Portrait of Pierre Luc Carrier

Pierre Luc Carrier

Senior Applied Research Scientist, Applied Machine Learning Research

Publications

Crystal-GFN: sampling materials with desirable properties and constraints
Mistal
Alex Hernandez-Garcia
Alexandra Volokhova
Alexandre AGM Duval
Divya Sharma
pierre luc carrier
Michał Koziarski
Victor Schmidt
Crystal-GFN: sampling crystals with desirable properties and constraints
Alex Hernandez-Garcia
Alexandre AGM Duval
Alexandra Volokhova
Divya Sharma
pierre luc carrier
Michał Koziarski
Victor Schmidt
Accelerating material discovery holds the potential to greatly help mitigate the climate crisis. Discovering new solid-state materials such … (see more)as electrocatalysts, super-ionic conductors or photovoltaic materials can have a crucial impact, for instance, in improving the efficiency of renewable energy production and storage. In this paper, we introduce Crystal-GFN, a generative model of crystal structures that sequentially samples structural properties of crystalline materials, namely the space group, composition and lattice parameters. This domain-inspired approach enables the flexible incorporation of physical and structural hard constraints, as well as the use of any available predictive model of a desired physicochemical property as an objective function. To design stable materials, one must target the candidates with the lowest formation energy. Here, we use as objective the formation energy per atom of a crystal structure predicted by a new proxy machine learning model trained on MatBench. The results demonstrate that Crystal-GFN is able to sample highly diverse crystals with low (median -3.1 eV/atom) predicted formation energy.
Predicting Infectiousness for Proactive Contact Tracing
Prateek Gupta
Nasim Rahaman
Martin Weiss
Tristan Deleu
Meng Qu
Victor Schmidt
Pierre-Luc St-Charles
Hannah Alsdurf
Olexa Bilaniuk
gaetan caron
pierre luc carrier
Joumana Ghosn
satya ortiz gagne
Bernhard Schölkopf … (see 3 more)
abhinav sharma
andrew williams
The COVID-19 pandemic has spread rapidly worldwide, overwhelming manual contact tracing in many countries and resulting in widespread lockdo… (see more)wns for emergency containment. Large-scale digital contact tracing (DCT) has emerged as a potential solution to resume economic and social activity while minimizing spread of the virus. Various DCT methods have been proposed, each making trade-offs between privacy, mobility restrictions, and public health. The most common approach, binary contact tracing (BCT), models infection as a binary event, informed only by an individual's test results, with corresponding binary recommendations that either all or none of the individual's contacts quarantine. BCT ignores the inherent uncertainty in contacts and the infection process, which could be used to tailor messaging to high-risk individuals, and prompt proactive testing or earlier warnings. It also does not make use of observations such as symptoms or pre-existing medical conditions, which could be used to make more accurate infectiousness predictions. In this paper, we use a recently-proposed COVID-19 epidemiological simulator to develop and test methods that can be deployed to a smartphone to locally and proactively predict an individual's infectiousness (risk of infecting others) based on their contact history and other information, while respecting strong privacy constraints. Predictions are used to provide personalized recommendations to the individual via an app, as well as to send anonymized messages to the individual's contacts, who use this information to better predict their own infectiousness, an approach we call proactive contact tracing (PCT). We find a deep-learning based PCT method which improves over BCT for equivalent average mobility, suggesting PCT could help in safe re-opening and second-wave prevention.
COVI-AgentSim: an Agent-based Model for Evaluating Methods of Digital Contact Tracing
Prateek Gupta
Martin Weiss
Nasim Rahaman
Hannah Alsdurf
abhinav sharma
Nanor Minoyan
Soren Harnois-Leblanc
Victor Schmidt
Pierre-Luc St-Charles
Tristan Deleu
andrew williams
Akshay Patel
Meng Qu
Olexa Bilaniuk
gaetan caron
pierre luc carrier
satya ortiz gagne
Marc-Andre Rousseau
Joumana Ghosn
Yang Zhang
Bernhard Schölkopf
Joanna Merckx
Diet Networks: Thin Parameters for Fat Genomics
pierre luc carrier
Akram Erraqabi
Tristan Sylvain
Alex Auvolat
Etienne Dejoie
Marc-André Legault
Marie-Pierre Dubé
Learning tasks such as those involving genomic data often poses a serious challenge: the number of input features can be orders of magnitude… (see more) larger than the number of training examples, making it difficult to avoid overfitting, even when using the known regularization techniques. We focus here on tasks in which the input is a description of the genetic variation specific to a patient, the single nucleotide polymorphisms (SNPs), yielding millions of ternary inputs. Improving the ability of deep learning to handle such datasets could have an important impact in medical research, more specifically in precision medicine, where high-dimensional data regarding a particular patient is used to make predictions of interest. Even though the amount of data for such tasks is increasing, this mismatch between the number of examples and the number of inputs remains a concern. Naive implementations of classifier neural networks involve a huge number of free parameters in their first layer (number of input features times number of hidden units): each input feature is associated with as many parameters as there are hidden units. We propose a novel neural network parametrization which considerably reduces the number of free parameters. It is based on the idea that we can first learn or provide a distributed representation for each input feature (e.g. for each position in the genome where variations are observed in data), and then learn (with another neural network called the parameter prediction network) how to map a feature's distributed representation (based on the feature's identity not its value) to the vector of parameters specific to that feature in the classifier neural network (the weights which link the value of the feature to each of the hidden units). This approach views the problem of producing the parameters associated with each feature as a multi-task learning problem. We show experimentally on a population stratification task of interest to medical studies that the proposed approach can significantly reduce both the number of parameters and the error rate of the classifier.
