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<!DOCTYPE html>
<html lang="en">
<head>
<title>News</title>
</head>
<body>
<div id="header"></div><br/>
<div class="container">
<!-- your content starts here-->
<div class="row tall-row">
<div class="col-lg-12">
<h1>News</h1>
<hr>
</div>
</div>
<div class="row">
<div class="col-md-12">
<h3>New pre-print</h3>
<div class="date">21 May 2019</div>
<p>
<a href="https://arxiv.org/abs/1905.08770">High-Resolution Road Vehicle Collision Prediction for the City of Montreal</a>.</p>
</div></div>
<div class="row">
<div class="col-md-12">
<h3>Thesis defense</h3>
<div class="date">11 Apr 2019</div>
</div></div>
<div class="row">
<div class="col-md-12">
<h3>New pre-print</h3>
<div class="date">8 Apr 2019</div>
<p>
<a href="https://arxiv.org/abs/1904.02666">Subject Cross Validation in Human Activity Recognition</a>.</p>
</div></div>
<div class="row">
<div class="col-md-12">
<h3>New pre-print</h3>
<div class="date">16 Dec 2018</div>
<p>
<a href="https://arxiv.org/pdf/1812.06492">Performance Evaluation of Big Data Processing Strategies for Neuroimaging</a>.</p>
</div></div>
<div class="row">
<div class="col-md-12">
<h3>Soudabeh Barghi defended her Master thesis</h3>
<div class="date">19 Nov 2018</div>
"Predicting Computational Reproducibility of Data Analysis Pipelines in Large Population Studies Using Collaborative Filtering".
</div></div>
<div class="row">
<div class="col-md-12">
<h3>Monika Sharma defended her Master thesis</h3>
<div class="date">2 Nov 2018</div>
"Data and Simulation Models for Route Optimization in Vehicle Routing Problem".
</div></div>
<div class="row">
<div class="col-md-12">
<h3>Lalet Scaria defended his Master thesis</h3>
<div class="date">07 June 2018</div>
<h4>A Framework to Evaluate Pipeline Reproducibility across Operating Systems</h4>
<p>The lack of computational reproducibility threatens data science
in several domains. In particular, it has been shown that different
operating systems can lead to different analysis results. This
study aims to identify and quantify the effect of the operating
system on neuroimaging analysis pipelines. We developed a framework
to evaluate the reproducibility of these neuroimaging pipelines
across operating systems. The framework essentially leverages
software containerization and system-call interception to record
results provenance without having to instrument the pipelines. A
tool (Repro-tools) was developed to compare results obtained in
different conditions. We used our framework to evaluate the effect
of the operating system on results produced by pipelines from the
Human Connectome Project (HCP), a large open- data initiative to
study the human brain. In particular, we focused on pre-processing
pipelines for anatomical and functional data, namely PreFreeSurfer,
FreeSurfer, Post- FreeSurfer and fMRIVolume. We used data from 5
subjects released by the HCP. Re- sults highlight substantial
differences in the output of the HCP pipelines obtained in two
versions of Linux (CentOS6 and CentOS7). Inter-OS differences
corresponding to normalized root mean square errors of up to 0.27
were observed, which corresponds to visually important differences.
We provide visualizations of the most important differences for
various pipeline steps. No meaningful inter-run differences were
observed, which shows that the inter-OS differences do not
originate from the use of pseudo- random numbers or silent crashes
of the pipelines. We hypothesize that the observed inter-OS
differences come from numerical instabilities in the pipelines,
triggered by rounding and truncation differences that originate in
the update of mathematical libraries in different systems. An
apparent solution to this issue is to freeze the execution
environment using, for instance, software containers. However, this
would only mask instabilities while they should ultimately be
corrected in the pipelines.</p>
</div>
</div>
<div class="row">
<div class="col-md-12">
<h3>Boutiques paper <img src="./images/boutiques.png" alt="boutiques logo"/></h3>
<div class="date">06 Jun 2018</div>
Read the <a href="https://academic.oup.com/gigascience/article/7/5/giy016/4951979">Boutiques paper</a> just published in GigaScience!
</div>
</div>
<div class="row">
<div class="col-md-12">
<h3>Boutiques release <img src="./images/boutiques.png" alt="boutiques logo"/></h3>
<div class="date">30 Mar 2018</div>
New <a href="http://boutiques.github.io">Boutiques<a> release (0.5.7), now supports pipeline tests.
