Publications

The 6 publications that contain the main part of my contributions and that I recommend for reading are listed by (1)(2)(3)(4)(5)(6):

Information - Cohomology - Data Analysis

• Sanos. F, Tewarie, Baudot P., Luchicchi, Barros de Souza, Girier, Milan, Broeders, Centeno, Cofre, Rosas, Carone, Kennedy, Stam, Hillebrand, Desroches, Rodrigues, Schoonheim, Douw, Quax. Emergence of High-Order Functional Hubs in the Human Brain. BioRxiv-2023.02.10.528083. 2023 (submitted to Nature communication). PDF

• Lang L., Baudot P., Quax R., Forré P., Information Decomposition Diagrams Applied beyond Shannon Entropy: A Generalization of Hu's Theorem.  arXiv:2202.09393. 2022 (submitted to Compositionality) . PDF

• Baudot P., On Information links. Lecture Notes in Computer Science Springer, 2021 PDF

• (1) Baudot P., Tapia M., Bennequin, D. , Goaillard J.M., Topological Information Data Analysis. 2019, Entropy, 21(9), 869    PDF . Entropy Best paper award 2019.  PDF

• (2) Baudot P., The Poincaré-Shannon Machine: Statistical Physics and Machine Learning aspects of Information Cohomology. 2019, Entropy , 21(9),  PDF

• (3) Tapia M., Baudot P., Dufour M., Formizano-Treziny C., Temporal S., Lasserre M., Kobayashi K., Goaillard J.M.. Neurotransmitter identity and electrophysiological phenotype are genetically coupled in midbrain dopaminergic neurons. Scientific Reports. 2018. PDF. BioArXiv168740. PDF

• (4) Baudot P., Elements of qualitative cognition: an Information Topology Perspective. Physics of Life Reviews. 2019 LINK. extended version on Arxiv. PDF

• (5) Baudot P., Bennequin D., The homological nature of entropy. Entropy, 2015, 17, 1-66; doi:10.3390. PDF

• Baudot P., Bennequin D., Topological forms of information. AIP conf. Proc., 2015. 1641, 213. PDF

Medical AI

• Munoz E., Baudot P., Le V.K., Voyton C., Renoust B., Francis D., Groza V., Brisset J.C., Geremia E., Iannessi A., Liu Y., Huet B., 3D-Morphomics, Morphological Features on CT scans for lung nodule malignancy diagnosis. Medical Image Computing and Computer Assisted Intervention - MICCAI 2022 - Workshop Caption. PDF

• Brag J., Auffret M., Ramos C., Liu Y., Baudot P., Ibiopsy for precision medicine. European Medical Journal. 2018, 3,4, 50-61 LINK 

Visual Information processing - Learning - Cortical Network - Perception

• Lebec B., Troncoso X., Desbois C., Pasarelli Y., Baudot P., Monier C., Pananceau M., Frégnac Y.,   Horizontal connectivity in V1: Prediction of coherence in contour and motion integration. PLOS ONE. 2022 PDF

• Baudot P., Physical model of qualitative cognition: Comment on "Physics of mind: Experimental confirmations of theoretical predictions" by F. Schoeller, L. Perlovsky and D. Arseniev. Phys Life Rev. 2018 PDF

• Baudot P., Levy M., Marre O., Monier C., Pananceau M., Frégnac Y., Animation of natural scene by virtual eye-movements evokes high precision and low noise in V1 neurons. Front Neural Circuits., 2013, Dec 27;7:206. PDF

• El Boustani S., Marre O., Béhuret S., Baudot P., Yger P., Bal T., Destexhe A., Frégnac Y., Network-state modulation of power-law frequency-scaling in visual cortical neurons. PLoS Comput Biol., 2009, Sep;5(9). PDF

• Fregnac Y., Baudot P., Chavane F., Marre O., Monier C., Pananceau M., Sadoc G., Multiscale functional imaging: reconstructing network dynamics from the synaptic echoes recorded in a single visual cortex neuron. Bull Acad Natl Med., 2009, Apr; 193(5):851-62. PDF

