I’m a senior researcher (DR) 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 typography).

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.

Selected articles

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.

Selected books

Scientific Visualization — Python & Matplotlib (2021) An open access book on scientific visualization using python and matplotlib. Sources are available on GitHub, the book is open-access and the printed book cost 49$. If you want to support the book, you can tip a few euros.

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.

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…


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November 2022

November 7, 2022 I’ll give a talk at Inria Rennes about reproducible science (one bit at a time).

November 3-4, 2022 I’ll give a Python beginner course at URFIST Bordeaux.

October 2022

October 31, 2022 Start of the coding week for our neuroscience master students.

October 24-25, 2022 Team green days in Lacanau.

October 19, 2022 I’ll talk about open science at the first editon of GT8 school

October 17, 2022 Plenary meeting of the software branch of the open science committee.

October 3, 2022 We had youjr first CauseeIES & Coffee (Season #1, Episode #1) to talk about scientific edition and information. Today, we’ll explore this question “Do I really need to pay 9500 euros to publish in Nature?”

September 2022

September 23-24, 2022 Hypermondes festival!!!

September 15, 2022 We got the best paper award at ICDL 2022 for Dual pathway architecture underlying vocal learning in songbirds

September 2, 2022 Just released sideframe for GNU Emacs.

September 1, 2022 The program for the Hypermondes festival is online.

August 2022

August 6, 2022 Just released a minibuffer header for GNU Emacs. It is available on ELPA.

July 2022

July 15, 2022 Joined the International Symposium on Benchmarking, Measuring and Optimizing program committee.

July 8, 2022 Victor Leroy defended his internship , co-supervised by myself and Nicolas Mallet.

July 7, 2022 Short interview by Yuvrak Singh about my work on GNU Emacs.

July 6, 2022 I’ll talk about Open Science for the Hacking Cognition Summer school in Paris.

June 2022

June 30, 2022 Our paper Create Efficient and Complex Reservoir Computing Architectures with ReservoirPy has been accepted to SAB 2022.

June 22, 2022 The final program for the Hypermondes festival (theme “Utopia”) is finished and will be soon be online.

June 15, 2022 Our paper Dual pathway architecture underlying vocal learning in songbirds has been accepted at ICDL 2022

June 14, 2022 Psyphine green days, celebrating ten year of multidisciplinary research between computer science, neuroscience, psychology, linguistic, philosophy and ahtropology.

June 1, 2022 Our paper From concrete to abstract rules : A computational sketch has been accepted at Brain Informatics 2022.

May 2022

May 18, 2022 I’ll give a talk about dataviz at INSEP.

May 18, 2022 Attenting the Swiss universities Open Science workshop for preparing expertise.

May 10, 2022 Two days training in economic intelligence at IHEDN (Paris) for the French Open Science Committee.

May 4, 2022 Attending the PhD thesis of Nathalie Azevedo as a reviewer.

April 2022

April 29, 2022 First meeting for the machine learning aspect of GPR 2030

April 13, 2022 First meeting of the Free Research Software college for the Commitee for Open Science. I’ll co-supervise the working group on international aspects.

April 7, 2022 New preprint available From implicit learning to explicit representations

April 3, 2022 New preprint available Dual pathway architecture underlying vocal learning in songbirds

March 2022

March 27, 2022 I published the Reviewer manifesto

March 18, 2022 Remya Sankar will present our work at Cosyne: Dual pathway architecture in songbirds boosts sensorimotor learning.

March 17, 2022 Fjola Hyseni will present our work at Cosyne: Temporal Dynamics in an Attractor Model of the Songbird’s Premotor Nucleus.

March 17, 2022 I’ll be present at CinéScience for commenting the documentary “Cinq nouvelles du cerveau”

February 2022

February 23, 2022 Joined the International Workshop on Self-Organizing Maps and Learning Vector Quantization, Clustering and Data Visualization (WSOM+ 2022) program committee

February 14, 2022 Movie from the AI trial is online.

February 4, 2022 Joined the Cognitive Science Conference (CogSci 2022 programm committee.

January 2022

January 31, 2022 Two abstracts accepted at COSYNE 2022: “Dual pathway architecture in songbirds boosts sensorimotor learning” & “Temporal Dynamics in an Attractor Model of the Songbird’s Premotor Nucleus”

January 11, 2022 I’ll vie a talk about Scientific Visualization at Open Planetary Lunch

January 8, 2022 The French Reproducibility Network in online

December 2021

December 24, 2021 Github update: 4.2k followers — Scientific Visualization book (6.4k ★) — From Python to Numpy (1.7k ★) — Matplotlib cheat sheets (5.8k ★) — 100 Numpy exercises (7.7k ★) — Matplotlib tutorial (2.2k ★) — Glumpy (1k ★) — Vispy (2.8k ★) — Freetype-gl (1.4k ★) - Emacs / N Λ N O (1.4k★)

December 22, 2021 I just entered the top 500 on GitHub (out of 80 million users).

