I’m a researcher in computational cognitive neuroscience at Inria and the
Institute of Neurodegenerative Diseases (Bordeaux, France). I’m investigating
decision making, learning and cognition using computational models of the brain
and distributed, numerical and adaptive computing, a.k.a. artificial neural
networks and machine learning. My research aims to irrigate the fields of
philosophy with regard to the mind-body problem, medicine to account for the
normal and pathological functioning of the brain and the digital sciences to
offer alternative computing paradigms.
Beside neuroscience and philosophy, I’m also interested in open and
reproducible science (I’ve co-founded ReScience C with Konrad Hinsen and
wrote the article Transforming Code into Scientific Contribution), scientific
visualization (I’ve created glumpy, co-created VisPy and authored the
popular Ten Simple Rules for Better Figures article), Science outreach
(e.g. The Conversation) and computer graphics (especially digital
Keywords: Neuroscience, Cognition, Enaction, Behavior, Embodiment,
Learning, Model, Decision Making, Distributed Computing, Neural
Networks, Machine Learning, Artificial Intelligence, Scientific
Computation, Scientific Visualization, Scientific Modelling, Open
Science, Reproducible Science.
A Robust Model of Gated Working Memory (Neural Computation, 2020)
In this article we introduce a robust yet simple reservoir model of gated
working memory with instantaneous updates. The model is able to store an
arbitrary real value at random time over an extended period of time. The
dynamics of the model is a line attractor that learns to exploit reentry and a
nonlinearity during the training phase using only a few representative values.
A Natural History of Skills (Progress in Neurobiology, 2018) In
this review, we propose to re-evaluate the function of the basal ganglia-cortical
network in light of the current experimental evidence concerning the anatomy
and physiology of the basal ganglia-cortical circuits in vertebrates. We
briefly review the current theories and show that they could be encompassed in
a broader framework of skill learning and performance.
A Computational Model of Dual Competition (eNeuro, 2018) We
propose a model that includes interactions between the cortex, the basal
ganglia and the thalamus based on a dual competition that endows the model with
two regimes. One is driven by reinforcement learning and the other by Hebbian
learning. The final decision is made according to a combination of these two
mechanisms with a gradual transfer from the former to the latter.
Sustainable Computational Science (PeerJ, 2017) Computer science
offers a large set of tools for prototyping, writing, running, testing,
validating, sharing and reproducing results; however, computational science
lags behind. In the best case, authors may provide their source code as a
compressed archive and they may feel confident their research is
reproducible. But this is not exactly true.
A Neural Field Model of the Somatosensory Cortex (PLOS One, 2012) We
investigated the formation and maintenance of ordered topographic maps in the
primary somatosensory cortex as well as the reorganization of representations
after sensory deprivation or cortical lesion. We hypothesized that feed-forward
thalamocortical connections are an adequate site of plasticity while
cortico-cortical connections are believed to drive a competitive mechanism that
is critical for learning.
Rules Without Symbols (PNAS, 2005) Human cognitive control is uniquely
flexible and has been shown to depend on prefrontal cortex (PFC). But exactly
how the biological mechanisms of the PFC support flexible cognitive control
remains a profound mystery. We show how this can occur when a set of
PFC-specific neural mechanisms interact with breadth of experience to self
organize abstract rule-like PFC representations that support flexible
generalization in novel tasks.
→ See my résumé for full bibliography.
Scientific Visualization — Python & Matplotlib (2020) An open access book on
scientific visualization using python and matplotlib to be released during
summer 2020 (hopefully). Sources will be available on GitHub, the PDF book will
be open-access and the printed book will cost 50$. If you want to support the
book, you can tip a few euros. If you want to have access to the private
repository during the writing, you can tip a few more euros (and let me know
abour your github handle). If you’re a company, you can also sponsor me. Note
that in any case, the GitHub repository will be made public at the end of the
writing and the PDF will be available for free.
Towards Reproducible Research (2019) This book takes a current perspective onto
a number of potentially dangerous situations and practices, to examplify and
highlight the symptoms of non-reproducibility in research. Each time, it
provides efficient solutions ranging from good-practices that are easily and
immediately implementable to more technical tools, all of which are free and
have been put to the test by the authors themselves.
