Aurobrata Ghosh

Aurobrata Ghosh
Diffusion MRI Scientist
Athéna, Inria, 2004 Route des Lucioles, Sophia Antipolis, 06902, France
Date: 25th March 2014
contact
[email protected]
https://sites.google.com/sit
e/brainconnectomics2
M: +33-(0)660474694 (Fra)
H: +91-(0)4132225995(Ind)
languages
English, French: fluent
Bengali, Hindi, Sanskrit
computers
prog: C, C++ (adept),
Java, Python, Fortran
computing: MATLAB,
Maple, Maxima
graphics: OpenGL,
VTK, Qt (GUI)
os: Linux, Windows
statement
objective: I seek a professional R&D career, private or academic, in medical imaging, where I can
create accessible products for hospitals and clinics, which deliver & broaden cutting edge
computational healthcare techniques (in particular Diffusion MRI) – to help improve in
vivo & non-invasive diagnosis and prognosis of cerebral pathologies. I am proficient in the
state-of-the-art of Diffusion MRI, I have strong mathematical and programming skills and
a proven track record for making advanced computing/mathematical tools accessible to
industrial users.
core-skills: 7 years experience in COMPUTATIONAL DIFFUSION MRI for modelling the connectivity &
integrity of the brain's white matter (includes a PhD & a Post-doctoral position).
summary: 10 years experience (academic & professional) in SCIENTIFIC RESEARCH & delivery of
ADVANCED MATHEMATICAL SOLUTIONS to medical, industrial & business domains.
publications: 39: Journals*: (5), Chapters: (4), Conferences*: (16), Abstracts*: (13), PhD-thesis: (1)
(*peer-reviewed)
available: November 2014 (to discuss), preferably in Europe.
experience
2013–2014
Research Engineer, OLEA MEDICAL & ATHÉNA, INRIA, FRANCE
(current)
- Providing an expert link between academic research and the medical imaging industry.
Developing a C++ library of diffusion MRI algorithms at Athéna, Inria which is being
integrated into Olea Medical's flagship product – Olea Sphere.
- key achievements: (estimation algorithms)
•
DTI: Linear, weighted-Linear, Cholesky (positive constraint)
•
Generalized-DTI: Linear, weight-Linear, Ternay Quartic (TQ: positive constraint)
•
DKI: Linear, weight-Linear, Cholesky+TQ (positive), Maximum likelihood (MLE)
- key tools: (software development)
•
templated C++ & generic programming, with a C/C++ interface
•
standard numerical libraries: LAPACK, NLOpt
•
standard tools: CMake, Git, Linux
2011–2012
Post-Doctoral Fellow, ATHÉNA, INRIA, SOPHIA ANTIPOLIS, FRANCE
- R&D local and global white-matter structures of the brain from Diffusion MRI (dMRI).
- key achievements:
•
Developed novel estimation algorithms for state-of-the-art dMRI models:
ODF, FOD (spherical deconvolution), EAP and constrained DKI.
•
Proposed new dMRI biomarkers from 3D rotation invariants of 4 th order tensors.
•
Fractality in human cerebral neuron axonal topography from dMRI tractography.
•
Guided an under-graduate intern, which resulted in a journal publication.
(*peer-reviewed)
- publications: 14
of which: Journals*: (5), Book-chapters: (3), Conferences*: (5), Abstracts*: (1).
date of birth
17th of May, 1979
nationality
Indian
permanent address
48 Francois Dessier St.
P.O. Padmininagar,
Pondicherry, 605012, India
2007–2011
2006
Ph.D, ATHÉNA, INRIA, SOPHIA ANTIPOLIS, FRANCE
Computer Science & Signal Processing (details below).
Game Programmer, VBEING SOFTWARE PVT. LTD. NEW DELHI, INDIA
- Designed & developed a common C++ API to interface standard physics gaming engines.
- key achievements:
•
Developed a C++ library/API to wrap the Open Dynamics Engine (ODE), but
also compatible with the commercial physics engine Havok.