• Fregnac Y., Monier C., Chavane F., Baudot P., Graham L., Shunting inhibition, a silent step in visual cortical computation. Journal of Physiology (Paris), 2003. Jul-Nov;97(4-6):441-51. PDF

• Monier, C., Chavane, F., Baudot, P., Borg-Graham, L., and Frégnac, Y., Orientation and direction selectivity of synaptic inputs in visual cortical neurons: a diversity of combinations produces spike tuning. Neuron, 2003. Vol. 37 .663-80. PDF

• Chavane, F., Monier, C., Bringuier, V., Baudot, P., Borg-Graham, L., Lorenceau, J. and Frégnac, Y., The visual cortical association field: a Gestalt concept or a physiological entity. Journal of Physiology (Paris), 2000. 94: 333-342. PDF

• Menegon A., Burgaya F., Baudot P., Dunlap D., Girault J.A., Valtorta F., FAK+ and PYK2/CAK, two related tyrosine kinases highly expressed in the central nervous system: similarities and differences in the expression pattern. European Journal of Neuroscience, 1999. vol.11, 3777-3788. PDF

Patent

• Method and system for computer aided diagnosis using ensembled 2D and 3D neural networks based on medical images. US Patent 11,810,299, 2023 Link

• Method and system for prediction of the severity risk of the disease of an organ based on morphological characteristics extracted from 3-dimensional medical images. 2023 (presubmission EU-US)

• Automated pattern recognition and scoring method of fibrosis from non invasive radiology imaging. US Patent App. 17/772,881, 2022. Link

Unpublished work

• (Book) Baudot P., Information topology: Mathematic and Physic of evolution and adaptation. Lecture Notes in Morphogenesis. Springer International publishing. Order Number: 86366129. In preparation.

• Baudot P., On Information (pseudo) metric. Arxiv, 2021 PDF

• Baudot P., Levy M., Marre O., and Frégnac, Y, (2006). Eye movement dynamic constrain V1 code precision and sparsening through adapted non-linearities. PDF. This is the second part of the study on coding in natural condition of viewing, submitted to nature in 2006 and rejected, and only published in my thesis. The results have been highlighted in a review for general public by T. Sejnowski and T. Delbruck “The language of neurons” (Pour la science 2013, Link).

Articles in edited books and thesis

• Frégnac Y., Baudot P., Chavane F., Lorenceau J., Marre O., Monier C., Pananceau M., Carelli P., and Sadoc G., Multiscale functional imaging in V1 and cortical correlates of apparent motion. In: Dynamics of visual motion processing (G. Masson & U. Ilg) Springer, 2010. 73-94. PDF.

• (6) Baudot P. Natural computation, much ado about nothing? Thesis Paris-6 University. 2006. PDF.

• Frégnac Y., Monier C., Chavanne F., Baudot P. and Graham L., Diversity of computation of orientation and direction preference by visual cortical neurons: an intracellular re-examination. In: "The Neural Basis of early Vision". (Eds. A. Kaneko) Springer-Verlag, 2002. pp. 68-69.

Publication in journal for general public

• René A., Baudot P., and Frégnac Y. Basse Vision (2005). Rééduquer le cerveau adulte. 19: 15-17. ISSN 1630-9146. PDF.

• Collective work - French Roadmap for complex Systems 2008-2009, PDF

Communications with acts

• Baudot P., Voyton C., De Bie G., Le VK, Francis D., Geremia E., Renoust B., Siot PH., Liu Y., Huet B. End to end model for nodule detection and characterization in lung cancer screening : performances and subpopulation analysis. NACLC, Chicago, IL, USA. December, 2023.

