Publications
Pre-prints
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Predicting Parkinson's disease progression using MRI-based white matter radiomic biomarker and machine learning: a reproducibility and replicability study
Mohanad Arafe, Nikhil Parag Bhagwat, Yohan Chatelain, Mathieu Dugré, Andrzej Sokolowski, Michelle Wang, Yiming Xiao, Madeleine Sharp, Jean-Baptiste Poline, Tristan Glatard
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Longitudinal brain structure changes in Parkinson's disease: a replication study
Andrzej Sokołowski, Nikhil Bhagwat, Yohan Chatelain, Mathieu Dugré, Alexandru Hanganu, Oury Monchi, Brent McPherson, Michelle Wang, Jean-Baptiste Poline, Madeleine Sharp, Tristan Glatard
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Numerical Stability of DeepGOPlus Inference
Inés Gonzalez Pepe, Yohan Chatelain, Gregory Kiar, Tristan Glatard
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Sea: A lightweight data-placement library for Big Data scientific computing
Valérie Hayot-Sasson, Mathieu Dugré, Tristan Glatard
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Mondrian Forest for Data Stream Classification Under Memory Constraints
Martin Khannouz, Tristan Glatard
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A Conceptual Marketplace Model for IoT Generated Personal Data
Victor Molina, Marta Kersten-Oertel, Tristan Glatard
Published papers
(including contributions from lab members as co-authors)Reproducibility of Tumor Segmentation Outcomes with a Depp Learning Model
Morgane des Ligneris, Axel Bonnet, Yohan Chatelain, Tristan Glatard, Micha ̈el Sdika, Ga ̈el Vila, Valentine Wargnier-Dauchelle, Sorina Pop, and Carole Frindel
2023 International Symposium on Biomedical Imaging-
PyTracer: Automatically profiling numerical instabilities in Python
Yohan Chatelain, Nigel Yong, Gregory Kiar, Tristan Glatard
IEEE Computers, 2022
Dynamic Ensemble Size Adjustment for Memory Constrained Mondrian Forest
Martin Khannouz, Tristan Glatard
7th Workshop on Real-time Stream Analytics, Stream Mining, CER/CEP & Stream Data Management in Big Data, Osaka, 2022
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NeuroCI: Continuous Integration of Neuroimaging Results Across Software Pipelines and Datasets
Jacob Sanz-Robinson, Arman Jahanpour, Natalie Phillips, Tristan Glatard, Jean-Baptiste Poline
IEEE eScience 2022
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Reducing numerical precision preserves classification accuracy in Mondrian Forests
Marc Vicuna, Martin Khannouz, Gregory Kiar, Yohan Chatelain, Tristan Glatard
6th Workshop on Real-time Stream Analytics, Stream Mining, CER/CEP & Stream Data Management in Big Data, 2021
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Can we Estimate Truck Accident Risk from Telemetric Data using Machine Learning?
Antoine Hébert, Ian Marineau, Gilles Gervais, Tristan Glatard, Brigitte Jaumard
2021 IEEE International Conference on Big Data, 2021
Data and Tools Integration in the Canadian Open Neuroscience Platform
Jean-Baptiste Poline, Samir Das, Tristan Glatard, Cécile Madjar, et al.
to appear in Scientific Data, 2021-
The benefits of prefetching for large-scale cloud-based neuroimaging analysis workflows
Valerie Hayot-Sasson, Tristan Glatard, Ariel Rokem
16th Workshop on Workflows in Support of Large-Scale Science, 2021
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A Recommender System for Scientific Datasets and Analysis Pipelines
Mandana Mazaheri, Gregory Kiar, Tristan Glatard
16th Workshop on Workflows in Support of Large-Scale Science, 2021
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Numerical Instabilities in Analytical Pipelines Lead to Large and Meaningful Variability in Brain Networks
Gregory Kiar, Yohan Chatelain, Pablo de Oliveira Castro, Eric Petit, Ariel Rokem, Gaël Varoquaux, Bratislav Misic, Alan C. Evans, Tristan Glatard
PLOS ONE, to appear, 2021
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Accurate simulation of operating system updates in neuroimaging using Monte-Carlo arithmetic
Ali Salari, Yohan Chatelain, Gregory Kiar, Tristan Glatard
2021 MICCAI workshop on Uncertainty for Safe Utilization of Machine Learning in Medical Imaging (UNSURE 2021)
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Centering inclusivity in the design of online conferences—An OHBM–Open Science perspective
Elizabeth Levitis, Cassandra D Gould van Praag, Rémi Gau et al.