•
Used this in a demo virtual first-person explorer of archeological sites of N. Delhi.
- key tools: (software development)
•
OOP, C++, MS Visual Studio, Windows 2000
•
physics engine: Open Dynamics Engine
reference: 1
2004–2005
Research Assistant, INDIAN INSTITUTE OF TECHNOLOGY KANPUR (IIT-K), INDIA
- Developed Yantrika, a GUI based complete design, analysis, path-planning & control
software for hyper-redundant robotic arms. It was comprised of research done at IIT-K.
Yantrika was sold to Indira Gandhi Centre for Atomic Research (IGCAR), Kalpakkam,
India for designing robotic manipulators to handle nuclear waste.
key
achievements:
•
Designed & developed a fully functional GUI based robotic software solution.
•
It was sold to IGCAR for designing manipulators to handle nuclear waste.
•
Lead a team of 3 M.Tech post-graduate students to develop Yantrika.
- key tools: (software development)
•
OOP, C++, C, OpenGL, Qt, Qt-Designer, KDevelop, Make, Linux
2003–2004
Associate Programmer, SAPIENT CORPORATION, INDIA
- Wrote key Java+Matlab code for a Sapient project to optimize the gas portfolio and
trading+risk management for the Dutch energy giant Essent Energie.
Designed & implemented core numerical optimization solvers in Matlab, wraped these
with Java via JNI and integrated & oversaw their robust functioning at the heart of the
Gas Optimization solution of the ParkMaster project that Sapient created for Essent
Energie. Collaborated with & worked in a 40 member team.
- key achievements:
•
2005: The Gas Optimization solution was nominated by Morgan Stanley and won
the Computerworld Honors Medal of Achievement. (Link1, Link2)
•
2006: The Gas Optimization solution won the “Best In-House Software System”
award by the EnergyRisk Magazine. (Link1, Link2)
•
“This [Gas Optimiz.] solution, which resulted in costs savings of 4MM [million]
Euros within 24 hours, literally paid for itself the first day it went live.” (Link)
- key tools: (software development)
•
OOP, Java, JNI, MATLAB, Oracle
•
Eclipse, Svn, Apache Ant, Windows
Dr. Rachid Deriche
[email protected]
Research Director & Leader,
Project Team Athéna,
Inria Sophia Antiplois –
Méditerranée,
2004 Rt des Lucioles,
Sophia Antipolis 06902,
France
W:+33-(0)492387832 (Fra)
reference: 2
Dr. Maxime Descoteaux
[email protected]
Associate Professor,
MOIVRE Centre,
Dept. of Computer Science,
Sherbrooke University,
2500 Blv Université,
Sherbrooke, Québec
Canada, J1K 2R1
W:+18198218000 (Can)
ext: 66129
awards
2007: PhD scholarship,
Ministère de l'Éducation
National, France (MESR)
2002: Joint CSIR & UGC
Junior Research Fellowship
in Mathematics
interests
aikido: since 7 years
music: Indian classical
music – Sitar, Tabla
education
2007–2011
- Ph.D in COMPUTER SCIENCE & SIGNAL PROCESSING
Project Team Athéna, Inria Sophia Antipolis – Méditerranée, France
2006–2007
- MS in COMPUTER SCIENCE
Campus STIC, Université de Nice – Sophia Antipolis, France
2001–2003
- MSc in MATHEMATICS
Indian Institute of Technology, Kanpur, India
phd thesis
title:
supervisor:
reviewers:
examiners:
achievements:
Higher Order Models in Diffusion MRI and Applications
Dr Rachid Deriche
Dr Peter J. Basser & Dr Baba C. Vemri
Dr Habib Benali, Dr Pierre Comon, Dr Rachid Deriche, Dr Nikos Paragios
Developed higher order & more accurate descriptors (than DTI) to model the
microstructure & integrity of the cerebral white matter from Diffusion MRI.
keywords: Diffusion MRI, 4th order tensor, DTI, DKI, G-DTI, ODF, EAP, positive diffusion constraint.