• Voyton C., Baudot P., Le V.K., Francis D., Munoz E., Development of an AI/ML Tech Based Pulmonary Nodule Malignancy Prediction Model: Application to Indeterminate Pulmonary Nodules and Early-Stage Cancers. RSNA 2022. 4040 W7-SSN06

• Grossi F., Le V.K., Baudot P., Voyton C., Francis D., Munoz E., Huet B., Artificial Intelligence Supporting Lung Cancer Screening: Computer Aided Diagnosis of Lung Lesions Driven by Morphological Feature Extraction.  ESMO 2022

• Baudot, P., Voyton, C., Francis, D., Baili-laya, A., Bobin, V., Renoust, B., Liu, Y., Iannessi, A., Huet, B.: Development and Validation of a Machine Learning Based CADx Designed to Improve Patient Management in Lung Cancer Screening Programs. In: Proceedings of ECR 2022. Vienna (2022) 

• Baudot P. , Bernardi M.,  The Poincaré-Boltzmann Machine: passing the information between disciplines, ENAC Toulouse France. 2019 LINK PDF

• Liu Y., Ramos C., Baudot P., Brag J., Lucidarme O. Imaging biomarker phenotyping system (iBiopsy) to accelerate hepatocellular carcinoma (HCC) drug development. Journal of Clinical Oncology 37, no. 15_supp LINK

• Baudot P. , Bernardi M.,  Information Cohomology methods for learning the statistical structures of data. DS3 Data Science, Ecole Polytechnique 2019 POSTER 

• Baudot P.  Pattern Recognition, Gestalt and Qualitative aspects of cognition: an information topology perspective. Cognitive Neuroscience 2018, Warsaw. J Neurol Neurophysiol 2018, Volume 9. p45  PDF

• Tapia M, Baudot P*, Formisano-Tréziny C, and Goaillard JM, Beyond cell identity: unraveling the structure of cell variability. NeuroFrance 2017 , Bordeaux, 17­19 Mai. POSTER

• Tapia M., Formisano-Tréziny C., Baudot P. and Goaillard J.M., Quantitative Channelomics of individual substantia nigra dopaminergic neurons. 2-6 July 2016 FENS Copenhagen, Denmark. 

• Baudot P., Tapia Pacheco M., Moubarak E., Haddjeri A., Goaillard J.M., Topological structures of information, theory, perspectives and applications to biological data and biological models. BigDataLifeScience 2016. Big Data Mathematical and Statistical Tools for Life Science, Amirkabir University of TeheranIPM, Tehran, Iran

• Baudot P., Information topology for Neural data analysis and theories. Linking cellular properties to neuronal network dynamic, int. Conference, Marseille, 16-18 april 2016 POSTER

• Baudot, P. Information topology, a mathematical theory of Complex Systems and data. CS-DC’15 Complex Systems Digital Campus e-satellites of international Conference on Complex Systems 2015. Link.

• Baudot, P., Information Topology: neural dynamics and adaptation. 2015. First International Conference on Mathematical NeuroScience, Juan-les-Pins, France. Link.

• Bal T., Béhuret S., Deleuze C., Gomez L., Piwkowska Z., Wolfart J., Debay D., Brette R., El Boustani S., Marre O., Baudot P., Yger P., Rudolph M., Le Masson G., Sadoc G., Destexhe A., and Frégnac Y., Hybrid biological-artificial neuronal networks,. Colloque Interface physique, chimie, biologie, soutient à la prise de risqué. 2009. Fréjus, France. 

• Kremkow J., Perrinet L., Baudot P., Levy M., Marre O., Monier C., Fregnac Y., Masson G., and Aertsen A. . Control of the temporal interplay between excitation and inhibition by the statistics of visual input: a V1 network modelling study. In Proceedings of the Society for Neuroscience conférence. 2008

• Marre O., El Boustani S., Baudot P., Levy M., Monier C., Huguet N., Pananceau M., Fournier J., Destexhe A. and Fregnac Y. . Stimulus-dependency of spectral scaling laws in V1 synaptic activity as a read-out of the effective network topology. In Society for Neuroscience Abstracts, 2007. 33: 790.6.