GigaScience, 10(8), giab051.
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Data Augmentation Through Monte Carlo Arithmetic Leads to More Generalizable Classification in Connectomics
Gregory Kiar, Yohan Chatelain, Ali Salari, Alan C Evans, Tristan Glatard
Neurons, Behavior, Data Analysis and Theory, 2021
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Brainhack: Developing a culture of open, inclusive, community-driven neuroscience
Rémi Gau, Stephanie Noble, Katja Heuer, Katherine L Bottenhorn, et al.
Neuron, 109(11), pp 1769-1775, 2021
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Modeling the Linux page cache for accurate simulation of data-intensive applications
Hoang-Dung Do, Valerie Hayot-Sasson, Rafael Ferreira da Silva, Christopher Steele, Henri Casanova, Tristan Glatard
to appear in IEEE Cluster 2021
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An Analysis of Security Vulnerabilities in Container Images for Scientific Data Analysis
Bhupinder Kaur, Mathieu Dugré, Aiman Hanna, Tristan Glatard
GigaScience, Volume 10, Issue 6, June 2021, giab025.
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A benchmark of data stream classification for human activity recognition on connected objects
Martin Khannouz, Tristan Glatard
Sensors, 2020, 20(22), 6486.
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File-based localization of numerical perturbations in data analysis pipelines
Ali Salari, Gregory Kiar, Lindsay Lewis, Alan C. Evans, Tristan Glatard
Giga Science, Volume 9, Issue 12, December 2020.
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Variability in the analysis of a single neuroimaging dataset by many teams
Rotem Botvinik-Nezer, Felix Holzmeister, Colin F. Camerer et al.
Nature, 582, 84-88 (2020).
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Comparing Perturbation Models for Evaluating Stability of Post-Processing Pipelines in Neuroimaging
Gregory Kiar, Pablo de Oliveira Castro, Pierre Rioux, Eric Petit, Shawn T. Brown, Alan C. Evans, Tristan Glatard
International Journal of High-Performance Computing Applications, May 21, 2020, arXiv:1908.10922.
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Performance benefits of Intel® Optane™ DC persistent memory for the parallel processing of large neuroimaging data
Valerie Hayot-Sasson, Shawn T Brown, Tristan Glatard
IEEE/ACM CCGrid 2020, arXiv:1912.11794.
A Quantitative Comparison of Overlapping and Non-Overlapping Sliding Windows for Human Activity Recognition Using Inertial Sensors
Akbar Dehghani, Omid Sarbishei, Tristan Glatard, Emad Shihab
Sensors 2019, 19(22), 5026
High-Resolution Road Vehicle Collision Prediction for the City of Montreal
Antoine Hébert, Timothée Guédon, Tristan Glatard, Brigitte Jaumard
2019 IEEE International Conference on Big Data, arXiv:1905.08770.
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A performance comparison of Dask and Apache Spark for data-intensive neuroimaging pipelines
Mathieu Dugré, Valérie Hayot-Sasson, Tristan Glatard
14th Workshop on Workflows in Support of Large-Scale Science - WORKS 2019, in conjunction with Supercomputing'19, arXiv:1907.13030.
OrpailleCC: a Library for Data Stream Analysis on Embedded Systems
Martin Khannouz, Bo Li, Tristan Glatard
Journal of Open-Source Software, 2019.
Evaluation of pilot jobs for Apache Spark applications on HPC clusters
Valerie Hayot-Sasson, Tristan Glatard, IEEE eScience 2019
Performance Evaluation of Big Data Processing Strategies for Neuroimaging
Valérie Hayot-Sasson, Shawn T Brown, Tristan Glatard
arXiv:1812.06492, IEEE/ACM CCGrid 2019.