From Python to Numpy(2017) There are a lot of techniques that you don’t find in
books and such techniques are mostly learned through experience. The goal of
this book is precisely to explain some of these techniques and to provide an
opportunity for making this experience in the process.
→ See other books on my résumé.
Some popular science
Why your cat is lousy at chess yet way smarter than even the most advanced AI
If you share your home with a dog or a cat, look at it carefully and you will
get a good overview of everything we don’t know how to do in artificial
intelligence. “But my cat does nothing all day except sleep, eat and wash
herself,” you may think. And yet your cat knows how to walk, run, jump (and
land on her feet), hear, see, watch, learn, play, hide, be happy, be sad, be
afraid, dream, hunt, eat, fight, flee, reproduce, educate her kittens – and the
list is still very long…
Silicon soul: The vain dream of electronic immortality If we want to “upload
our brain” without going insane, it’s imperative for the uploaded brain to be
connected to an artificial body that can perceive the outside world and act on
it. But what kind of artificial body do we have today? Robotic bodies where
retinas are replaced by cameras and muscles by motors?
Why you’ll never be able to upload your brain If we consider the whole central
nervous system, we are facing an average of 86 billion neurons, and each of
these neurons contacts an average of 10,000 other neurons, representing a grand
total of approximately 860 trillion connections. This is really huge…
- July 10, 2020 I’ve designed brand new cheatsheets for matplotlib, with the financial support of NumFOCUS. 700 retweets, 1900 likes and 1400 stars on GitHub. This was much needed.
- June 12-19, 2020 Our computational neuroscience crash course will be online this year.
- June 9, 2020 My Ten Years Reproducibility Challenge entry just got published. It’s a reproduction of a 32 years old program that I published when I was a teenager. Coded in Applesoft Basic on an Appel IIe.
- May 27, 2020 The VisPy project that I co-funded with C.Rossant, A.Klein and L.Campagnola and now lead by David Hoese got funded by the Chan Zuckerberg Initiative.
- May 22, 2020 Articles (x10) and editorial from the 2019 NeurIPS Reproducibility Challenge are online.
- May 18, 2020 I’m now review editor for Decision Neuroscience, shared between Frontiers in Neuroscience and Frontiers in Psychology.
- May 14, 2020 I’ve made a minimal but elegant theme for emacs.
- May 13, 2020 Our article Identification of distinct pathological signatures induced by patient-derived α-synuclein structures in nonhuman primates is online at Science Advances.
- May 12, 2020 Joining the Bordeaux University expert group.
- May 5, 2020 New comment in Nature about the upcoming creation of ReScience X with Etienne Roesch.
- May 3, 2020 24 entries sor far for the Ten Years Reproducibility Challenge and a few more need extra time.
- April 17, 2020 Arthur Leblois and me have been awarded a PhD Grant in Theoretical Neuroscience by the University of Bordeaux.
- May 1, 2020 Ten Years Reproducibility Challenge deadline! Only a few hours to submit your entries.
- March 29, 2020 The Ten Years Reproducibility Challenge workshop is postponed sometime later in the year.
- March 29, 2020 The Ten Years Reproducibility Challenge deadline has been extended to 30/04/2020.
- March 28, 2020 100 Numpy exercises reached 5000 ★.
- March 27, 2020 New experimental Matplotlib 3d axis
- March 21, 2020 New preprint Transfer between long-term and short-term memory using Conceptors available on arXiv.
- March 17, 2020 France global lockdown
- March 13, 2020 Universities shutdown in France because of COVID-19.
- March 5, 2020 Le 5 mars l’université et la recherche s’arrêtent.
- March 4, 2020 Joining the Technical Commitee of the upcoming
SAB 2020 : From Animals to Animats 16, the 16th international conference on the simulation of adaptive behavior.
- March 3, 2020 I’ll give a keynote at the upcoming European Neuroscience Conference by Doctoral Students (ENCODS) 2020 in Glasgow (UK), a FENS event.