• Yger P., Marre O., El Boustani S., Baudot P., Monier C., Levy M., Davison A. and Frégnac Y., Chaos control: reliable signal propagation and pattern completion in chaotic neuronal networks. In American Society for Neuroscience Abstract. 2007. 33: 792.3. Link

• Marre O., Baudot P., Levy M. and Frégnac, Y., High timing precision and reliability, low redundancy and low entropy code in V1 neuron during visual processing of natural scene. Society for Neuroscience Abstracts. Washington, USA. 2005. Link.

• Baudot P., Levy M., Marre O., Fregnac Y. An intracellular view of time coding and sparseness of cortical representation in V1. Journées du Réseau de Sciences Cognitives d'Ile-de-France RESCIF. 2005. Link

• Frégnac Y., Marre O., Baudot P., Levy M., Sparse representation and time coding in V1, when processing continuous streams of animated sequences of natural images. International SenseMaker Workshop, 2005 .School of computing Intelligence, University of Ulster, Derry, Ireland. 

• Frégnac Y., Baudot P., Levy M. and Marre O. . An intracellular view of time coding and sparseness of cortical representation in V1 neurons during virtual oculomotor exploration of natural scenes. Cosyne Computational and Systems Neuroscience. 2005. March 17-20, - Salt Lake City, USA. Link submission article. Link abstract.

• Frégnac Y., Sadoc G., Kopysova I., Huguet N., Marre O., René A., Baudot P., Levy M. and Pananceau M. ,Network state dependency in the evoked subthreshold dynamics of visual cortical receptive fields. In "4th Forum of European Neuroscience". FENS Abstracts. 2004. 2: A085.085. Lisbon, Portugal.

• René A., Huguet N., Pananceau M., Baudot P., Marre O. and Frégnac Y., Revisiter in vivo l'impact de la plasticité synaptique dépendante de l'ordre temporel entre activités pré- et post-synaptiques dans la réorganisation fonctionnelle des champs récepteurs dans le cortex visuel primaire adulte. In Roscoff. 2004.

• Huguet N., Sadoc G., Baudot P., Kopysova I., Levy M., Marre O., Pananceau M., René A. and Frégnac Y. Conditional maps of visual cortical receptive fields: Up- and Down- state dependency in visually evoked dynamics. In "34th Annual Meeting of the Society for Neuroscience". Society for Neuroscience Abstracts. San Diego, USA. 2004.

• Levy M., Baudot P., Pananceau M., Marre O., Huguet N., Rene A., Grant K. and Fregnac Y. An intracellular view of the temporal encoding of contrast in cat visual cortex during viewing of natural scenes. In "34th Annual Meeting of the Society for Neuroscience". Society for Neuroscience Abstracts. San Diego, USA. Link.

• Baudot P., Levy M., Monier C., Chavane F., René A., Huguet N., Marre O., Pananceau, M., Kopysova, I. and Fregnac, Y., Time-coding, low noise Vm Attractors, and trial-by-trial spiking reproducibility during natural scene viewing in V1 cortex. In "34th Annual Meeting of the Society for Neuroscience". Society for Neuroscience Abstracts. San Diego, USA. 2004. Link.

• Baudot P., Levy M., Fregnac Y. An intracellular view of the temporal encoding of natural stimuli in V1 neurons. Gordon Research conferences ‘Sensory Coding & the Natural Environment’. Queen’s college. UK. 2004. Link.

• René A., Huguet N., Pananceau M., Baudot P., Marre O. and Frégnac Y., Revisiting the impact of spike-timing-dependent plasticity in the shaping of adult visual cortical receptive fields in vivo. In "The Monte Verita Workshop on STDP".Ascona, Suisse. Orgs: W. Gerstner, H. Markram and W. Senn. Invited. 2004.

• Frégnac Y., Baudot P., An intracellular view of computation in V1: from high conductance states to the processing of natural images. National Network for Computational Neuroscience. Bernstein Centers for Computational Neuroscience Kick-off meeting Oct. 14th – 16th, Berlin, Germany. 2004. Link.