Diet Networks: Thin Parameters for Fat Genomics
pierre luc carrier
Akram Erraqabi
Tristan Sylvain
Alex Auvolat
Etienne Dejoie
Marc-André Legault
Marie-Pierre Dubé
Learning tasks such as those involving genomic data often poses a serious challenge: the number of input features can be orders of magnitude… (see more) larger than the number of training examples, making it difficult to avoid overfitting, even when using the known regularization techniques. We focus here on tasks in which the input is a description of the genetic variation specific to a patient, the single nucleotide polymorphisms (SNPs), yielding millions of ternary inputs. Improving the ability of deep learning to handle such datasets could have an important impact in medical research, more specifically in precision medicine, where high-dimensional data regarding a particular patient is used to make predictions of interest. Even though the amount of data for such tasks is increasing, this mismatch between the number of examples and the number of inputs remains a concern. Naive implementations of classifier neural networks involve a huge number of free parameters in their first layer (number of input features times number of hidden units): each input feature is associated with as many parameters as there are hidden units. We propose a novel neural network parametrization which considerably reduces the number of free parameters. It is based on the idea that we can first learn or provide a distributed representation for each input feature (e.g. for each position in the genome where variations are observed in data), and then learn (with another neural network called the parameter prediction network) how to map a feature's distributed representation (based on the feature's identity not its value) to the vector of parameters specific to that feature in the classifier neural network (the weights which link the value of the feature to each of the hidden units). This approach views the problem of producing the parameters associated with each feature as a multi-task learning problem. We show experimentally on a population stratification task of interest to medical studies that the proposed approach can significantly reduce both the number of parameters and the error rate of the classifier.
Diet Networks: Thin Parameters for Fat Genomic
pierre luc carrier
Akram Erraqabi
Tristan Sylvain
Alex Auvolat
Etienne Dejoie
Marc-andr'e Legault
M. Dubé
Learning tasks such as those involving genomic data often poses a serious challenge: the number of input features can be orders of magnitude… (see more) larger than the number of training examples, making it difficult to avoid overfitting, even when using the known regularization techniques. We focus here on tasks in which the input is a description of the genetic variation specific to a patient, the single nucleotide polymorphisms (SNPs), yielding millions of ternary inputs. Improving the ability of deep learning to handle such datasets could have an important impact in precision medicine, where high-dimensional data regarding a particular patient is used to make predictions of interest. Even though the amount of data for such tasks is increasing, this mismatch between the number of examples and the number of inputs remains a concern. Naive implementations of classifier neural networks involve a huge number of free parameters in their first layer: each input feature is associated with as many parameters as there are hidden units. We propose a novel neural network parametrization which considerably reduces the number of free parameters. It is based on the idea that we can first learn or provide a distributed representation for each input feature (e.g. for each position in the genome where variations are observed), and then learn (with another neural network called the parameter prediction network) how to map a feature's distributed representation to the vector of parameters specific to that feature in the classifier neural network (the weights which link the value of the feature to each of the hidden units). We show experimentally on a population stratification task of interest to medical studies that the proposed approach can significantly reduce both the number of parameters and the error rate of the classifier.
