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Serge Cohen

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**Thèmes de recherche** ![-](https://ipanema.cnrs.fr/squelettes-dist/puce.gif) modélisation stochastique d’image spectrale, approche par estimation de densité conditionnelle et critère de sélection de modèle pour l’optimisation discrète ![-](https://ipanema.cnrs.fr/squelettes-dist/puce.gif) factorisation positive d’image spectrale, combinaison des approches factorisation de matrice et factorisation de tenseur ; prise en compte de la « nature image » des matrices d’activation ![-](https://ipanema.cnrs.fr/squelettes-dist/puce.gif) reconstruction 3D, développement de nouvelles modalités de mesure et de reconstruction ![-](https://ipanema.cnrs.fr/squelettes-dist/puce.gif) traitement d’image : algorithmes pour implémentations rapides sur architectures SIMD ou GP-GPU **Recherches actuelles** Mon activité, à l’interface des statistiques, du traitement du signal/image et de l’analyse par méthode synchrotron des matériaux anciens. L’analyse des données issues de l’observation de matériaux anciens est rendue complexe par le faible échantillonnage, conséquence de la rareté des objets et de leur fragilité, ainsi que par la complexité des mesures et par la faible connaissance a priori des processus ayant conduit aux matériaux tels qu’observés. Ces contraintes conduisent à des développements mathématiques spécifiques et motivent la recherche de garanties théoriques sur les résultats de la modélisation. La localisation à IPANEMA permet d’ancrer le développement méthodologique dans la problématique et l’expérience d’application pour assurer une bonne adéquation des approches développées. **Parcours de recherche** Après une formation initiale en mathématiques et physique, ma thèse en biologie structurale (EMBL, Grenoble) avec en particulier la mise en oeuvre des techniques synchrotron m’a permis d’aborder en post-doctorat les méthodes mathématiques pour la biologie structurale (NKI, Amsterdam). Jai alors développé des méthodes algorithmiques permettent d’accélérer dun facteur 100 à 1000 la construction du modèle moléculaire pour les protéines. Depuis fin 2007 j’ai une activité de recherche dans le cadre du projet puis de l’unité IPANEMA, avec une première phase de prospectives qui m’a permis de condenser les caractéristiques déterminantes communes à l’ensemble des matériaux anciens du point de vue de leur étude physico-chimique et de l’analyse des données correspondante. La deuxième phase de mon activité au sein d’IPANEMA, commencée fin 2009, correspond aux premiers développement de méthodes mathématique pour l’analyse des image de spectro-microscopie de matériaux hétérogènes complexes.
**Research area** \- stochastic modelling of spectral image, conditional density estimation approach and model selection criterion for discrete optimisation \- positive factorisation of spectral image, combining matrix factorisation and tensor factorisation approaches; taking into account the "image nature" of activation matrices \- 3D reconstruction, development of new measurement and reconstruction modalities \- image processing: algorithms for fast implementation on SIMD or GP-GPU architectures **Current research** My activity stands at the interface of statistics, signal/image processing and synchrotron analysis of ancient materials. The analysis of data resulting from the observation of ancient materials is made complex by the low sampling rate, a consequence of the rarity of the objects and their fragility, as well as by the complexity of the measurements and by the poor *a priori* knowledge of the processes that led to the materials as observed. These constraints lead to specific mathematical developments and motivate the search for theoretical guarantees on the modelling results. The location at IPANEMA allows the methodological development to be anchored in the problematic and the application experience to ensure a good adequacy of the developed approaches. **Research background** After an initial training in mathematics and physics, my thesis in structural biology (EMBL, Grenoble) using, in particular, the implementation of synchrotron techniques allowed me to approach mathematical methods for structural biology (NKI, Amsterdam) as a post-doctorate fellow. I then developed algorithmic methods, mostly machine learning and pattern recognition based, to accelerate by a factor of 100 to 1000 the construction of molecular models for proteins. Since the end of 2007, I have been involved in research activities within the IPANEMA project and unit, with a first phase of prospective work that allowed me to condense the determining characteristics common to all ancient materials from the point of view of their physicochemical study and the corresponding data analysis. The second phase of my activity within IPANEMA, which began at the end of 2009, corresponds to the first development of mathematical methods for the analysis of spectro-microscopy images of complex heterogeneous materials.

