Health and social sciences

Health and social sciences

Electronic health records

Electronic health records are typically data collected by the care system. As a result, they cover a large number of individuals over a long period of time. However, they are observational data: interventions, such as drug prescription, have not been done according to a systematic experimental plan. As such, they raise many causal inference challenges (which we study in link with machine learning). In addition, they are complex relational data, structured for clinical practices or accounting, and not research. Analyzing them faces challenges of missing values, as well as statistical modeling across multiple sources of relational data with varying representations. The databases are full of non normalized snippets of text, for which we develop dedicated NLP approaches.

We apply our statistical learning research on large electronic health records (in partnership with APHP, HAS, and on the French healthcare system: SNDS). The related questions are that of personalized medicine (individualized prediction models) as well as treatment efficacy, for instance to answer public-health questions.

Epidemiological reasoning

From a health-research perspective, the questions are typical of epidemiology and draw from the corresponding line of thoughts: all kind of biases must be accounted for, such as a sampling bias between the study population and the target. Where we innovate is that we strive to replace the traditional parametric models with non-parametric estimates built from machine-learning models.

AP-HP’s “entrepot de données de santé”

We have a tight collaboration with AP-HP, the Paris hospitals, that unite 39 different hospital in a consistent database covering 10 million patients a year. This collaboration was born at the beginning of the COVID crisis, where we used the corresponding database (known as the EDS, “entrepôt de données de santé”) to follow the unfolding of a new disease, building on the fly prognosis models and evaluating treatment efficiency.

Educational data mining, learning analytics

Learning platforms collect a large amount of data that can be used to personalize learning. Educational data mining is about developing mathematical models of student learning (knowledge tracing, spaced repetition systems), for example students attempting programming exercises. Learning analytics is focused on representing information for teacher decision-making (e.g. dashboards in MOOCs).

Related publications

Medical applications

Publications HAL titre medicine de gael varoquaux

titre
Prediction, Not Association, Paves the Road to Precision Medicine
auteur
Danilo Bzdok, Gael Varoquaux, Ewout Steyerberg
article
JAMA Psychiatry, Chicago, IL : American Medical Association, [2013]-, 2021, 78 (2), pp.127. ⟨10.1001/jamapsychiatry.2020.2549⟩
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Education-related

Publications HAL titre student de jill-jenn vie

titre
DAS3H: Modeling Student Learning and Forgetting for Optimally Scheduling Distributed Practice of Skills
auteur
Benoît Choffin, Fabrice Popineau, yolaine Bourda, Jill-Jênn Vie
article
JDSE 2019 – Paris-Saclay Junior Conference on Data Science and Engineering, Sep 2019, Gif-sur-Yvette, France
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https://hal.archives-ouvertes.fr/hal-03427048/file/DAS3H_JDSE_2019.pdf BibTex