- February 29, 2020 ReScience C will publish a special issue on the NeurIPS 2019 Reproducibility Challenge in association with Joelle Pineau and Koustuv Sinha.
- February 25, 2020 I’ve been officially appointed as a scientific expert by the University of Bordeaux.
- February 24, 2020 Happy to be a keynote for the upcoming NeuroDoWo 2020 in Cologne organized by German PhD students in Neurobiology under the patronage of the German Neuroscience Society.
- February 21, 2020 Our article Identification of distinct pathological signatures induced by patient-derived α-synuclein structures in non-human primates has been accepted at Science Advances.
- February 19, 2020 Our book Vers une recherche reproductible, faire évoluer ses pratiques is now available at the Bibliothèque Nationale de France (ISBN: 979-10-97595-04-3)
- February 17, 2020 Participating to the PhD defense of Aliaa Moualla at
Cergy University about a robot
wandering in a musem while developping a sense of aesthetic.
- February 6 & 7, 2020 Meeting of the Drôles d’objets, un nouvel art de faire
scientific committee in Nancy. We established the program of the conference
that promises to be fun and interesting.
- January 27, 2020 Official start of the Hypermondes festival. Follow us on
- January 24, 2020 Our Saraswati associated team proposal has been accepted.
- January 21, 2020 My interview for GrandLabo is
- January 20, 2020 Start of the AI4Industry workshop. 5 days of conferences,
training and hackatons.
- January 7, 2020 Just submitted the reproduction of my very first (non
scientific) published article 32 years ago for the Ten Years Reproducibility
- December 20, 2019 “Scandale à la Macropole !”, the (fake) trial of an
artificial intelligence is online.
- December 17, 2019 On strike and demonstrating!
- December 10, 2019 On strike and demonstrating!
- December 5, 2019 My former internship student Bhargav Teja Nallapu will defend
his PhD Thesis: “A closed-loop framework of decision-making and learning in
primate prefrontal circuits : Computational modeling and virtual
- December 3, 2019 I’ll give an invited talk(“Boostrapping Cognition”) at the
NeuroDevRob : robotics, development and neurosciences conference.
- November 29, 2019 I’ll participate to the national meeting of digital
libraries in Bordeaux.
- November 26, 2019 Attending the Robotic GDR workshop (GT8, robotic &
neuroscience). Very nice talks, especially the one by Olivier Ly at the end
of the day.
- November 20, 2019 “Scandale à la Macropole !”, a FACTS event. I will testify
at the (fake) trial of an artificial intelligence. Trial will start at 19h at
the Hôtel de Région in Bordeaux.
- November 18, 2019 Submission deadline is today for the conference Drôles
d’objets, un nouvel art de faire
- November 13, 2019 I added a new entry for the Ten Years Reproducibility
Challenge with my very first published article in a (non-scientific) journal,
published 31 years ago (for apple IIe).
- November 5, 2019 Our article about the emergence of money under information
scarcity has been accepted in Palgrave Communications (Springer Nature).
- November 4, 2019 You can now sponsor me using the Github sponsorship
program. From $1/month up to 100$/month (for companies).
- November 2, 2019 Together with T.Boraud and C.Brun, we submitted our ERC
Synergy project “BRAINCRAFT: Unraveling cognition using systemic,
computational & intelligible models: from newts to non-human primates”
- October 31, 2019 New preprint online: Identification of distinct pathological
signatures induced by patient-derived α-synuclein structures in non-human
- October 29, 2019 Challenge to test reproducibility of old computer
code. Correspondence in Nature about the Ten Years Reproducibility Challenge.
- October 22, 2019 Kick-off meeting at La Rochelle for our EcoMob project
funded by Région Nouvelle-Aquitaine.
- October 21, 2019 Why your cat is lousy at chess yet way smarter than even the
most advanced AI in The Conversation.
- October 18, 2019 Fastest peer-review in my personal history. Six hours
between submission and acceptance for a correspondence in Nature: “Putting
Reproducibility to the test”.