Publications

Heritage research at the PUMA beamline

S. Schöder , Katharina Müller , Laurent Tranchant , Angélique Rouquié , Pierre Gueriau
Applied physics. A, Materials science & processing, 2024, 130 (11), pp.848. ⟨10.1007/s00339-024-08026-0⟩
Journal articles hal-04766397v1

International study day on "New research on mineralised textiles"

Clémence Iacconi , Loïc Bertrand , Corentin Reynaud , Agathe Chave , Ariane Thomas
Archaeological Textiles Review, 2023, 65, pp.157-159
Journal articles hal-04398759v1
Image document

Hierarchical clustering of spectral images with spatial constraints for the rapid processing of large and heterogeneous data sets

Gilles Celeux , Serge X. Cohen , Agnès Grimaud , Pierre Gueriau
SN Computer Science, 2022, 3 (194), ⟨10.1007/s42979-022-01074-4⟩
Journal articles hal-03104488v4
Image document

Disentangling the chemistry of Australian plant exudates from a unique historical collection

Rafaella Georgiou , Rachel Popelka-Filcoff , Dimosthenis Sokaras , Victoria Beltran , Ilaria Bonaduce
Proceedings of the National Academy of Sciences of the United States of America, 2022, 119 (22), pp.2116021119. ⟨10.1073/pnas.2116021119⟩
Journal articles hal-03680015v1
Image document

Micro-computed tomography for discriminating between different forming techniques in ancient pottery: new segmentation method and pore distribution recognition

Vanna Lisa Coli , Louise Gomart , Didier F Pisani , Serge X. Cohen , Laure Blanc-Féraud
Archaeometry, 2021, ⟨10.1111/arcm.12693⟩
Journal articles hal-03225382v2
Image document

Deciphering the Chemistry of Cultural Heritage: Targeting Material Properties by Coupling Spectral Imaging with Image Analysis

Loïc Bertrand , Mathieu Thoury , Pierre Gueriau , Étienne Anheim , Serge X. Cohen
Accounts of Chemical Research, 2021, 54 (13), pp.2823-2832. ⟨10.1021/acs.accounts.1c00063⟩
Journal articles hal-03329879v1
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Robust framework and software implementation for fast speciation mapping

Serge X. Cohen , Samuel Webb , Pierre Gueriau , Emmanuel Curis , Loïc Bertrand
Journal of Synchrotron Radiation, 2020, 27 (4), pp.1049-1058. ⟨10.1107/S1600577520005822⟩
Journal articles hal-02915778v1
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IPANEMA, un laboratoire dédié à l'étude des matériaux anciens et patrimoniaux par méthodes synchrotron

Loïc Bertrand , Serge X. Cohen , Mathieu Thoury , Sophie David , Sebastian Schoeder
Reflets de la Physique, 2019, 63, pp.21. ⟨10.1051/refdp/201963021⟩
Journal articles hal-02377530v1
Image document

Three-dimensional imaging of flat natural and cultural heritage objects by a Compton scattering modality

Mai K. Nguyen , Laurent Dumas , Serge X. Cohen , Patricio Guerrero
Journal of Electronic Imaging, 2017, 26 (1), pp.11026 - 11026. ⟨10.1117/1.JEI.26.1.011026⟩
Journal articles hal-01472451v1
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Unsupervised Segmentation of Spectral Images with a Spatialized Gaussian Mixture Model and Model Selection

Serge X. Cohen , E. Le Pennec
Oil & Gas Science and Technology - Revue d'IFP Energies nouvelles, 2014, 69 (2), pp.245-259. ⟨10.2516/ogst/2014013⟩
Journal articles hal-01933379v1
Image document

Trace Elemental Imaging of Rare Earth Elements Discriminates Tissues at Microscale in Flat Fossils

Pierre Gueriau , Cristian Mocuta , Didier B. Dutheil , Serge X. Cohen , Dominique Thiaudière
PLoS ONE, 2014, 9 (1), pp.e86946. ⟨10.1371/journal.pone.0086946⟩
Journal articles hal-01360897v1