COVID-related

Publications HAL titre covid de gael varoquaux

titre
Evolving phenotypes of non-hospitalized patients that indicate long COVID
auteur
Hossein Estiri, Zachary Strasser, Gabriel Brat, yevgeniy Semenov, Chirag Patel, Shawn Murphy, James Aaron, Giuseppe Agapito, Adem Albayrak, Mario Alessiani, Danilo Amendola, Li Anthony, Bruce Aronow, Fatima Ashraf, Andrew Atz, Paul Avillach, James Balshi, Brett Beaulieu-Jones, Douglas Bell, Antonio Bellasi, Riccardo Bellazzi, Vincent Benoit, Michele Beraghi, José Luis Bernal Sobrino, Mélodie Bernaux, Romain Bey, Alvar Blanco Martínez, Martin Boeker, Clara-Lea Bonzel, John Booth, Silvano Bosari, Florence Bourgeois, Robert Bradford, Stéphane Bréant, Nicholas Brown, William Bryant, Mauro Bucalo, Anita Burgun, Tianxi Cai, Mario Cannataro, Aldo Carmona, Charlotte Caucheteux, Julien Champ, Jin Chen, Krista Chen, Luca Chiovato, Lorenzo Chiudinelli, Kelly Cho, James Cimino, Tiago Colicchio, Sylvie Cormont, Sébastien Cossin, Jean Craig, Juan Luis Cruz Bermúdez, Jaime Cruz Rojo, Arianna Dagliati, Mohamad Daniar, Christel Daniel, Anahita Davoudi, Batsal Devkota, Julien Dubiel, Loic Esteve, Shirley Fan, Robert Follett, Paula Gaiolla, Thomas Ganslandt, Noelia García Barrio, Lana Garmire, Nils Gehlenborg, Alon Geva, Tobias Gradinger, Alexandre Gramfort, Romain Griffier, Nicolas Griffon, Olivier Grisel, Alba Gutiérrez-Sacristán, David Hanauer, Christian Haverkamp, Bing He, Darren Henderson, Martin Hilka, John Holmes, Chuan Hong, Petar Horki, Kenneth Huling, Meghan Hutch, Richard Issitt, Anne Sophie Jannot, Vianney Jouhet, Mark Keller, Katie Kirchoff, Jeffrey Klann, Isaac Kohane, Ian Krantz, Detlef Kraska, Ashok Krishnamurthy, Sehi L’yi, Trang Le, Judith Leblanc, Andressa Leite, Guillaume Lemaitre, Leslie Lenert, Damien Leprovost, Molei Liu, Ne Hooi Will Loh, Sara Lozano-Zahonero, yuan Luo, Kristine Lynch, Sadiqa Mahmood, Sarah Maidlow, Alberto Malovini, Kenneth Mandl, Chengsheng Mao, Anupama Maram, Patricia Martel, Aaron Masino, Maria Mazzitelli, Arthur Mensch, Marianna Milano, Marcos Minicucci, Bertrand Moal, Jason Moore, Cinta Moraleda, Jeffrey Morris, Michele Morris, Karyn Moshal, Sajad Mousavi, Danielle Mowery, Douglas Murad, Thomas Naughton, Antoine Neuraz, Kee yuan Ngiam, James Norman, Jihad Obeid, Marina Okoshi, Karen Olson, Gilbert Omenn, Nina Orlova, Brian Ostasiewski, Nathan Palmer, Nicolas Paris, Lav Patel, Miguel Pedrera Jimenez, Emily Pfaff, Danielle Pillion, Hans Prokosch, Robson Prudente, Víctor Quirós González, Rachel Ramoni, Maryna Raskin, Siegbert Rieg, Gustavo Roig Domínguez, Pablo Rojo, Carlos Sáez, Elisa Salamanca, Malarkodi Samayamuthu, Arnaud Sandrin, Janaina Santos, Maria Savino, Emily Schriver, Petra Schubert, Juergen Schuettler, Luigia Scudeller, Neil Sebire, Pablo Serrano Balazote, Patricia Serre, Arnaud Serret-Larmande, Zahra Shakeri, Domenick Silvio, Piotr Sliz, Jiyeon Son, Charles Sonday, Andrew South, Anastasia Spiridou, Amelia Tan, Bryce Tan, Byorn Tan, Suzana Tanni, Deanne Taylor, Ana Terriza Torres, Valentina Tibollo, Patric Tippmann, Carlo Torti, Enrico Trecarichi, yi-Ju Tseng, Andrew Vallejos, Gael Varoquaux, Margaret Vella, Guillaume Verdy, Jill-Jênn Vie, Shyam Visweswaran, Michele Vitacca, Kavishwar Wagholikar, Lemuel Waitman, Xuan Wang, Demian Wassermann, Griffin Weber, Zongqi Xia, Nadir yehya, William yuan, Alberto Zambelli, Harrison Zhang, Daniel Zoeller, Chiara Zucco