A Serverless Tool for Platform Agnostic Computational Experiment Management
Gregory Kiar, Shawn T Brown, Tristan Glatard, Alan C Evans
arXiv:1809.07693, Frontiers in Neuroinformatics, vol 13, 2019.
A multi-dimensional extension of the Lightweight Temporal Compression method
Bo Li, Omid Sarbishei, Hosein Nourani, Tristan Glatard
3rd Workshop on Real-time and Stream Analytics in Big Data & Stream Data Management, in conjunction with IEEE Big Data 2018.
Data models for service failure prediction in supply-chain networks
Monika Sharma, Tristan Glatard, Éric Gélinas, Mariam Tagmouti, Brigitte Jaumard
2018 IEEE International Conference on Big Data.
Predicting computational reproducibility of data analysis pipelines in large population studies using collaborative filtering
Soudabeh Barghi, Lalet Scaria, Ali Salari, Tristan Glatard
2018 IEEE International Conference on Big Data.
Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure
Olivier Commowick, Audrey Istace, Michaël Kain, Baptiste Laurent, Florent Leray, Mathieu Simon, Roxana Améli, Jean-Christophe Ferré, Thomas Tourdias, Frédéric Cervenansky, Tristan Glatard, Jérémy Beaumont, Senan Doyle, Florence Forbes, Jesse Knight, April Khademi, Amirreza Mahbod, Chunliang Wang, Richard McKinley, Franca Wagner, John Muschelli, Elizabeth Sweeney, Eloy Roura, Xavier Lladó, Michel M. Santos, Wellington P. Santos, Abel G. Silva-Filho, Xavier Tomas-Fernandez, Hélène Urien, Isabelle Bloch, Sergi Valverde, Mariano Cabezas, Francisco Javier Vera-Olmos, Norberto Malpica, Charles Guttmann, Sandra Vukusic, Gilles Edan, Michel Dojat, Martin Styner, Simon K. Warfield, François Cotton, Christian Barillot
Scientific Reports volume 8, Article number: 13650 (2018).
Evaluation through Realistic Simulations of Data Placement Strategies for Large Heterogeneous Distributed Systems
Anchen Chai, Sorina Camarasu-Pop, Tristan Glatard, Hugues Benoit-Cattin, and Frédéric Suter
Sixteenth International Workshop for Parallel Computing on Heterogeneous Platforms (HeteroPar'2018), August 27th, 2018, Turin, Italy
Best paper from the best Euro-Par 2018 workshop award
The first MICCAI challenge on PET tumor segmentation
Mathieu Hatt, Baptiste Laurent, Anouar Ouahabi, Hadi Fayad, Shan Tan, Laquan Li, Wei Lu, Vincent Jaouen, Clovis Tauber, Jakub Czakon, Filip Drapejkowski, Witold Dyrka, Sorina Camarasu-Pop, Frédéric Cervenansky, Pascal Girard, Tristan Glatard, Michael Kain, Yao Yao, Christian Barillot, Assen Kirov, Dimitris Visvikis
Medical Image Analysis, 44 (2018) 177–195.
Boutiques: a flexible framework to integrate command-line applications in computing platforms
Tristan Glatard, Gregory Kiar, Tristan Aumentado-Armstrong, Natacha Beck, Pierre Bellec, Rémi Bernard, Axel Bonnet, Shawn T Brown, Sorina Camarasu-Pop, Frédéric Cervenansky, Samir Das, Rafael Ferreira da Silva, Guillaume Flandin, Pascal Girard, Krzysztof J Gorgolewski, Charles R G Guttmann, Valérie Hayot-Sasson, Pierre-Olivier Quirion, Pierre Rioux, Marc-Etienne Rousseau Alan C Evans
GigaScience, Volume 7, Issue 5, 1 May 2018.
Sequential algorithms to split and merge ultra-high resolution 3D images
Valérie Hayot-Sasson, Yongping Gao, Yuhong Yan, Tristan Glatard
2017 IEEE International Conference on Big Data, Boston, MA, 2017, pp. 415-424.
Software architectures to integrate workflow engines in science gateways
Tristan Glatard, Marc-Etienne Rousseau, Sorina Camarasu-Pop, Reza Adalat, Natacha Beck, Samir Das, Rafael Ferreira da Silva, Najmeh Khalili-Mahani, Vladimir Korkhov, Pierre-Olivier Quirion, Pierre Rioux, Silvia D. Olabarriaga, Pierre Bellec, Alan C. EvansFuture Generation Computer Systems, Volume 75, October 2017, Pages 239-255.