Partition-Based Conditional Density Estimation

Serge X. Cohen , Erwan Le Pennec
ESAIM: Probability and Statistics, 2013, 17, pp.672--697. ⟨10.1051/ps/2012017⟩
Journal articles hal-00915854v1

The medieval iron market in Ariège (France). Multidisciplinary analytical approach and multivariate analyses

Stéphanie Leroy , Serge X. Cohen , Catherine Verna , Bernard Gratuze , Florian Téreygeol
Journal of Archaeological Science, 2012, 39 (4), pp.1080-1093. ⟨10.1016/j.jas.2011.11.025⟩
Journal articles hal-02130578v1

Cultural heritage and archaeology materials studied by synchrotron spectroscopy and imaging

Loïc Bertrand , Laurianne Robinet , Mathieu Thoury , Koen Janssens , Serge X. Cohen
Applied physics. A, Materials science & processing, 2012, 106 (2), pp.377-396. ⟨10.1007/s00339-011-6686-4⟩
Journal articles hal-02130649v1

The medieval iron market in Ariège (France). Multidisciplinary analatycal approach and multivariate analyses

Catherine Verna , Stéphanie Leroy , Serge X Cohen
Journal of Archaeological Science, 2012, 39 (4), pp.1080-1093
Journal articles halshs-00669129v1

Native mass spectrometry provides direct evidence for DNA mismatch-induced regulation of asymmetric nucleotide binding in mismatch repair protein MutS

Serge X. Cohen , Maria Chiara Monti , Alexander Fish , Herrie H K Winterwerp , Arjan Barendregt
Nucleic Acids Research, 2011, 39 (18), pp.8052-8064. ⟨10.1093/nar/gkr498⟩
Journal articles hal-03522064v1

Identification of the finishing technique of an early eighteenth century musical instrument using FTIR spectromicroscopy

Loïc Bertrand , Laurianne Robinet , Serge X. Cohen , Christophe Sandt , Anne-Solenn Le Hô
Analytical and Bioanalytical Chemistry, 2011, 399 (9), pp.3025-3032. ⟨10.1007/s00216-010-4288-1⟩
Journal articles hal-02130652v1

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank

Robbie P Joosten , Krista Joosten , Serge X. Cohen , Gert Vriend , Anastassis Perrakis
Bioinformatics, 2011, 27 (24), pp.3392-3398. ⟨10.1093/bioinformatics/btr590⟩
Journal articles hal-03522068v1
Image document

European research platform IPANEMA at the SOLEIL synchrotron for ancient and historical materials

Loïc Bertrand , Marie-Angélique Languille , Serge X. Cohen , Laurianne Robinet , Claire Gervais
Journal of Synchrotron Radiation, 2011, 18 (5), pp.765-772. ⟨10.1107/S090904951102334X⟩
Journal articles hal-00618143v1

Insights into the DNA cleavage mechanism of human LINE-1 retrotransposon endonuclease

Kostas Repanas , Gloria Fuentes , Serge X. Cohen , Alexandre M J J Bonvin , Anastassis Perrakis
Proteins - Structure, Function and Bioinformatics, 2009, 74 (4), pp.917-928. ⟨10.1002/prot.22201⟩
Journal articles hal-03522061v1

“Conditional Restraints”: Restraining the Free Atoms in ARP/wARP

Wijnand T.M. Mooij , Serge X. Cohen , Krista Joosten , Garib N Murshudov , Anastassis Perrakis
Structure, 2009, 17 (2), pp.183-189. ⟨10.1016/j.str.2008.12.011⟩
Journal articles hal-03521573v1

ARP / wARP and molecular replacement: the next generation

Serge X. Cohen , Marouane Ben Jelloul , Fei Long , Alexei Vagin , Puck Knipscheer
Acta crystallographica Section D : Structural biology [1993-..], 2008, 64 (1), pp.49-60. ⟨10.1107/S0907444907047580⟩
Journal articles hal-03521551v1

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

Serge X. Cohen , Gerrit Langer , Victor S Lamzin , Anastassis Perrakis
Nature Protocols, 2008, 3 (7), pp.1171-1179. ⟨10.1038/nprot.2008.91⟩
Journal articles hal-03521562v1

