnela
Albert Powers
David Silbersweig
John H. Krystal
2021-09-08
Frontiers in Psychiatry (publié)
doi.org
Assessing the Electronic Evidence System Needs of Canadian Public Health Professionals: A Cross-Sectional Study (Preprint)
Bandna Dhaliwal
Sarah E Neil-Sztramko
Nikita Boston-Fisher
David L Buckeridge
Maureen Dobbins
BACKGROUND True evidence-informed decision making in public health relies on incorporating evidence from a number of sources in addition to… (voir plus) traditional scientific evidence. Lack of access to these types of data, as well as ease of use and interpretability of scientific evidence contribute to limited uptake of evidence-informed decision making in practice. An electronic evidence system that includes multiple sources of evidence and potentially novel computational processing approaches or artificial intelligence holds promise as a solution to overcoming barriers to evidence-informed decision making in public health. OBJECTIVE To understand the needs and preferences for an electronic evidence system among public health professionals in Canada. METHODS An invitation to participate in an anonymous online survey was distributed via listservs of two Canadian public health organizations. Eligible participants were English or French speaking individuals currently working in public health. The survey contained both multiple choice and open-ended questions about needs and preferences relevant to an electronic evidence system. Quantitative responses were analyzed to explore differences by public health role. Inductive and deductive analysis methods were used to code and interpret the qualitative data. Ethics review was not required by the host institution. RESULTS Respondents (n = 371) were heterogeneous, spanning organizations, positions, and areas of practice within public health. Nearly all (98.0%) respondents indicated that an electronic evidence system would support their work. Respondents had high preferences for local contextual data, research and intervention evidence, and information about human and financial resources. Qualitative analyses identified a number of concerns, needs, and suggestions for development of such a system. Concerns ranged from personal use of such a system, to the ability of their organization to use such a system. Identified needs spanned the different sources of evidence including local context, research and intervention evidence, and resources and tools. Additional suggestions were identified to improve system usability. CONCLUSIONS Canadian public health professionals have positive perceptions towards an electronic evidence system that would bring together evidence from the local context, scientific research, and resources. Elements were also identified to increase the usability of an electronic evidence system.
2021-09-06
JMIR Public Health and Surveillance (publié)
doi.org
Simple Video Generation using Neural ODEs
David Kanaa
Vikram Voleti
Samira Ebrahimi Kahou
Christopher Pal
Despite having been studied to a great extent, the task of conditional generation of sequences of frames, or videos, remains extremely chall… (voir plus)enging. It is a common belief that a key step towards solving this task resides in modelling accurately both spatial and temporal information in video signals. A promising direction to do so has been to learn latent variable models that predict the future in latent space and project back to pixels, as suggested in recent literature. Following this line of work and building on top of a family of models introduced in prior work, Neural ODE, we investigate an approach that models time-continuous dynamics over a continuous latent space with a differential equation with respect to time. The intuition behind this approach is that these trajectories in latent space could then be extrapolated to generate video frames beyond the time steps for which the model is trained. We show that our approach yields promising results in the task of future frame prediction on the Moving MNIST dataset with 1 and 2 digits.
2021-09-06
arXiv (prépublication)
doi.org
arxiv.org
Learning Neural Causal Models with Active Interventions
Nino Scherrer
Olexa Bilaniuk
Yashas Annadani
Anirudh Goyal
Patrick Schwab
Bernhard Schölkopf
Michael Curtis Mozer
Yoshua Bengio
Stefan Bauer
Nan Rosemary Ke
Discovering causal structures from data is a challenging inference problem of fundamental importance in all areas of science. The appealing … (voir plus)scaling properties of neural networks have recently led to a surge of interest in differentiable neural network-based methods for learning causal structures from data. So far, differentiable causal discovery has focused on static datasets of observational or interventional origin. In this work, we introduce an active intervention-targeting mechanism which enables quick identification of the underlying causal structure of the data-generating process. Our method significantly reduces the required number of interactions compared with random intervention targeting and is applicable for both discrete and continuous optimization formulations of learning the underlying directed acyclic graph (DAG) from data. We examine the proposed method across multiple frameworks in a wide range of settings and demonstrate superior performance on multiple benchmarks from simulated to real-world data.
2021-09-05
ArXiv (prépublication)
openreview.net
openreview.net