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 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
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
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…
- December 5, 2019 My former internship student Bhargav Teja Nallapu will defen his PhD Thesis: “A closed-loop framework of decision-making and learning in primate prefrontal circuits : Computational modeling and virtual experimentation”
- 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
- November 5, 2019 Our article about the emergence of money under
information scarcity has been accepted in Palgrave Communications (Springer
- 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
- October 29, 2019 Challenge to test reproducibility of old computer
code. Correspondence in
Nature about the Ten Years Reproducibility
- 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
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
(in French in The Conversation, France)
- October 12, 2019 I’ll be present at the Discussion with the general
science, fiction and AI at Cap-Sciences (17h-19h). This event is part of the
AI Trial and Bordeaux
- 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
- 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 &
online. You can support it and have access to the private repository while I
- 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
(ANRT) in Nancy in order
to meet Jérémie Hornus from Black[Foundry].
- June 6, 2019 Auditions for a MdC LRU position at
- 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 https://drolesdobjets20.sciencesconf.org/
- 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
- 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
- May 23, 2019 Many contributions from Jérémy Fix to the machine
learning recipes repository.
- May 22, 2019 Our brand new ReScience C website with a smoother
and simpler submission and publishing process is live. Have a look
- 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 project.
- 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 discussions.
- 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
at the iBags conference to be held in
Biarritz, France from April 28 to May 2, 2019.
- April 26, 2019 Third and last lesson for the theoretical part of
our computational neuroscience crash
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
at Scipy Japan to be held
in Tokyo, 23-24 April 2019.
- April 23, 2019 The 100 Numpy
exercises repository reached
3,000 stars on GitHub and the open access book From Python to
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
(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
- April 12, 2019 Second lesson of our computational neuroscience
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
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
- 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
(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
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
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
Palgrave Communications (Nature), volume 5 (2019).
- March 27, 2019 Pre-selection phase for the Inria
Sophia-Antipolis Méditerranée (SAM) young graduate scientist
recruiting campaign. Long day ahead.
- March 26, 2019 My open access book “From Python to
is now runnable at
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
co-directed by myself and Arthur
Registrations are now closed (we already have too many people). All
the material will be available online for those who could not
- 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 variational fonts.
- 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 https://github.com/rougier/tiny-renderer.
- March 7, 2019 In collaboration with
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
- 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
- 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
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
- February 1, 2019 Together with Sophie
Sakka and Natacha
participate to the “Conférence Décalée” during the Reboot science
We’ll try to answer the question whether robots will dominate us
- 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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