A knowledge-driven approach for crystallographic protein model completion

Krista Joosten , Serge X. Cohen , Paul Emsley , Wijnand Mooij , Victor S Lamzin
Acta crystallographica Section D : Structural biology [1993-..], 2008, 64 (4), pp.416-424. ⟨10.1107/S0907444908001558⟩
Journal articles hal-03521536v1

SPINE workshop on automated X-ray analysis: a progress report

M. Bahar , C. Ballard , Serge X. Cohen , K. Cowtan , E. Dodson
Acta crystallographica Section D : Structural biology [1993-..], 2006, 62 (10), pp.1170-1183. ⟨10.1107/S0907444906032197⟩
Journal articles hal-03521526v1

Co-expression of protein complexes in prokaryotic and eukaryotic hosts: experimental procedures, database tracking and case studies.

Christophe Romier , Marouane Ben Jelloul , Shira Albeck , Gretel Buchwald , Didier Busso
Acta crystallographica Section D : Structural biology [1993-..], 2006, 62 (Pt 10), pp.1232-42. ⟨10.1107/S0907444906031003⟩
Journal articles hal-00188127v1

Breaking good resolutions with ARP/wARP

Richard J Morris , Petrus H Zwart , Serge X. Cohen , Francisco J Fernandez , Mattheos Kakaris
Journal of Synchrotron Radiation, 2004, 11 (1), pp.56-59. ⟨10.1107/s090904950302394x⟩
Journal articles hal-03521453v1

Developments in the CCP 4 molecular-graphics project

Liz Potterton , Stuart Mcnicholas , Eugene Krissinel , Jan Gruber , Kevin Cowtan
Acta crystallographica Section D : Structural biology [1993-..], 2004, 60 (12), pp.2288-2294. ⟨10.1107/S0907444904023716⟩
Journal articles hal-03521466v1

Towards complete validated models in the next generation of ARP / wARP

Serge X. Cohen , Richard J Morris , Francisco J Fernandez , Marouane Ben Jelloul , Mattheos Kakaris
Acta crystallographica Section D : Structural biology [1993-..], 2004, 60 (12), pp.2222-2229. ⟨10.1107/S0907444904027556⟩
Journal articles hal-03521488v1

Structure of the GCM domain-DNA complex: a DNA-binding domain with a novel fold and mode of target site recognition

Serge X. Cohen , Martine Moulin , Said Hashemolhosseini , Karin Kilian , Michael Wegner
EMBO Journal, 2003, 22 (8), pp.1835-1845. ⟨10.1093/emboj/cdg182⟩
Journal articles hal-03521438v1

The GCM domain is a Zn-coordinating DNA-binding domain

Serge X. Cohen , Martine Moulin , Oliver Schilling , Wolfram Meyer-Klaucke , Jörg Schreiber
FEBS Letters, 2002, 528 (1-3), pp.95-100. ⟨10.1016/s0014-5793(02)03257-x⟩
Journal articles hal-03521393v1

“It takes a village”: An integrated approach to pottery production in the early Neolithic settlements of the Aisne Valley (Picardy, France)

Marzia Gabriele , Michael Ilett , Gilles Fronteau , Bruno Robert , Florian Couderc
Modelling households: economy & sociology of Europe’s first farmer population, Closing conference HOMES project, Nov 2023, Paris Institut national d’histoire de l’art (INHA), France
Conference papers hal-04485641v1

Tomographic imaging: two examples of medical and archaeological applications

Vanna Lisa Coli , Didier Binder , Laure Blanc-Féraud , Juliette Leblond , Serge X. Cohen
MIA-MIVA - 1st French-Italian workshop on the Mathematics of Imaging, Vision and their Applications, Sep 2022, Sophia Antipolis, France
Conference papers hal-03959834v1

The IAEA Collaborating Center Atoms for Heritage at Université Paris-Saclay

Loïc Bertrand , Sébastien Nomade , Mathieu Thoury , Sophie David , Lucile Beck
IAEA Workshop on Innovative Approaches of Accelerator Science and Technology for Sustainable Heritage Management, IAEA, Jun 2022, Vienne, Austria
Conference papers hal-03924484v1