- October 17, 2019 Pourquoi votre chat est nul aux éches at pourtant plus
intelligent qu’une IA (in French in The Conversation, France)
- October 12, 2019 I’ll be present at the Discussion with the general public
about science, fiction and AI at Cap-Sciences (17h-19h). This event is part
of the AI Trial and Bordeaux Macropole.
- October 11, 2019 Announcing the Ten Years Reproducibility Challenge whose
goal is to try to run your old code (older than 10 years). Good
luck. Deadline set to 01/04/2020.
- October 9, 2019 Submission of our associated team Saraswati (Hindu goddess of
knowledge, music, art, wisdom, and learning) with our Indian partners from
Hyderabad (Raju Surampudi Bapi) and Chenai (Srinivasa Shakravarty).
- October 8, 2019 Science outreach day at the Montendre high-school to talk
about Artificial Intelligence and do some experiment on unplugger AI.
- September 23, 2019 Our article Attributing and Referencing (Research)
Software: Best Practices and Outlook from Inria has been accepted to CiSE
special issue on Software and Data Citations.
- September 18, 2019 Github update: From Python to Numpy (1.2k ★) — Matplotlib
cheat sheet (1.1k ★) — 100 Numpy exercises (4.1k ★) — Matplotlib tutorial
(1.0k ★) — Glumpy (660 ★) — Vispy (2.1k ★) - Freetype-gl (1k ★)
- September 2, 2019 Our paper on a robust model of working memory has been
accepted in Neural Computation.
- September 1, 2019 Recursive voronoi are fascinating mathematical objects. I
had to try to make one using matplotlib and shapely.
- August 30, 2019 Interesting meeting with P.Couillard, former Premier of
Québec, to talk about AI, health & medicine.
- August 16, 2019 My 2020 book project Scientific Visualization — Python &
Matplotlib is online. You can support it and have access to the private
repository while I write it.
- August 11, 2019 I designed a matplotlib cheatsheet from figures I’ve made for
the upcoming scientific viualization book.
- August 3, 2019 Just released a calendar heatmap made with matplotlib (from my
upcoming book on scientific visusalization)
- July 30, 2019 Our paper ReScience C: A Journal for Reproducible Replications
in Computational Science has been published in Reproducible Research in
Pattern Recognition (Lecture Notes in Computer Science)
- July 23, 2019 Preparation of the Artificial Intelligence trial that will be
held on November 20 2019, somewhere in Bordeaux.
- July 20, 2019 Our project EcoMob with the University of La Rochelle has been
accepted and funded. We’ll study and model the formation of habits in Humans
with a special emphasis on the cortex and the basal ganglia.
- July 7-12, 2019 En route for Oslo to attend the International Society for the
History, Philosophy and Social Studies of Biology. I’ll give a talk about the
difficulties in evaluating non-predictive models.
- July 1-5, 2019 Start of the Computational Neuroscience Crash Course week with
Arthur Leblois and in association with the Bordeaux Neuroscience Grad School.
- June 24, 2019 Meeting with Etienne Coutureau’s lab. Anthony Strock will
present our (robust) model of working memory.
- June 21, 2019 APEIA day (Artificial Intelligence & Education) at Inria
BSO. I’ll introduce some unplugged AI activities: maze building & solving and
perceptrons with pen, papers and dices.
- June 11, 2019 We are movie stars ! The team is shooting a short movie about
our ongoing cooperation with our fellow neurobiologist colleagues.
- June 7, 2019 Very much excited to visit The Atelier National de Recherche
Typographique (ANRT) in Nancy in order to meet Jérémie Hornus from
- June 6, 2019 Auditions for a MdC LRU position at centrale-supélec Metz.
- June 4, 2019 Our book Vers une recherche reproductible, faire évoluer ses
pratiques has been edited and is now online.
- May 28, 2019 The website for the upcoming conference Drôles d’objets, un
nouvel art de faire (2020) is online at
- May 25, 2019 Our preprint Attributing and Referencing (Research) Software:
Best Practices and Outlook from Inria is online. Submitted to CiSE for the
special issue on Software and Data Citations.
