Publications, Communications and students


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 Publications: 

Articles in Journals:

    • 19- Inconsistency of Template Estimation by Minimizing of the Variance/Pre-Variance in the Quotient Space. L. Devilliers, S. Allassonnière, A. Trouvé, X. Pennec. Entropy 201719(6), 288; doi:10.3390/e19060288
    • 18- Template estimation in computational anatomy: Fréchet means top and quotient spaces are not consistent, L. Devilliers, S. Allassonnière, A. Trouvé, X. Pennec. Accepted for publication in SIAM journal on Imaging Science (2017).
    • 17- Phase-based Metamorphosis of Diffusion Lesion in Relation to Perfusion Values in Acute Ischemic StrokeI. Rekik, S. Allassonniere, M. Luby, T. Carpenter and J. Wardlaw. NeuroImage Clinical 9(C):44-49, 2015. DOI: 10.1016/j.nicl.2015.07.007.
    • 16- Bayesian Mixed Effect Atlas Estimation under Diffeomorphic constraint on the deformation model. S.Allassonnière, S.Durrleman and E.Kuhn. 
      SIAM Journal on Imaging Science., 8(3), 1367–1395, 2015.  (pdf)
    • 15- Convergent stochastic Expectation Maximization algorithm with efficient sampling in high dimension. Application to deformable template model estimation. S. Allassonniere and E. Kuhn. Journal of Computational Statistics & Data Analysis, Volume 91(C), 2015. 
    • 14- Using longitudinal metamorphosis to examine ischemic stroke lesion dynamics on perfusion- weighted and relation to final outcome on T2-w images. I. Rekik, S. Allassonniere, T. Carpenter and J. Wardlaw. NeuroImage Clinical, 5, 2014, pp 332-340. 
    • 13- Bayesian estimation of Probabilisitic atlas for tissue segmentation. H. Xu, B.Thirion and S. Allassonniere, IRBM Journal, 35(1), 2014, pp 27-32.
    • 12- Probabilistic Atlas and Geometric Variability Estimation to Drive Tissue Segmentation. H. Xu, B.Thirion and S. Allassonniere, Statistics in Medicine, 33(20), 2014, pp 3576–3599. 
    • 11- Statistical models for deformable templates in image and shape analysis. S. Allassonniere, J. Bigot, J.A. Glaunes, F. Maire and F.J.P. Richard. Annales mathématiques Blaise Pascal, vol 20(1), 2013.
    • 10- Spacio-temporal dynamic simulation of acute perfusion/diffusion ischemic stroke lesions evolution: a pilot study derived from longitudinal MR patient data. I. Rekik, S. Allassonniere, S. Durrleman, T. Carpenter and J. Wardlaw. Computational and Mathematical Methods in Medicine, vol 2013, doi:10.1155/2013/283593, 2013 (pdf).
    • 9- A Review of Medical Image Analysis Methods in MR/CT-imaged Acute-subacute Ischemic Stroke Lesion: Segmentation, Prediction and Insights into Dynamic Evolution Simulation Models. I. Rekik, S. Allassonniere, T. Carpenter and J. Wardlaw. NeuroImage Clinical Volume 1, Issue 1, (2012), (164-178) (pdf).
    • 8- Sparse Adaptive Parameterization of Variability in Image Ensembles. S. Durrleman, S. Allassonniere, S.Joshi. IJCV, 2012, (DOI) 10.1007/s11263-012-0556-1.
    • 7- Aircraft classification with a low resolution infrared sensor. S. Lefebvre, S. Allassonniere, J. Jakubowicz, T. Lasne, and E. Moulines. Machine Vision and Application Journal, 2013, Vol. 24(1), pp 175-186 (pdf).
    • 6- Tumor Growth Parameters Estimation and Source Localization From a Unique Time Point: Application to Low-grade Gliomas. I. Rekik, S. Allassonniere, H. Deslingette, O. Clatz, E. Geremia, N. Ayache.  Computer Vision and Image Understanding, 117(3), 2013, pp 238-249.
    • 5- A Stochastic Algorithm for Probabilistic Independent Component Analysis. S. Allassonnière, L. Younes.  Annals of Applied Statistics, 2012, Vol. 6, No. 1, 125-160 (.pdf)
    • 4- Bayesian Consistent Estimation in Deformable Models using Stochastic Algorithms: Applications to Medical ImagesS. Allassonnière, E. Kuhn, A. Trouvé. Journal de la Société Française de Statistiques. Vol. 151(1) p. 1-16, 2010.
    • 3- Stochastic Algorithm For Parameter Estimation For Dense Deformable Template Mixture Model. S. Allassonnière, E. Kuhn.  ESAIM-PS 2010, Vol 14, p. 382_408. (.pdf)
    • 2- Construction of Bayesian deformable models via stochastic approximation algorithm: A convergence study.  S. Allassonnière, E. Kuhn, A. Trouvé. Bernoulli Journal, Vol 16(3), p.641-678, 2010. (pdf)
    • 1- Toward a coherent statistical framework for dense deformable template estimation. S. Allassonnière, Y. Amit, A. Trouvé. Volume 69, part 1 (2007), pages 3-29, of the Journal of the Royal Statistical Society, Series B.  (pdf)
        