December 20, 2021 I’ve released a GNU Emacs notebook-mode for orgmode.

December 10, 2021 I’ve been invited to gove a talk on AI for the conference L’intelligence artificielle dans le domaine de la santé

December 9, 2021 I’ve just released an experimental GNU Emacs notebook.

December 9, 2021 Lise Aubin’s PhD defense for which I served as reviewer.

December 7, 2021 Louis Annabi’s PhD defense for which I served as examiner.

November 2021

November 29, 2021 Almost 100,000 downloads in 2 weeks for my book on scientific visualization (see Seems to be a huge success.

November 24, 2021 Team green days (2) in Gradigan.

November 22, 2021 Our replication of A Reservoir Computing Model of Reward-Modulated Motor Learning and Automaticity is online

November 23, 2021 We got a small grant from FNSO (Fond National pour la Science Ouver) to migrate ReScience C to open journals.

November 19, 2021 I attended the Emacs conference over the week-end. Great conference with many great talks. Mine was on the design of text editors, using Emacs, of course.

November 15, 2021 My book on scientific visualization is online and you can buy a printed edition.

November 8, 2021 We organized our first R4 workshop in Bidard (Pays Basque).

October 2021

October 29, 2021 Knowledge extraction from the learning of sequences in a long short term memory (LSTM) architecture has been published

October 27, 2021 Opening of the conference Drôles d’objets, Un nouvel art de faire that I’m co-organizing with the Psyphine group.

October 25, 2021 Our paper “Computational benefits of structural plasticity, illustrated in songbirds” has been accepted in Neuroscience and Biobehavioral Reviews.

October 14, 2021 I’ve been invited to give a talk on embodied cognition at the Journées Scientifiques.

October 12, 2021 nano-agenda.el is now on ELPA.

October 3, 2021 nano-theme.el is now on ELPA.

October 1, 2021 AI Trial (in French) to be played during the science festival.

October 1, 2021 Welcome to Naomi Chaix who will start her PhD under the co-supervision of my self and Thomas Boraud.

September 2021

September 30, 2021 I’ll participate to the 8th edition of the URFIST symposium a about numerical methods and scientific practices.

September 28, 2021 svg-lib.el is now on ELPA.

September 21, 2021 Our climackathon event get rewarded by the University of Bordeaux (“Talents U”)

September 13, 2021 First meeting of the French network of international Open Science experts.

September 1, 2021 Back to the lab!

August 2021

August 31, 2021 We got a grant from the Chan Zuckerberg Initiative to work on Vispy 2.0!

August 22, 2021 Start of the 13th Advanced Scientific Python Programming Summer school in Bordeaux

July 2021

July 15, 2021 Interview for the Data Analytics Post (in French).

July 5, 2021 Computational Neuroscience Crash Course starts.

July 2, 2021 Anthologie Hypermondes #1 Robots announced!

June 2021

June 25, 2021 Working on a Matplotlib course for NumFocus Academy to be launched early September 2021.

June 18, 2021 Final dates for the hypermondes festival have been announced: Friday 1st October to Sunday 3rd October 2021.

June 16, 2021 I’ve been appointed Director of Research at Inria.

June 14, 2021 I’ve been nominated permanent expert for the Open Research Europe publishing platform (for French Ministère de l’Enseignement Supérieur, de la Recherche et de l’Innovation)

June 8, 2021 Get my first vaccine shot for Sars-Cov2.

June 8, 2021 Slides for “The Art of Braincrafting” are online

June 4, 2021 I’ll give a keynote lecture at the European Neuroscience Conference by Doctoral Students (ENCODS) about the Art of Braincrafting.

June 2, 2021 Nice Report on my talk for Inachevé d’imprimer (in French).

May 2021

May 27, 2021 I’ve been invited by Inachevé d’imprimer group to talk about my typographic perenigrations and Emacs hacking.

May 26, 2021 Our article “Randomized Self-Organizing Map” is online at Neural Computation (open access).

May 17, 2021 Just reached 3k followers on GitHub.

May 10, 2021 I’ve been invited by the “Société Informatique de France” to talk about long term reproducibility.

May 5, 2021 We (with Cyrille Rossant) will publish a department article in Computer in Science & Engineering about Datoviz and the future of Vispy.

May 2, 2021 The Bordeaux Neurocampus GitHub organization is now live and will host our computational neuroscience crash course in association with the Bordeaux Neurocampus Graduate School.

May 1, 2021 Our Vispy/CZI grant passed first phase. We now have 2 week to write the full proposal.

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