- May 23, 2019 Our very first ReScience C special issue is online. Many thanks
to Joelle Pineau, Koustuv Sinha and all the students that worked hard on
the ICLR 2019 Reproducibility Challenge.
- May 23, 2019 Many contributions from Jérémy Fix to the machine learning
- May 22, 2019 Our brand new ReScience C website with a smoother and simpler
submission and publishing process is live. Have a look at
- May 15, 2019 SOMA meeting at Inria Lille (following the BioComp conference in
Lille). Each of us will give update on their research concerning the
- May 13, 2019 Lab retreat in Lacanau for 2 days. Second and third year PhD
students will introduce their work.
- May 9, 2019 Audition and selection for the Inria National young graduate
scientist recruiting campaign. One long day for auditions, one day for
- May 7, 2019 Preselection for an assistant professor position in machine
Learning for Central/Supélec, Metz.
- May 2, 2019 Audition and selection for the Inria Sophia-Antipolis
Méditerranée (SAM) young graduate scientist recruiting campaign. One day
for auditions, one day for discussions.
- April 28-30, 2019 We’ll present a poster on the Natural History of Skills at
the iBags conference to be held in Biarritz, France from April 28 to May 2,
- April 26, 2019 Third and last lesson for the theoretical part of our
computational neuroscience crash course for the Bordeaux Neurocampus
Graduate Program. Today, we’ll review and practice signal processing.
- April 24, 2019 Fabien Benureau will present our work on Transforming Code
into Scientific Contribution at Scipy Japan to be held in Tokyo, 23-24
- April 23, 2019 The 100 Numpy exercises repository reached 3,000 stars on
GitHub and the open access book From Python to Numpy reached 1,000 stars.
- April 19, 2019 Amazing, we did it! We wrote a complete book on reproducible
science in three days. The book is now edited and will be online (open
access) in a few weeks.
- April 16, 2019 A brand new Mag U (University of Bordeaux) has been published
where I give a short interview on brain and artificial intelligence.
- April 15, 2019 I’ll participate in a book sprint organized by Sabrina Granger
(URFIST) with Loïc Desquilbet, Boris Hejblum, Arnaud Legrand and Pascal
Pernot. We are supposed to write a complete book on reproducible science in
three days. Quite a challenge indeed.
- April 14, 2019 I just published another absurd dialogue between two
immortals: Immortel (dialogues) (in French).
- April 12, 2019 Second lesson of our computational neuroscience crash course
for the Bordeaux Neurocampus Graduate Program. Today, we’ll review and
practice differential equations.
- April 9, 2019 Videos of our initiation to Artifical Intelligence for math
teachers are now online (part 1 & part 2) thanks to Didier Roy who also
organised this meeting in 2018.
- April 5, 2019 First lesson of our computational neuroscience crash course for
the Bordeaux Neurocampus Graduate Program. Today, we’ll review and practice
basic linear algebra.
- April 4, 2019 Our talk proposal with Fabien Benureau has been accepted for
Scipy 2019 but none of us can attend the conference. We had to decline.
- April 4, 2019 Pre-selection phase for the Inria National young graduate
scientist recruiting campaign in Paris. Another long day ahead.
- April 3, 2019 Joint interview with Natacha Vas-Deyres for the Bordeaux Geek
Festival (BGF) whose theme, this year, is the rise of the machines.
- April 2, 2019 Just published another absurd dialogue “Connecté (dialogues)”
(in French) between a man and a door.
- April 1, 2019 I’ll give a course on neural field and cortical plasticity at
the University Côte d’Azur for the master of science in Modelling for
Neurosciences and Cognitives Systems.
- March 30, 2019 Just published “Autonome (dialogues)”, a short and absurd
dialogue (in French) between an autonomous car and its principal user,
inspired by a recent and ongoing collaboration with the blOp artistic
- March 29, 2019 During the workshop organized by URFIST and Inria, Etienne
Roesch gave a very nice talk and introduced ReScience X, a journal
dedicated to the publication of experimental replications that we’ll launch
this summer (hopefully). Stay tuned!