Hough Transform and Image Processing: An Application to Neolithic Pottery

Vanna Lisa Coli , Didier Binder , Laure Blanc-Féraud , Serge X. Cohen , Louise Gomart
IS 2020 - SIAM Conference on Imaging Science, Jul 2020, Virtual, Canada
Conference papers hal-03225403v1

Des macro-traces au synchrotron : premiers résultats et enjeux relatifs aux méthodes de montage des céramiques

Louise Gomart , Didier Binder , Laure Blanc-Féraud , Serge X. Cohen , Vanna Lisa Coli
Céramiques imprimées de Méditerranée occidentale. Matières premières, productions, usages, Didier Binder; Stéphane Azoulay; Alain Burr; Claire Manen; Martine Regert; Chrystèle Vérati, Mar 2019, Nice, France
Conference papers hal-02398865v1

Détection et modélisation des réseaux poreux dans les céramiques néolithiques : perspectives pour l'identification des techniques et des usages

Vanna Lisa Coli , Didier Binder , Laure Blanc-Féraud , Serge X. Cohen , Drieu Léa
2ème Journée Matériaux Université Côte d'Azur, Sep 2019, Sophia Antipolis, France
Conference papers hal-03252965v1
Image document

Factorisation d'images spectrales de matériaux anciens

Alexandre Aiello , Serge X. Cohen , Axel Davy , Agnès Desolneux , Guillaume Le Mailloux
GRETSI 2019, Aug 2019, Lille, France
Conference papers hal-03341714v1

Modélisation 3D des fabriques et identification des techniques : nouvelles méthodes de segmentation et de reconnaissance de formes

Vanna Lisa Coli , Didier Binder , Laure Blanc-Féraud , Serge X. Cohen , Louise Gomart
Céramiques imprimées de Méditerranée occidentale. Matières premières, productions, usages, Didier Binder; Stéphane Azoulay; Alain Burr; Claire Manen; Martine Regert; Chrystèle Vérati, Mar 2019, Nice, France
Conference papers hal-02398835v1
Image document

Segmentation d'images spectrales à l'aide d'un algorithme hiérarchique avec contrainte spatiale

Agnès Grimaud , Gilles Celeux , Serge X. Cohen
51es Journées de Statistique, Jun 2019, Nancy, France
Conference papers hal-04420543v1

Céramiques imprimées de Méditerranée occidentale: apports de la micro-tomographie à la restitution des traditions céramiques en contexte archéologique

Vanna Lisa Coli , Louise Gomart , Didier Binder , Laure Blanc-Féraud , Serge Cohen
Journée d'échanges "Applications de la tomographie par rayons X", Réseau Tomo3D, CNRS-INEE, Muséum National d'Histoire Naturelle, Nov 2018, Paris, France
Conference papers hal-02112471v1

Céramiques imprimées de Méditerranée occidentale : apports de la micro-tomographie à la restitution des traditions techniques

Louise Gomart , Didier Binder , Marzia Gabriele , Gilles Durrenmath , Sabine Sorin-Mazouni
Archéologie : Imagerie Numérique Et 3D. Séminaire scientifique et technique organisé par l'Inrap, l’Institut national de recherche en informatique et en automatique (Inria) et l’Institut de recherche en informatique et systèmes aléatoires (IRISA)., May 2018, Rennes, France
Conference papers hal-03934431v1

Multiscale Tomography - Imaging and Modelling Ancient Materials

Vanna Lisa Coli , Didier Binder , Laure Blanc-Féraud , Serge Cohen , Louise Gomart
Journées du Programme structurant UCA-JEDI "Matière, Lumière, Interactions", 2018, Villa Clythia de Fréjus, France, France
Conference papers hal-02112470v1

The Extra Dimension of Energy - Strategies for the Collection and Analysis of Complex Synchrotron Data Sets

Sam Webb , Nicholas Edwards , Serge X. Cohen , Loïc Bertrand
IPC5 - Session : 3D imaging of fossils: novel approaches, advances and data management, Jul 2018, Paris, France
Conference papers hal-02290150v1

