Simon Lemieux

Louis Gagnon

Raphaelle Giguère

Alexandre Hains

Marie-Hélène Lévesque

Simon Nepveu

Lorne Rosenbloom

An Tang

Issac Yang

Nathalie Duchesne … (see 1 more)

Simon Duchesne

2022-04-13

Scientific Reports (published)

Tracking and predicting COVID-19 radiological trajectory on chest X-rays using deep learning

Daniel Gourdeau

Olivier Potvin

Patrick Archambault

Carl Chartrand‐lefebvre

Louis Dieumegarde

Reza Forghani

Alexandre Hains

David Hornstein

Huy Khiem Le

Marie‐hélène Lévesque

Diego R. Martin

Lorne Rosenbloom

An Tang

Fabrizio Vecchio

Issac Y Yang

N. Duchesne

Simon Duchesne

2022-04-04

Scientific Reports (published)

Tracking and predicting COVID-19 radiological trajectory on chest X-rays using deep learning

Daniel Gourdeau

Olivier Potvin

Patrick Archambault

Carl Chartrand-Lefebvre

Louis Dieumegarde

Reza Forghani

Alexandre Hains

David Hornstein

Marie-Hélène Lévesque

Diego Martin

Lorne Rosenbloom

An Tang

Fabrizio Vecchio

Issac Yang

Nathalie Duchesne

Simon Duchesne

2022-04-04

Scientific Reports (published)

Tracking and predicting COVID-19 radiological trajectory on chest X-rays using deep learning

Daniel Gourdeau

Olivier Potvin

Patrick Archambault

Carl Chartrand-Lefebvre

Louis Dieumegarde

Reza Forghani

Alexandre Hains

David Hornstein

Marie-Hélène Lévesque

Diego Martin

Lorne Rosenbloom

An Tang

Fabrizio Vecchio

Issac Yang

Nathalie Duchesne

Simon Duchesne

Radiological findings on chest X-ray (CXR) have shown to be essential for the proper management of COVID-19 patients as the maximum severity… (see more) over the course of the disease is closely linked to the outcome. As such, evaluation of future severity from current CXR would be highly desirable. We trained a repurposed deep learning algorithm on the CheXnet open dataset (224,316 chest X-ray images of 65,240 unique patients) to extract features that mapped to radiological labels. We collected CXRs of COVID-19-positive patients from an open-source dataset (COVID-19 image data collection) and from a multi-institutional local ICU dataset. The data was grouped into pairs of sequential CXRs and were categorized into three categories: ‘Worse’, ‘Stable’, or ‘Improved’ on the basis of radiological evolution ascertained from images and reports. Classical machine-learning algorithms were trained on the deep learning extracted features to perform immediate severity evaluation and prediction of future radiological trajectory. Receiver operating characteristic analyses and Mann-Whitney tests were performed. Deep learning predictions between “Worse” and “Improved” outcome categories and for severity stratification were significantly different for three radiological signs and one diagnostic (‘Consolidation’, ‘Lung Lesion’, ‘Pleural effusion’ and ‘Pneumonia’; all P 0.05). Features from the first CXR of each pair could correctly predict the outcome category between ‘Worse’ and ‘Improved’ cases with a 0.81 (0.74–0.83 95% CI) AUC in the open-access dataset and with a 0.66 (0.67–0.64 95% CI) AUC in the ICU dataset. Features extracted from the CXR could predict disease severity with a 52.3% accuracy in a 4-way classification. Severity evaluation trained on the COVID-19 image data collection had good out-of-distribution generalization when testing on the local dataset, with 81.6% of intubated ICU patients being classified as critically ill, and the predicted severity was correlated with the clinical outcome with a 0.639 AUC. CXR deep learning features show promise for classifying disease severity and trajectory. Once validated in studies incorporating clinical data and with larger sample sizes, this information may be considered to inform triage decisions.

2022-04-04

Scientific Reports (published)

TRACKING AND PREDICTING COVID-19 RADIOLOGICAL TRAJECTORY USING DEEP LEARNING ON CHEST X-RAYS: INITIAL ACCURACY TESTING

Simon Duchesne

Olivier Potvin

Daniel Gourdeau

Patrick Archambault

Carl Chartrand-Lefebvre

Louis Dieumegarde

Reza Forghani

Alexandre Hains

David Hornstein

Marie-Hélène Lévesque

Diego Martin

Lorne Rosenbloom

An Tang

Fabrizio Vecchio

Issac Yang

Nathalie Duchesne

2022-04-04

Scientific Reports (published)

Nicolas Boulanger-Lewandowski

Theano: A Python framework for fast computation of mathematical expressions

Rami Al-rfou'

Guillaume Alain

Amjad Almahairi

Christof Angermüller

Dzmitry Bahdanau

Nicolas Ballas

Frédéric Bastien

Justin S. Bayer

A. Belikov

A. Belopolsky

J. Bergstra

Josh Bleecher Snyder

Xavier Bouthillier

Alexandre De Brébisson

Olivier Breuleux … (see 92 more)

Paul F. Christiano

Marc-Alexandre Côté

Myriam Côté

Julien Demouth

Sander Dieleman

M'elanie Ducoffe

Samira Ebrahimi Kahou

Dumitru Erhan

Ziye Fan

Orhan Firat

Mathieu Germain

Xavier Glorot

Ian J. Goodfellow

Matthew Graham

Balázs Hidasi

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

Nicolas Boulanger-Lewandowski

Nicholas Léonard

Zhouhan Lin

J. Livezey

Cory R. Lorenz

Jeremiah L. Lowin

Qianli M. Ma

Pierre-Antoine Manzagol

R. McGibbon

Mehdi Mirza

Alberto Orlandi

Chris Pal

Razvan Pascanu

Mohammad Pezeshki

Colin Raffel

Daniel Renshaw

Matthew David Rocklin

Adriana Romero Soriano

Markus Dr. Roth

Peter Sadowski

John Salvatier

François Savard

Jan Schlüter

John D. Schulman

Gabriel Schwartz

Iulian V. Serban

Dmitriy Serdyuk

Samira Shabanian

Etienne Simon

Sigurd Spieckermann

S. Subramanyam

Jakub Sygnowski

Jeremie Tanguay

Gijs van Tulder

Joseph P. Turian

Sebastian Urban

Dustin J. Webb

M. Willson

Lijun Xue

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.

2016-05-09

ArXiv (preprint)

arxiv.org

Theano: A Python framework for fast computation of mathematical expressions

Rami Al-rfou'

Guillaume Alain

Amjad Almahairi

Christof Angermüller

Dzmitry Bahdanau

Nicolas Ballas

Frédéric Bastien

Justin S. Bayer

A. Belikov

A. Belopolsky

Josh Bleecher Snyder

Xavier Bouthillier

Alexandre De Brébisson

Olivier Breuleux … (see 92 more)

Paul F. Christiano

Marc-Alexandre Côté

Myriam Côté

Julien Demouth

Sander Dieleman

M'elanie Ducoffe

Samira Ebrahimi Kahou

Dumitru Erhan

Ziye Fan

Orhan Firat

Mathieu Germain

Xavier Glorot

Ian G Goodfellow

Matthew Graham

Balázs Hidasi

Arjun Jain

Kai Jia

Mikhail V. Korobov

Vivek Kulkarni

Alex Lamb

Pascal Lamblin

Eric Larsen

César Laurent

S. Lee

Simon-mark Lefrancois