article
BMC Medicine, BioMed Central, 2021, 19 (1), pp.249. ⟨10.1186/s12916-021-02115-0⟩
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titre
Multinational characterization of neurological phenotypes in patients hospitalized with COVID-19
auteur
Trang Le, Alba Gutiérrez-Sacristán, Jiyeon Son, Chuan Hong, Andrew South, Brett Beaulieu-Jones, Ne Hooi Will Loh, yuan Luo, Michele Morris, Kee yuan Ngiam, Lav Patel, Malarkodi Samayamuthu, Emily Schriver, Amelia Tan, Jason Moore, Tianxi Cai, Gilbert Omenn, Paul Avillach, Isaac Kohane, Shyam Visweswaran, Danielle Mowery, Zongqi Xia, James Aaron, Giuseppe Agapito, Adem Albayrak, Mario Alessiani, Danilo Amendola, François Angoulvant, Li Anthony, Bruce Aronow, Andrew Atz, James Balshi, Douglas Bell, Antonio Bellasi, Riccardo Bellazzi, Vincent Benoit, Michele Beraghi, José Luis Bernal Sobrino, Mélodie Bernaux, Romain Bey, Alvar Blanco Martínez, Martin Boeker, Clara-Lea Bonzel, John Booth, Silvano Bosari, Florence Bourgeois, Robert Bradford, Gabriel Brat, Stéphane Bréant, Nicholas Brown, William Bryant, Mauro Bucalo, Anita Burgun, Mario Cannataro, Aldo Carmona, Charlotte Caucheteux, Julien Champ, Krista Chen, Jin Chen, Luca Chiovato, Lorenzo Chiudinelli, James Cimino, Tiago Colicchio, Sylvie Cormont, Sébastien Cossin, Jean Craig, Juan Luis Cruz Bermúdez, Jaime Cruz Rojo, Arianna Dagliati, Mohamad Daniar, Christel Daniel, Anahita Davoudi, Batsal Devkota, Julien Dubiel, Loic Esteve, Shirley Fan, Robert Follett, Paula Gaiolla, Thomas Ganslandt, Noelia García Barrio, Lana Garmire, Nils Gehlenborg, Alon Geva, Tobias Gradinger, Alexandre Gramfort, Romain Griffier, Nicolas Griffon, Olivier Grisel, David Hanauer, Christian Haverkamp, Bing He, Darren Henderson, Martin Hilka, John Holmes, Petar Horki, Kenneth Huling, Meghan Hutch, Richard Issitt, Anne Sophie Jannot, Vianney Jouhet, Ramakanth Kavuluru, Mark Keller, Katie Kirchoff, Jeffrey Klann, Ian Krantz, Detlef Kraska, Ashok Krishnamurthy, Sehi L’yi, Judith Leblanc, Andressa Leite, Guillaume Lemaitre, Leslie Lenert, Damien Leprovost, Molei Liu, Sarah Lozano-Zahonero, Kristine Lynch, Sadiqa Mahmood, Sarah Maidlow, Adeline Makoudjou Tchendjou, Alberto Malovini, Kenneth Mandl, Chengsheng Mao, Anupama Maram, Patricia Martel, Aaron Masino, Michael Matheny, Thomas Maulhardt, Maria Mazzitelli, Michael Mcduffie, Arthur Mensch, Fatima Ashraf, Marianna Milano, Marcos Minicucci, Bertrand Moal, Cinta Moraleda, Jeffrey Morris, Karyn Moshal, Sajad Mousavi, Douglas Murad, Shawn Murphy, Thomas Naughton, Antoine Neuraz, James Norman, Jihad Obeid, Marina Okoshi, Karen Olson, Nina Orlova, Brian Ostasiewski, Nathan Palmer, Nicolas Paris, Miguel Pedrera Jimenez, Emily Pfaff, Danielle Pillion, Hans Prokosch, Robson Prudente, Víctor Quirós González, Rachel Ramoni, Maryna Raskin, Siegbert Rieg, Gustavo Roig Domínguez, Pablo Rojo, Carlos Sáez, Elisa Salamanca, Arnaud Sandrin, Janaina Santos, Maria Savino, Juergen Schuettler, Luigia Scudeller, Neil Sebire, Pablo Serrano Balazote, Patricia Serre, Arnaud Serret-Larmande, Zahra Shakeri, Domenick Silvio, Piotr Sliz, Charles Sonday, Anastasia Spiridou, Bryce Tan, Byorn Tan, Suzana Tanni, Deanne Taylor, Ana Terriza-Torres, Valentina Tibollo, Patric Tippmann, Carlo Torti, Enrico Trecarichi, yi-Ju Tseng, Andrew Vallejos, Gael Varoquaux, Margaret Vella, Jill-Jênn Vie, Michele Vitacca, Kavishwar Wagholikar, Lemuel Waitman, Demian Wassermann, Griffin Weber, yuan William, Nadir yehya, Alberto Zambelli, Harrison Zhang, Daniela Zoeller, Chiara Zucco