Theano: A Python framework for fast computation of mathematical expressions
Rami Al-rfou'
Guillaume Alain
Amjad Almahairi
Christof Angermüller
Nicolas Ballas
Frédéric Bastien
Justin S. Bayer
A. Belikov
A. Belopolsky
Arnaud Bergeron
J. Bergstra
Valentin Bisson
Josh Bleecher Snyder
Nicolas Bouchard
Nicolas Boulanger-Lewandowski
Xavier Bouthillier
Alexandre De Brébisson
Olivier Breuleux … (see 92 more)
pierre luc carrier
Kyunghyun Cho
Jan Chorowski
Paul F. Christiano
Tim Cooijmans
Marc-Alexandre Côté
Myriam Côté
Yann Dauphin
Olivier Delalleau
Julien Demouth
Guillaume Desjardins
Sander Dieleman
Laurent Dinh
M'elanie Ducoffe
Vincent Dumoulin
Dumitru Erhan
Ziye Fan
Orhan Firat
Mathieu Germain
Xavier Glorot
Ian J. Goodfellow
Matthew Graham
Caglar Gulcehre
Philippe Hamel
Iban Harlouchet
Jean-philippe Heng
Balázs Hidasi
Sina Honari
Arjun Jain
S'ebastien Jean
Kai Jia
Mikhail V. Korobov
Vivek Kulkarni
Alex Lamb
Pascal Lamblin
Eric P. Larsen
César Laurent
S. Lee
Simon-mark Lefrancois
Simon Lemieux
Nicholas Léonard
Zhouhan Lin
J. Livezey
Cory R. Lorenz
Jeremiah L. Lowin
Qianli M. Ma
Pierre-Antoine Manzagol
Olivier Mastropietro
R. McGibbon
Roland Memisevic
Bart van Merriënboer
Vincent Michalski
Mehdi Mirza
Alberto Orlandi
Razvan Pascanu
Mohammad Pezeshki
Colin Raffel
Daniel Renshaw
Matthew David Rocklin
Markus Dr. Roth
Peter Sadowski
John Salvatier
Francois Savard
Jan Schlüter
John D. Schulman
Gabriel Schwartz
Iulian V. Serban
Dmitriy Serdyuk
Samira Shabanian
Etienne Simon
Sigurd Spieckermann
S. Subramanyam
Jakub Sygnowski
Jérémie Tanguay
Gijs van Tulder
Joseph P. Turian
Sebastian Urban
Francesco Visin
Harm de Vries
David Warde-Farley
Dustin J. Webb
M. Willson
Kelvin Xu
Lijun Xue
Li Yao
Saizheng Zhang
Ying Zhang
Theano is a Python library that allows to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficie… (see more)ntly. Since its introduction, it has been one of the most used CPU and GPU mathematical compilers - especially in the machine learning community - and has shown steady performance improvements. Theano is being actively and continuously developed since 2008, multiple frameworks have been built on top of it and it has been used to produce many state-of-the-art machine learning models. The present article is structured as follows. Section I provides an overview of the Theano software and its community. Section II presents the principal features of Theano and how to use them, and compares them with other similar projects. Section III focuses on recently-introduced functionalities and improvements. Section IV compares the performance of Theano against Torch7 and TensorFlow on several machine learning models. Section V discusses current limitations of Theano and potential ways of improving it.
Theano: A Python framework for fast computation of mathematical expressions
Rami Al-rfou'
Guillaume Alain
Amjad Almahairi
Christof Angermüller
Nicolas Ballas
Frédéric Bastien
Justin S. Bayer
A. Belikov
A. Belopolsky
Arnaud Bergeron
James Bergstra
Valentin Bisson
Josh Bleecher Snyder
Nicolas Bouchard
Nicolas Boulanger-Lewandowski
Xavier Bouthillier
Alexandre De Brébisson
Olivier Breuleux … (see 92 more)
pierre luc carrier
Kyunghyun Cho
Jan Chorowski
Paul F. Christiano
Tim Cooijmans
Marc-Alexandre Côté
Myriam Côté
Yann Dauphin
Olivier Delalleau
Julien Demouth
Guillaume Desjardins
Sander Dieleman
Laurent Dinh
M'elanie Ducoffe
Vincent Dumoulin
Dumitru Erhan
Ziye Fan
Orhan Firat
Mathieu Germain
Xavier Glorot
Ian G Goodfellow
Matthew Graham
Caglar Gulcehre
Philippe Hamel
Iban Harlouchet
Jean-philippe Heng
Balázs Hidasi
Sina Honari
Arjun Jain
Sébastien Jean
Kai Jia
Mikhail V. Korobov
Vivek Kulkarni
Alex Lamb
Pascal Lamblin
Eric Larsen
César Laurent
S. Lee
Simon-mark Lefrancois
Simon Lemieux
Nicholas Léonard
Zhouhan Lin
J. Livezey
Cory R. Lorenz
Jeremiah L. Lowin
Qianli M. Ma
Pierre-Antoine Manzagol
Olivier Mastropietro
R. McGibbon
Roland Memisevic
Bart van Merriënboer
Vincent Michalski
Mehdi Mirza
Alberto Orlandi
Razvan Pascanu
Mohammad Pezeshki
Colin Raffel
Daniel Renshaw
Matthew David Rocklin
Markus Dr. Roth
Peter Sadowski
John Salvatier
Francois Savard
Jan Schlüter
John D. Schulman
Gabriel Schwartz
Iulian V. Serban
Dmitriy Serdyuk
Samira Shabanian
Etienne Simon
Sigurd Spieckermann
S. Subramanyam
Jakub Sygnowski
Jérémie Tanguay
Gijs van Tulder
Joseph P. Turian
Sebastian Urban
Francesco Visin
Harm de Vries
David Warde-Farley
Dustin J. Webb
M. Willson
Kelvin Xu
Lijun Xue
Li Yao
Saizheng Zhang
Ying Zhang
Theano is a Python library that allows to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficie… (see more)ntly. Since its introduction, it has been one of the most used CPU and GPU mathematical compilers - especially in the machine learning community - and has shown steady performance improvements. Theano is being actively and continuously developed since 2008, multiple frameworks have been built on top of it and it has been used to produce many state-of-the-art machine learning models. The present article is structured as follows. Section I provides an overview of the Theano software and its community. Section II presents the principal features of Theano and how to use them, and compares them with other similar projects. Section III focuses on recently-introduced functionalities and improvements. Section IV compares the performance of Theano against Torch7 and TensorFlow on several machine learning models. Section V discusses current limitations of Theano and potential ways of improving it.