    PhD and HDR dissertations:

    • HDR manuscript: Statistical analysis of Deformable Template Models for medical image understanding. (pdf)
    • PhD Dissertation: Representation and Statistical Estimation of Deformable Template Models for Shape Recognition and Computational Anatomy. S.Allassonnière. (pdf)

    Conference Articles:

    •  Statistical Learning of Spatiotemporal Patterns from Longitudinal Manifold-Valued NetworksI. Koval, J.-B. Schiratti, A. Routier, M. Bacci, O. Colliot, S. Allassonnière, S. Durrleman. MICCAI 2017

    • Optimisation d'arbre de décision pour un problème de détection précoce d'anomalies foetales. R. Besson, E. Le Pennec, S. Allassonnière. JDS2017.

    • Inconsistency of Template Estimation with the Fréchet mean in Quotient SpaceLoïc DevilliersXavier Pennec, and Stéphanie Allassonnière. In Information Processing in Medical Imaging 2017, Boone, United States, June 2017.

    • Estimating the Template in the Total Space with the Fréchet Mean on Quotient Spaces may have a Bias: a Case Study on Vector Spaces Quotiented by the Group of Translations. S. Allassonnière, L. Devilliers, X. Pennec. Proceedings of the fifth international workshop on Mathematical Foundation sof Computational Anatomy (MFCA'15), Munich, Germany, pages 131-142, 2015

    • Learning spatiotemporal trajectories from manifold-valued longitudinal data. J.J Schiratti, S. Allassonnière, O. Colliot, S. Durrleman. NIPS 2015.

    • Innovation-based sparse estimation of functional connectivity from multivariate autoregressive models. F. Deloche, F. De Vico Fallani, S. Allassonnière. Proc. SPIE 9597, Wavelets and Sparsity XVI, 95971I (August 24, 2015); doi:10.1117/12.2189640; Conference Volume 9597

    •  Mixed-effects model for the spatiotemporal analysis of longitudinal manifold-valued data. J-B.  Schiratti, S. Allassonnière, O. Colliot, S. Durrleman. MFCA 2015

    • Estimating the Template in the Total Space with the Fréchet Mean on Quotient Spaces may have a Bias: a Case Study on Vector Spaces Quotiented by the Group of Translations.  S. Allassonnière, L. Devilliers, X. Pennec. MFCA 2015.