- March 28, 2019 A Robust Model of Gated Working Memory, a work where we
introduce a robust yet simple reservoir model of gated working memory with
instantaneous updates is now online on biorXiv.
- March 27, 2019 Our experimental and theoretical work on decision making with
limited information has been published: A.Nioche, B.Garcia, T.Boraud,
N.Rougier & S. Bourgeois-Gironde, Interaction effects between consumer
information and firms’ decision rules in a duopoly: how cognitive features
can impact market dynamics, Palgrave Communications (Nature), volume 5
- March 27, 2019 Pre-selection phase for the Inria Sophia-Antipolis
Méditerranée (SAM) young graduate scientist recruiting campaign. Long day
- March 26, 2019 My open access book “From Python to Numpy” is now runnable at
educative.io who provides interactive in-browser environments that keep you
engaged and test your progress as you go.
- March 23, 2019 Huge success for our computational neuroscience crash course
co-directed by myself and Arthur Leblois. Registrations are now closed (we
already have too many people). All the material will be available online
for those who could not register.
- March 20, 2019 Welcome to Gabriel Gouraud who will work with me for three
months on spatial distributed and adaptive computing.
- March 15, 2019 En route for La Rochelle to give a 4 hours course on
dataviz. We’ll use INSEE database (“mariages in 2016”) and try to achieve
some nice visualization.
- March 13, 2019 I’m visiting Black[Foundry]
with Samuel Hornus and Adrien Tétar. We are collaborating on the design of
a flawless font hardware-accelerated rendering engine, including
- March 10, 2019 Psyphine, our multidisciplinary group (computer science,
psychology, philosophy, linguistic, neuroscience, ethnology) for the
theoretical and experimental study on cognition has been funded for one
more year (CNRS PEPS).
- March 9, 2019 I’ve coded a small and pure Python 3D renderer (100 lines with
loader, z-buffer, transformation, texture & light) available at
- March 7, 2019 In collaboration with URFIST and EDMI, I’ll give a talk on
scientific integrity for Bordeaux PhD students, based on the preprint Ten
Simple Rules for Scientific Fraud and Misconduct I wrote with John Timmers
from Ars Technica.
- March 3, 2019 Our session “Idealizations in Computational Neuroscience:
Facticity, Pragmatics and the Coding Heuristics”, with Daniel Kostic and
Cédric Brun, has been accepted for the biennal meeting of the International
Society for the History, Philosophy and Social Studies of Biology to take
place in Oslo, Norway, July 7-12, 2019.
- February 28, 2019 I’ve created a small GitHub repository at
https://github.com/rougier/ML-Recipes with stand-alone Python recipes for
some basic machine learning algorithms. Very far from scikit-learn coverage
or quality, but this might come handy for a quick experiment.
- February 28, 2019 I’ll be teaching advanced scientific Python to Bordeaux PhD
students (and faculty as well). Make sure to have conda installed and to
know the basics of Python.
- February 26, 2019 The UNESCO Paris Call I helped to review is now online at
https://en.unesco.org/foss/paris-call-software-source-code. It emphasizes
the importance of the Software Heritage archive to collect, preserve and
share software source code.
- February 21, 2019 Fourth year I’m teaching scientific Python for beginners to
Bordeaux PhD students. It was sold out (actually it is free) after only a
few days following the annoucement.
- February 19, 2019 Our ANR grant proposal on reproducible research (Software
Heritage, Inria, CBM, CASCaD, Leo, LIG and MAP5) coordinated by Konrad
Hinsen has passed the first stage.
- February 1, 2019 Together with Sophie Sakka and Natacha Vas-Deyres, I’ll
participate to the “Conférence Décalée” during the Reboot science festival.
We’ll try to answer the question whether robots will dominate us one day.
- January 14, 2019 First Psyphine meeting of the year. We met at the FMSM
(Fondation des Maison des Sciences de l’Homme) in Paris in order to prepare
our conference to be held next year in La Rochelle.
- January 7, 2019 Olivia Guest and myself will chair the track on Neuroscience
and Cognitive science during the SciPy conference to be held in Austin,
Texas, USA, July 10–12, 2019.
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