</div>
</div>
<div class="row">
<div class="col-md-12">
<h3>Read and comment on our abstracts accepted to <a href="https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3821">HBM</a> 2018</h3>
<div class="date">2 Mar 2018</div>
<ul>
<li><a href="https://docs.google.com/document/d/1ILaoahMegNjFz38nHE3TTFjpdyK3mfHyZtV4R6xVwuU/edit#heading=h.vu2plg8vn0bh">Numerical error propagation in the HCP structural pre-processing pipelines</a></li>
<li><a href="https://docs.google.com/document/d/1NtaqkKb3fBjtcmULuU3wi-cM0c_HRdvydoTH8qMCRH8/edit#heading=h.6dtpemobk43v">Numerical stability of motion estimation in fMRI time series</a> (with P. Bellec)</li>
<li><a href="https://docs.google.com/document/d/1ywPXGDlZ1OBt6s15eQ97j1RMx6WfH1CK_sZsRaYgriE/edit">sim: An Apache Spark-based pipeline framework for neuroimaging</a></li>
</ul>
</div>
</div>
<div class="row">
<div class="col-md-12">
<h3>Yongping Gao will defend his Master thesis on December 12 at 10am in EV 3.309</h3>
<div class="date">28 Nov 2017</div>
<h4>A New Algorithm to Split and Merge Ultra-High Resolution 3D Images</h4>
<p>Splitting and merging ultra-high resolution 3D images is a requirement for parallel or distributed
processing operations. Naive algorithms to split and merge 3D blocks from ultra-high resolution images
perform very poorly, due to the number of seeks required to reconstruct spatially-adjacent blocks from
linear data organizations on disk. The current solution to deal with this problem is to use file formats
that preserve spatial proximity on disk, but this comes with additional complexity. We introduce a new
algorithm called Multiple reads/writes to split and merge ultra-high resolution 3D images efficiently
from simple file formats. Multiple reads/writes write contiguously in the reconstructed image, which
leads to substantial performance improvements compared to existing algorithms. We parallelize our
algorithm using multi-threading, which further improves the performance for data stored on a Hadoop
cluster. We also show that on-the-fly lossless compression with the lz4 algorithm reduces the split and
merge time further. </p>
</div>
</div>
<div class="row">
<div class="col-md-12">
<a href="https://arxiv.org/abs/1711.09713"> <h3>New preprint: Boutiques: a flexible framework for automated application integration in computing platforms</h3></a>
<div class="date">7 Nov 2017</div>
<p>We present Boutiques, a system to automatically publish, integrate and execute applications across computational platforms. Boutiques applications are installed through
software containers described in a rich and flexible JSON language. A set of core tools facilitate the construction, validation, import, execution, and publishing of applications.
Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect
Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster
Open Science.</p>
</div>
</div>
<div class="row">
<div class="col-md-12">
<a href="https://docs.google.com/presentation/d/1tUeopkiGX3Czd_x_2MG3_WeNilXsYSFy5E28jM0w7nE/edit#slide=id.g16edeca75c_0_89"> <h3>Presentation at BigBrain workshop</h3></a>
<div class="date">3 Nov 2017</div>
<p>See complete workshop schedule <a href="http://mcin-cnim.ca/bigbrain-workshop-2017-montreal-schedule/">here</a>.</p>
</div>
</div>
<div class="row">
<div class="col-md-12">
<a href="http://neuroscience.uchicago.edu/hackathon/"><h3>Neurostorm Hackathon</h3></a>
<div class="date">24-27 Oct 2017</div>
<p>Valérie Hayot participated to the Neurostorm hackathon in Woodshole.</p>
</div>
</div>
<div class="row">
<div class="col-md-12">
<a href="https://docs.wixstatic.com/ugd/004e4a_c24ac7b3c0954b3f814f356e3881f923.pdf"> <h3>New paper accepted!</h3></a>
<div class="date">12 Oct 2017</div>
<p>To be presented at IEEE Big Data
2017: <a href="https://docs.wixstatic.com/ugd/004e4a_c24ac7b3c0954b3f814f356e3881f923.pdf">Sequential
algorithms to split and merge ultra-high resolution 3D
images</a>, Valérie Hayot-Sasson, Yongping Gao,
Yuhong Yan, Tristan Glatard.</p>
</div>
</div>
<div class="row">
<div class="col-md-12">
<a href="https://docs.wixstatic.com/ugd/004e4a_c24ac7b3c0954b3f814f356e3881f923.pdf"> <h3>Colloquium:
Towards a Sustainable Digital Society: From Clouds
to Connected Objects</h3></a>
<div class="date">06 Oct 2017</div>
<p>Towards a Sustainable Digital Society: From Clouds to Connected Objects</p>
<p>Organized at Concordia as part of the
<a href="http://www.centrejacquescartier.com/les-entretiens-jacques-cartier/">Entretiens
Jacques Cartier</a> event. The aim of the
symposium is to allow interactions between
researchers working on different perspectivesin
communication networks, terminal equipment,
connected object and data centers, but sharing a
common concern to design the digital society of
tomorrow in a development perspective Sustainable
development.</p>
<p><a href="https://www.weezevent.com/vers-une-societe-numerique-a-developpement-durable">Register here</p></a>
</div>
</div>
<div class="row">
<div class="col-md-12">
<a href="https://neurohackweek.github.io/nhw2017/"> <h3>Neurohackweek</h3></a>
<div class="date">September 2017</div>
<p>Valérie Hayot-Sasson and Lalet Scaria
have been selected to participate
to Neurohackweek
2017, congratulations!</p>
</div>
</div>
<div class="row">
<div class="col-md-12">
<a href="http://reproducibility.stanford.edu/2nd-annual-crn-coding-sprint-open-call-for-applications/"> <h3>Stanford
CRN coding sprint</h3></a>
<div class="date">28 Aug 2017</div>
<p>Lalet Scaria, Greg Kiar, Valérie
Hayot-Sasson and Tristan Glatard participate to
the Coding Sprint organized by
the Stanford
Center for Reproducible Neuroscience.</p>
</div>
</div>
<div class="row">
<div class="col-md-12">
<a href="http://neuroinformatics2017.org"> <h3>Neuroinformatics 2017</h3></a>
<div class="date">20-21 Aug 2017</div>
<p>Lalet Scaria presented an abstract
at Neuroinformatics
2017: Reproducibility of Human Connectome Project pipelines across
operating systems.</p>
</div>
</div>
<div class="row">
<div class="col-md-12">
<a href="https://github.com/big-data-lab-team/paper-sequential-split-merge/releases/download/0.1/paper.pdf"> <h3>New
preprint</h3></a>
<div class="date">20 Aug 2017</div>
<p>New pre-print
available: Sequential
algorithms to split and merge ultra-high
resolution 3D images.</p>
</div>
</div>
</div>
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