Early Western Mediterranean Impressed Wares (Early 6th millennium BCE): new interdisciplinary research on pottery paste processing at Pendimoun rock-shelter (Alpes-Maritimes, France)

Marzia Gabriele , Léa Drieu , Louise Gomart , Alain Burr , Serge X. Cohen
EMAC2017: European Meeting on Ancient Ceramics, 2017, Bordeaux, France
Conference papers hal-02112459v1

Backprojection of a conical Radon Transform in Compton scatter tomography

Patricio Guerrero , Laurent Dumas , Mai K. Nguyen , Serge X. Cohen
CANUM 2016, May 2016, Obernai, France
Conference papers hal-01440265v1

Simulation d'une nouvelle modalité d'imagerie basée sur le rayonnement X diffusé

Patricio Guerrero Prado , Mai K. Nguyen , Laurent Dumas , Serge Cohen
Congrès d’Analyse Numérique (CANUM), Institut Elie Cartan de Lorraine et SMAI, May 2016, Obernai (Alsace), France
Conference papers hal-01760008v1

Segmentation non supervisée d'image hyperspectrale par mélange de gausiennes spatialisé

Serge X. Cohen , Erwan Le Pennec
GRETSI 2011, Sep 2011, Bordeaux, France
Conference papers inria-00638432v1

Multiscale Tomography. Imaging and Modelling Ancient Materials

Vanna-Lisa Coli , Didier Binder , Laure Blanc-Féraud , Serge X. Cohen , Louise Gomart
Winter school IHP The Mathematics of Imagining, CIRM - Centre International de Rencontres Mathématiques, Jan 2009, Marseille, France
Conference papers hal-02399427v1
Image document

NOIRoeS project: Total study of the historical and technical background of Soulages' paintings to define the conservation strategy

Pauline Helou-de la Grandière , Shadé ALAO AFOLABI , Marouane Ben Jelloul , Serge X. Cohen , Lionel Simonot
5th international conference on Innovation in Art Research and Technology, Jun 2022, Paris, France
Conference poster hal-04294449v1
Image document

Hierarchical clustering of spectral images with spatial constraints for the rapid processing of large and heterogeneous datasets from ancient material studies

Serge Cohen , Gilles Celeux , Agnès Grimaud , Pierre Gueriau , Sajjad Mahdavi
GRC : Scientific Methods in Cultural Heritage Research, Jul 2022, Les Diablerets, Switzerland.
Conference poster hal-04420576v1

Archaeology and Biodiversity research databases: how are the user communities articulated?

Pauline Lefebvre , Cécile Callou , Serge X. Cohen , Chloé Martin , Frédérique Chlous
6th Young Natural History Scientists’Meeting, MNHN, Mar 2019, Paris, France. 2019
Conference poster hal-03204649v1
Image document

Archaeology research databases: how are the user communities articulated?

Pauline Lefebvre , Serge X. Cohen , Cécile Callou , Chloé Martin , Frédérique Chlous
Symposium « Heritages Sciences and Technologies », Institut de France, Feb 2019, Paris, France. 2019
Conference poster hal-03204636v1

In-depth imaging of flat ancient material objects: backprojection reconstruction of a 2D conical Radon Transform.

Patricio Guerrero , Serge X. Cohen , Mai K. Nguyen , Laurent Dumas
Atelier scientifique interdisciplinaire "Matériaux du patrimoine et patrimoine matériel", Mar 2016, Plateau Saclay - École Polytechnique, France., Mar 2016, Palaiseau, France.
Conference poster hal-01436931v1

From macrotraces to micro-tomography: a multi-scale approach for detecting and characterizing the “Spiralled Patchwork Technology” in Northern Mediterranean Neolithic pottery assemblages

Louise Gomart , Didier Binder , Laure Blanc-Féraud , Laura Cassard , Serge X. Cohen
D. Binder et C. Manen. Céramiques imprimées de Méditerranée occidentale (VIe millénaire AEC) : données, approches et enjeux nouveaux / Western Mediterranean Impressed Wares (6th millennium BCE): new data, approaches and challenges, Actes de la Séance de la Société préhistorique française, Nice, 18-20 mars 2019, 18, 2022, Séances de la Société préhistorique française
Book sections hal-03908897v1