article
Scientific Reports, Nature Publishing Group, 2021, 11 (1), pp.20238. ⟨10.1038/s41598-021-99481-9⟩
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titre
International Analysis of Electronic Health Records of Children and Youth Hospitalized With COVID-19 Infection in 6 Countries
auteur
Florence Bourgeois, Alba Gutiérrez-Sacristán, Mark Keller, Molei Liu, Chuan Hong, Clara-Lea Bonzel, Amelia Tan, Bruce Aronow, Martin Boeker, John Booth, Jaime Cruz Rojo, Batsal Devkota, Noelia García Barrio, Nils Gehlenborg, Alon Geva, David Hanauer, Meghan Hutch, Richard Issitt, Jeffrey Klann, yuan Luo, Kenneth Mandl, Chengsheng Mao, Bertrand Moal, Karyn Moshal, Shawn Murphy, Antoine Neuraz, Kee yuan Ngiam, Gilbert Omenn, Lav Patel, Miguel Pedrera Jiménez, Neil Sebire, Pablo Serrano Balazote, Arnaud Serret-Larmande, Andrew South, Anastasia Spiridou, Deanne Taylor, Patric Tippmann, Shyam Visweswaran, Griffin Weber, Isaac Kohane, Tianxi Cai, Paul Avillach, Jaime Cruz-Rojo, Noelia García-Barrio, Miguel Pedrera-Jiménez, Pablo Serrano-Balazote, James Aaron, Giuseppe Agapito, Adem Albayrak, Mario Alessiani, Danilo Amendola, François Angoulvant, Li Llj Anthony, Andrew Atz, James Balshi, Brett Beaulieu-Jones, Douglas Bell, Antonio Bellasi, Riccardo Bellazzi, Vincent Benoit, Michele Beraghi, José Luis Bernal Sobrino, Mélodie Bernaux, Romain Bey, Alvar Blanco Martínez, Silvano Bosari, Robert Bradford, Gabriel Brat, Stéphane Bréant, Nicholas Brown, William Bryant, Mauro Bucalo, Anita Burgun, Mario Cannataro, Aldo Carmona, Charlotte Caucheteux, Julien Champ, Krista Chen, Jin Chen, Luca Chiovato, Lorenzo Chiudinelli, James Cimino, Tiago Colicchio, Sylvie Cormont, Sébastien Cossin, Jean Craig, Juan Luis Cruz Bermúdez, Arianna Dagliati, Mohamad Daniar, Christel Daniel, Anahita Davoudi, Julien Dubiel, Scott Duvall, Loic Esteve, Shirley Fan, Robert Follett, Paula Sa Gaiolla, Thomas Ganslandt, Lana Garmire, Tobias Gradinger, Alexandre Gramfort, Romain Griffier, Nicolas Griffon, Olivier Grisel, Christian Haverkamp, Bing He, Darren Henderson, Martin Hilka, John Holmes, Petar Horki, Kenneth Huling, Anne Sophie Jannot, Vianney Jouhet, Ramakanth Kavuluru, Katie Kirchoff, Ian Krantz, Detlef Kraska, Ashok Krishnamurthy, Sehi L’yi, Trang Le, Judith Leblanc, Andressa Rr Leite, Guillaume Lemaitre, Leslie Lenert, Damien Leprovost, Ne Hooi Will Loh, Kristine Lynch, Sadiqa Mahmood, Sarah Maidlow, Alberto Malovini, Anupama Maram, Patricia Martel, Aaron Masino, Michael Matheny, Thomas Maulhardt, Maria Mazzitelli, Michael Mcduffie, Arthur Mensch, Marianna Milano, Marcos Minicucci, Jason Moore, Cinta Moraleda, Jeffrey Morris, Michele Morris, Sajad Mousavi, Danielle Mowery, Douglas Murad, Thomas Naughton, James Norman, Jihad Obeid, Marina Okoshi, Karen Olson, Nina Orlova, Brian Ostasiewski, Nathan Palmer, Nicolas Paris, Emily