Modeling Distributed Platforms from Application Traces for Realistic File Transfer Simulation
Anchen Chai, Mohammad Bazm, Sorina Camarasu-Pop, Tristan Glatard, Hugues Benoit-Cattin, Frédéric Suter17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid), Madrid, Spain, pp. 54-63., 2017.
Standards for Best Practices in Data Analysis and Sharing in Neuroimaging using MRI
Thomas E. Nichols, Samir Das, Simon B. Eickhoff, Alan C. Evans, Tristan Glatard, Michael Hanke, Nikolaus Kriegeskorte, Michael P. Milham, Russell A. Poldrack, Jean-Baptiste Poline, Erika Proal, Bertrand Thirion, David C. Van Essen, Tonya White, B.T. Thomas YeoNature Neuroscience 20, 299-303, 2017.
Cyberinfrastructure for Open Science at the Montreal Neurological Institute
S. Das, T. Glatard, C. Rogers, J. Saigle, S. Paiva, L. MacIntyre, M. Safi-Harab, M.-E. Rousseau, J. Stirling, N. Khalili-Mahani, D. MacFarlane, P. Kostopoulos, P. Rioux, C. Madjar, X. Lecours-Boucher, S. Vanamala, R. Adalat, Z. Mohaddes, V. S. Fonov, S. Milot, I.R. Leppert, C., T. M Durcan, T. Campbell, J. Moreau, A. Dagher, D L. Collins, J. Karamchandani, A. Bar-Or, E. A Fon, R. Hoge, S. Baillet, G. Rouleau, A. C. EvansFrontiers in Neuroinformatics, 10:53, 2017
Abstracts
- Ali Salari, Lalet Scaria, Gregory Kiar, Tristan Glatard, Numerical error propagation in the HCP structural pre-processing pipelines, Annual Meeting of the Organization for Human Brain Mapping, June 2018.
- Valérie Hayot-Sasson, Yongping Gao, Lalet Scaria, Tristan Glatard, sim: An Apache Spark-based pipeline framework for neuroimaging, 2018 Annual Meeting of the Organization for Human Brain Mapping, June 2018.
- Valérie Hayot-Sasson, Lindsay B. Lewis, Alan C. Evans, Tristan Glatard, Towards easy and efficient processing of large brain imaging data, 4th Annual PERFORM Centre Research Conference, May 2017.
- Lalet Scaria; Lindsay B. Lewis; Najmeh Khalili-Mahani; Alan C. Evans; Tristan Glatard, Reproducibility of Human Connectome Project pipelines across operating systems, 4th Annual PERFORM Centre Research Conference, May 2017.
- Andrew Doyle, Pierre Rioux, Natacha Beck, Tristan Aumentado-Armstrong, Samir Das, Marc-Etienne Rousseau, Tristan Glatard, Alan Evans, CBRAIN as a computational platform for Open Science, Annual Meeting of the Organization for Human Brain Mapping, 2017.
- Satrajit Ghosh, Tibor Auer, Guillaume Flandin, Tristan Glatard, Krzysztof Gorgolewski, Yaroslav Halchenko, Dorota Jarecka, David Keator, Camille Maumet, Thomas Nichols, Smruti Padhy, Jean-Baptiste Poline, Capturing and Reusing Computation Details with the Neuroimaging Data Model (NIDM), Annual Meeting of the Organization for Human Brain Mapping, 2017.
- AmanPreet Badhwar, Pierre-Olivier Quirion, Yassine Benhajali, Tristan Glatard, Christian Dansereau, Pierre Orban, Simon Duchesne, Alan Evans, Roger Dixon, Pierre Bellec, A reproducible, standardized workflow for the generation of fMRI markers of neurodegeneration, Annual Meeting of the Organization for Human Brain Mapping, 2017.