    • A mixed effect model with time reparametrization for longitudinal univariate manifold valued data}. \textsc{J.B. Schiratti, S. Allassonni\`ere, O. Colliot, S. Durrleman}. Information Processing in Medical Imaging (IPMI) 2015

    • Bayesian Estimation of Probabilistic Atlas for Anatomically-Informed Functional MRI Group Analyses. H. Xu, B. Thirion and S. Allassonniere. MICCAI, Nagoya, 2013

    • A 4D Patient-specific metamorphosis-based method to model ischemic stroke lesion evo- lution from acute diffusion-weighted to final T2-defined outcome. I. Rekik, S. Allas- sonnie`re, T. Carpenter and J. Wardlaw. International Stroke Conference, Honolulu, 2013. 
    • 4D spatio-temporal perfusion-diffusion Evolution scenarios estimation in Acute-subacute ischemic stroke. 

      I. Rekik, S. Allassonniere, S. Durrleman, T.K. Carpenter, J.M. Wardlaw, ISMRM, Melbroune, 2012.
    • Dynamic Patient-specific Modeling of Ischemic Stroke Lesion Evolution: From Presentation to Final Damage using Diffusion, Perfusion and T2 MR imaging, I. Rekik, S. Allassonniere, S. Durrleman, T.K. Carpenter, J.M. Wardlaw, ESC, Lisbon, 2012.
    • Mathematical Image Processing Algorithms in determining Stroke Tissue Status and Pre- dicting its Fate: Systematic Review reveals Untapped Potentials. I. Rekik, S. Allas- sonnie`re, T. Carpenter and J. Wardlaw.. European Stroke Conference, Hamburg 2011. 
    • Detection and classification of poorly known aircraft with a low-resolution infrared sensor. S. Lefebvre, S. Allassonnière, G. Durand, J. Jakubowicz, E. Moulines, A. Roblin. Proc. of SPIE volume 8050 (2011).
    • Detecting long distance conditional correlations between anatomical regions using Gaussian Graphical Models

      .
      S. Allassonnière, P.Jolivet, C.Giraud. Mathematical Fundation of Computational Anatomy
       (MFCA) workshop of the MICCAI 2011 conference. (pdf)
    • Consistent Atlas Estimation on BME Template Model: Applications to 3D Biomedical Images. S. Allassonnière, E. Kuhn, J. T. Ratnanather, A. TrouvéProbabilistic Models for Medical Image Analysis (PMMIA) worshop of the MICCAI 2009 conference. (pdf)
    •  MAP Estimation of Statistical Deformable Template Via Nonlinear Mixed Effect Models~:
      Deterministic and Stochastic Approaches.
      S.Allassonnière, E.Kuhn, A.Trouvé. Mathematical Foundations of Computational Anatomy (MFCA) workshop of MICCAI 2008 conference. (pdf)
    • Generative Model and consistent estimation algorithms for non-rigid deformable models. S.Allassonnière, E.Kuhn, Y.Amit, A.Trouvé. ICASSP conference, 2006 in Toulouse, France  (pdf)
    • Geodesic Shooting and Diffeomorphic Matching Via Textured Meshes. S.Allassonnière, A.Trouvé, L.Younes. EMMCVPR 2005, St Augustine, Florida, USA. (pdf)

    Grants:
    • PEPS Egalité (PI)
    • MMoVNI : Digiteo project (PI)
    • ANR_HM-TC (PI : Olivier Colliot)
    • ANR IRMGroup (PI : Stéphane Mallat)

    Students:

    • Master students
      • Pierre Jolivet (M1)
      • Islem Rekik (M2)
      • James Newling (M1)
    • PhD students
      • Jean-Baptiste Schirratti (01/09/2013-)
      • Islem Rekik (09/2010-31/03/2014)
      • Hao XU (03/2011-30/03/2014)

     

    Several Presentations and Seminars:

     
    • Seminar at the Institut National de Recherche Agronomique (INRA)  in Toulouse (November 2013)
    • Seminar at the University Paris Dauphine (November 2013)
    • Seminar at the CIMI thematic trimester on image processing (May 2013)
    • Presentation of the AMALA sampler at the conference Méthodes Mathématiques pour l'Image (Orléans, June 2012)
    • Presentation of the AMALA sampler at the BigMC seminar (January 2012)
    • Mini-course on  Computational Anatomy at the Forum des jeunes mathématiciennes (November 2011)
    • Seminar at the Institut des mathématiques in Toulouse for the Statistics and Imaging meeting (June 2011)
    • Presentation of current work at the annual Shape meeting, Imperial College London (May 2011)
    • Tutorial on Computational Anatomy at the KTH university in Stockholm (October 2010)
    • Image lunch seminar at the Scientific Computing and Imaging Institute (University of Utah September 2010)
    • Organization of the mini-symposium on Statistics for medical Image Analysis, part of the IMA conference on Imaging Science (April 2010)
    • Poster presentation at the  Probabilistic Models for Medical Image Analysis (PMMIA) worshop of the MICCAI 2009 conference. (pmmiabis.pdf)
    • Presentation at the Summer School Mathematics in Brain Imaging   in the Institute of Pure and Applied Mathematics (UCLA)  Generative Models and Stochastic Algorithms for Population Average Estimation and Image Analysis."(07/15/08).
    •  Seminar at the Applied Mathematics and Statistics department in Johns Hopkins University (03/04/08) :  Representation and Statistical Estimation of Deformable Template Models for Shape Recognition and Computational Anatomy.
    • Seminar Siemens Corporate Research (04/02/08) :  Representation and Statistical Estimation of Deformable Template Models for Shape Recognition and Computational Anatomy.
    • Seminar in University of Maryland Baltimore County (UMBC),  Department of Mathematics and Statistics (16/11/07) :  Representation and Statistical Estimation of Deformable Template Models for Shape Recognition and Computational Anatomy.
    • Presentation in the New Researcher Session of the SAMSI Summer 2007 Program on the Geometry and Statistics of Shape Spaces (July 7-13, 2007) : Representation and Statistical Estimation of Deformable Template Models for Shape Recognition and Computational Anatomy
    • Thesis defense, University Paris 13 (07/04/07)  : Representation and Statistical Estimation of Deformable Template Models for Shape Recognition and Computational Anatomy.
    • Seminar in LATP University of Provense, Marseille (12/01/06)  Toward a coherent statistical framework for dense deformable template estimation.
    • Presentation in the colloquim of Centre de Mathematiques et leurs Applications, Cachan, France, (05/18/06)  : Toward a coherent statistical framework for dense deformable template estimation.
    • Presentation in the ICASSP conference, Toulouse (05/16/06) : Generative Model and consistent estimation algorithms for non-rigid deformable models.
    • Poster session in the workshop in IMA on Shape Spaces (02-06/04/06) : Generative Model and consistent estimation algorithms for non-rigid deformation model.
    • Presentation in the ENST for the "groupe de travail" ISIS and MSPC (09/06/05) : Geodesic Shooting and Diffeomorphic Matching Via Textured Meshes.
    • Presentation in the LAGA probability and statistics seminar (13/04/05): Large Deformations and Triangulation for Image Matching Problems.
    • Presentation in the Center for Imaging Science in Johns Hopkins University (Baltimore) (15/03/05): Large Deformations and Triangulation for Image Matching Problems. 


    Conferences: 


    • MICCAI 2009. London. Sept 20th to Sept 24th.
    • MICCAI 2008. New York City. Sept 6th to Sept 10th.
    • Summer School in UCLA: Mathematics in Brain Imaging (2008)
    • SAMSI Summer 2007 Program on the Geometry and Statistics of Shape Spaces (July 7-13, 2007)
    • Workshop in Paris Dauphine University on Mathematics and Image Analysis ( 2004 and 2006)
    • IMA workshop on Shape Spaces (Apr 2006)
    • International Conference on Acoustics, Speech, and Signal Processing (ICASSP 2006)
    • Energy Minimisation Methods for Computer Vision and Pattern Recognition (EMMCVPR 2005)  
    • Summer School in UCLA: Mathematics in Brain Imaging (2004)