Pfaff, Danielle Pillion, Hans Prokosch, Robson Prudente, Víctor Quirós González, Rachel Ramoni, Maryna Raskin, Siegbert Rieg, Gustavo Roig Domínguez, Pablo Rojo, Carlos Sáez, Elisa Salamanca, Malarkodi Samayamuthu, Arnaud Sandrin, Janaina Cc Santos, Maria Savino, Emily Schriver, Juergen Schuettler, Luigia Scudeller, Patricia Serre, Domenick Silvio, Piotr Sliz, Jiyeon Son, Charles Sonday, Bryce Wq Tan, Byorn Wl Tan, Suzana Tanni, Ana Terriza Torres, Valentina Tibollo, Carlo Torti, Enrico Trecarichi, yi-Ju Tseng, Andrew Vallejos, Gael Varoquaux, Jill-Jênn Vie, Michele Vitacca, Kavishwar Wagholikar, Lemuel Waitman, Demian Wassermann, yuan William, Zongqi Xia, Nadir yehya, Alberto Zambelli, Harrison Zhang, Chiara Zucco
article
JAMA Network Open, American Medical Association, 2021, 4 (6), pp.e2112596. ⟨10.1001/jamanetworkopen.2021.12596⟩
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titre
International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium
auteur
Gabriel A. Brat, Griffin M. Weber, Nils Gehlenborg, Paul Avillach, Nathan P. Palmer, Luca Chiovato, James Cimino, Brett K. Beaulieu-Jones, Sehi L’yi, Mark S. Keller, Douglas S. Bell, Robert W. Follett, Lav P. Patel, Anne Sophie Jannot, Lemuel R. Waitman, Gilbert Omenn, Alberto Malovini, Jason H. Moore, Valentina Tibollo, Shawn N Murphy, Riccardo Bellazzi, David A Hanauer, Arnaud Serret-Larmande, Alba Gutierrez-Sacristan, John J Holmes, Douglas Bell, Kenneth D. Mandl, Jeffrey G Klann, Douglas A Murad, Luigia Scudeller, Mauro Bucalo, Katie Kirchoff, Jean Craig, Jihad Obeid, Vianney Jouhet, Romain Griffier, Sébastien Cossin, Bertrand Moal, Antonio Bellasi, Hans U Prokosch, Detlef Kraska, Piotr Sliz, Amelia L.M. Tan, Kee yuan Ngiam, Alberto Zambelli, Danielle L Mowery, Emily Schiver, Batsal Devkota, Robert Bradford, Mohamad Daniar, Christel Daniel, Vincent Benoit, Romain Bey, Nicolas Paris, Patricia Serre, Nina Orlova, Julien Dubiel, Martin Hilka, Stephane Breant, Judith Leblanc, Nicolas Griffon, Anita Burgun, Melodie Bernaux, Arnaud Sandrin, Elisa Salamanca, Sylvie Cormont, Thomas Ganslandt, Tobias Gradinger, Julien Champ, Martin Boeker, Patricia Martel, Loïc Estève, Alexandre Gramfort, Olivier Grisel, Damien Leprovost, Thomas Moreau, Gael Varoquaux, Jill-Jênn Vie, Demian Wassermann, Arthur Mensch, Charlotte Caucheteux, Christian Haverkamp, Guillaume Lemaître, Silvano Bosari, Andrew South, Tianxi Cai, Isaac Kohane
article
npj Digital Medicine, Nature Research 2020, 3 (1), pp.#109. ⟨10.1038/s41746-020-00308-0⟩
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https://hal.archives-ouvertes.fr/hal-02918344/file/covid_ehr.pdf BibTex
titre
Hydroxychloroquine with or without azithromycin and in-hospital mortality or discharge in patients hospitalized for COVID-19 infection: a cohort study of 4,642 in-patients in France
auteur
Emilie Sbidian, Julie Josse, Guillaume Lemaître, Imke Mayer, Melodie Bernaux, Alexandre Gramfort, Nathanaël Lapidus, Nicolas Paris, Antoine Neuraz, Ivan Lerner, Nicolas Garcelon, Bastien Rance, Olivier Grisel, Thomas Moreau, Ali Bellamine, Pierre Wolkenstein, Gaël Varoquaux, Eric Caumes, Marc Lavielle, Armand Mekontso Dessap, Etienne Audureau
article
2020
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