• Frégnac Y., Sadoc G., Kopysova I., Huguet N., Marre O., René A., Baudot P., Levy M. and Pananceau M. . Network state dependency in the evoked subthreshold dynamics of visual cortical receptive fields. In "4th Forum of European Neuroscience". Lisbon, Portugal. 2004.

• Kopysova I., Sadoc G., Baudot P., Huguet N., René A., Pananceau M., Chavane F., Monier C. and Frégnac Y. . Synaptic functional imaging of visual cortical receptive fields: network dependency in visually evoked dynamics. 33nd Annual Meeting of the Society for Neuroscience". Society for Neuroscience Abstracts. 2003. 338.334. New Orleans, USA.

• Sadoc G., Kopysova I., Baudot P., Huguet N., René A., Levy M., Pananceau M., Chavane F., Monier C. and Frégnac Y., Synaptic functional imaging of recurrent activity in visual cortex. In "3 ème Conférence Ladislas Tauc". Gif sur Yvette. Orgs:T. Bal, A. Destexhe, Y. Frégnac, K. Grant, M. Pananceau and D.E. Shulz. 2003.

• René A., Panaceau M., Huguet N., Baudot P. and Frégnac Y. . An in vivo generalization of spike-timing-dependent plasticity to multiple pairs of pre/post synaptic spikes in adult visual cortex. In "3 ème Conférence Ladislas Tauc". Gif sur Yvette. Orgs:T. Bal, A. Destexhe, Y. Frégnac, K. Grant, M. Pananceau and D.E. Shulz. 2003.

• Monier C., Chavane F., Baudot P., Graham L. and Frégnac Y. Sélectivité à l'orientation et à la direction des entrées synaptiques dans les neurones du cortex visuel primaire du chat: Une diversité de combinaison produit la sélectivité de la décharge. In "6ème Colloque de la Société des Neurosciences". Livre des Résumés. 145. Rouen, France. 2003.

• Frégnac Y., Monier C., Chavanne F., Baudot P. and Graham L. . Diversity of computation of orientation and direction preference by visual cortical neurons: an intracellular re-examination. In: "The Neural Basis of early Vision". (Eds. Kaneko, A.) Springer-Verlag, 2002. pp. 68-69.

• Sériès P., Georges S., Baudot P., Lorenceau J. and Frégnac Y.. Apparent motion perception is constrained by center/surround synaptic dynamics in V1. In "Neural Information and Coding Workshop". Les Houches, France. 2002.

• René A., Pananceau M., Levy M., Baudot P., Tsomaya V. and Frégnac Y. Reconfiguration of synaptic dynamics and visual subthreshold receptive field following theta-burst conditioning in cat primary visual cortex. In "32nd Annual meeting of the Society for Neuroscience". Society for Neuroscience Abstracts. 2002. 28: Orlando, USA.

• Frégnac Y., Monier C., Chavane F., Baudot P. and Graham L. . Diversity of inhibitory input tuning and its contribution to the genesis of orientation and direction selectivity in primary visual cortex. In "The structure of the cortical microcircuit". Instituto Juan March Report, Madrid, Spain. 2002. 

• Frégnac Y., Chavane F., Monier C., Baudot P., Borg-Graham L. and Lorenceau J., Space and time imaging of synaptic activity in visual cortex: from single receptive fields to intracortical wave propagation. In "From Synaptic to Brain Imaging".Institut Henri Poincaré, Paris. 2002.

• Monier C., Chavane F., Baudot P., Borg-Graham L. and Frégnac Y., Intracellular evidence for diverse functional role of inhibition in the primary visual cortex. In "Neural Plasticity". Abstracts of the 10th Annual Meeting of the Israel Society for Neurosciences. 2001. 189. Eilat, Israel.

• Borg-Graham L., Frégnac Y., Monier C., Chavane F. and Baudot P., Biophysical dynamical signatures in visual cortex. In "First SIAM-EMS Conference AMCW01". Proceedings of the First SIAM-EMS Conference. 2001. Berlin, Germany.

• Lorenceau J., Baudot P., Seriès P., Georges S., Pananceau Y. and Frégnac Y. Modulation of apparent motion speed by horizontal intracortical dynamics. J Vis December 1, 2001 1(3): 400. Link.

• Frégnac Y., Monier C., Chavane F., Baudot P. and Borg-Graham L., Shunting inhibition and "horizontal" connectivy: A necessary silent step in visual cortical processing. In "Aspect of Neuronal Dynamics". Hanse Wissenschaftkolleg, Bremen, Germany. Org: K. Pawelzik. 2000.

• Georges S., Seriès P., Baudot P., Frégnac Y. and Lorenceau J. La vitesse apparente: une image du temps de traitement. In "Assises du Réseau de Sciences Cognitives". 2000. 25. Collège de France, Paris, France.

• Baudot P., Chavane F., Pananceau M., Edet V., Gutkin B., Lorenceau J., Grant K. and Frégnac Y., Cellular correlates of apparent motion in the association field of cat area 17 neurons. In "30th Annual Meeting of the Society for Neuroscience". Society for Neuroscience Abstracts. 2000. 26: 446. New Orleans, USA.

• Monier C., Chavane F., Baudot P., Borg-Graham L. and Frégnac Y. Shunting inhibition and horizontal propagation, a dual signature of visual cortical processing? In "FENS". European Journal of Neuroscience. 12 Supp. 2000. 11: 285 (128.213). Brighton, England.

• Monier C., Chavane F., Baudot P., Borg-Graham L., and Frégnac Y., Direct evidence for a role of inhibition in orientation and direction selectivity in V1 neurons. In "30th Annual Meeting of the Society for Neuroscience". Society for Neuroscience Abstracts. 2000. 139. New Orleans, USA.

• Chavane F., Monier C., Baudot P., Borg-Graham L. J. and Frégnac Y., Early inhibitory control of spiking evoked activity in area 17 neurons. In "30th Annual Meeting of the Society for Neuroscience". Society for Neuroscience Abstracts. 2000. 26: 1968. New Orleans, USA.

• Monier C., Borg-Graham L.J., Chavane F., Lucas-Meunier E., Baudot P. and Frégnac Y., Non-linear interaction between synaptic excitation and inhibition in visual cortical neurons in vivo and in vitro. In "Perception and sensorimotor control of action". 1999. 3. Collège de France, Paris. Org: L. Janin, Y. Frégnac and J. Bullier.

• Monier C., Chavane F., Baudot P., Borg-Graham L. and Frégnac Y., Rôle de la balance entre l'excitation et l'inhibition dans la genèse de la sélectivité à l'orientation dans le cortex visuel primaire. In "4ème Colloque de la Société des Neurosciences". 1999. 4. 304 (M316). Marseille, France.

• Monier C., Borg-Graham L. J., Chavane, F. Lucas-Meunier E., Baudot P. and Frégnac Y., Nature and function of the shunting inhibition in visual cortical neurons in-vivo and in-vitro. In "Conférences J. Monod: Synaptic Plasticity, Assembly Dynamics and Flexibility of Cognitive Representations". 1998. Aussois, France. .

• Chavane F., Baudot P., Lorenceau J., Bringuier V. and Frégnac Y. Functional predictions derived from spatio-temporal constraints in the synaptic integration field of area 17 neurons. In "Conférences J. Monod: Synaptic Plasticity, Assembly Dynamics and Flexibility of Cognitive Representations". 1998. Aussois, France.

• Chavane F., Monier C., Baudot P., Borg-Graham L. and Frégnac Y. Dynamics of the on/off balance of subthreshold versus spike receptive fields in cat area 17. In "28th Annual Meeting of the Society for Neuroscience". Society for Neuroscience Abstracts. 1998. 24: 897. Los Angeles, USA.