(*peer-reviewed)
- publications: 23
of which: Book-chapters: (1), Conferences*: (10), Abstracts*: (11), PhD-thesis: (1)
communication skills
Invited Talks & Oral Presentations
(highlights)
Higher Order Tensors in Diffusion MRI: Think Positive, STBB, NIH, Bethesda, USA, 2008
Extracting the Maxima of Spher. Func., BioMedical Image Analysis, T.U.E., Eindhoven, Holland, 2009
Fast & Analytical EAP Approx., International Symp. on Biomed. Imag., Rotterdam, Holland, 2010
High Order Models in D-MRI, Indian Statistical Institute & NIMHANS, Bangalore, India, 2011
Estimation of 4th order tensors in D-MRI, Dagstuhl Seminar, Vis. & Proc. Of Tensors., Germany, 2011
Maxima Extraction & Tractography in HARDI, Information Proc. in Med. Imag. IPMI, Germany, 2011
Scalar Indices for D-MRI from Higher Order Models, Max Planck Institute, Leipzig, Germany, 2012
+ Posters in numerous international conferences.
(annexe: publications, P.T.O.)
1.
2.
3.
4.
5.
6.
7.
publications
2013
Journal Articles (peer reviewed)
1.
2.
3.
2012
4.
5.
2014
Book Chapters
1.
2.
2013
3.
2009
4.
2013
2012
1.
2.
4.
5.
6.
7.
8.
2010
A. Ghosh and R. Deriche
4th Order Symmetric Tensors and Positive ADC Modelling. In Visualization and Processing of Tensors and
Higher Order Descriptors for Multi-Valued Data. PC Chairs: B. Burgeth, A. Vilanova and C. F. Westin.
Dagstuhl Seminar 2011. In print.
T. Schultz, A. Fuster, A. Ghosh, R. Deriche, L. Florack, L.-H. Lim
Higher-Order Tensors in Diffusion Imaging: A Survey. In Visualization and Processing of Tensors and Higher
Order Descriptors for Multi-Valued Data. PC Chairs: B. Burgeth, A. Vilanova and C. F. Westin. Dagstuhl
Seminar 2011. In print.
A. Ghosh and R. Deriche
From Diffusion MRI to Brain Connectomics. In Modeling in Computational Biology and Biomedicine: A
Multidisciplinary Endeavor, Lectures Notes in Mathematical and Computational Biology, chapter: 6, pages:
193–231, publisher: Springer, editors: Frederic Cazals and Pierre Kornprobst, 2013.
A. Ghosh and R. Deriche
From second to higher order tensors in diffusion MRI. In Tensors in Image Processing and Computer Vision,
Advances in Pattern Recognition, Chapter 9. Springer London, May 2009, Editors: Santiago Aja-Fernandez,
Rodrigo de Luis Garcia, Dacheng Tao, and Xuelong Li, 2009.
Conference Articles (peer reviewed)
3.
2011
S. Merlet, E. Caruyer, A. Ghosh and R. Deriche
A computational diffusion MRI and parametric dictionary learning framework for modeling the diffusion signal
and its features. Medical Image Analysis, vol. 17:7, pages: 830–843, October 2013.
A. Ghosh, T. Milne and R. Deriche
Constrained Diffusion Kurtosis Imaging Using Ternary Quartics & MLE. Magnetic Resonance in Medicine.
Article first published online: 2 July 2013.
A. Ghosh, E. Tsigaridas, B. Mourrain and R. Deriche
A polynomial approach for extracting the extrema of a spherical function and its application in diffusion MRI.
Medical Image Analysis, vol: 17:5, pages: 503–514, July 2013.
A. Ghosh and R. Deriche
Fast & Analytical EAP Approximation from a 4th Order Tensor. International Journal of Biomedical Imaging,
Special Issue: Advanced Signal Processing Methods for Biomedical Imaging, vol. 2012, Article ID 192730, 9
pages, 2012.
P. Katsaloulis, A. Ghosh, A.C. Philippe, A. Provata and R. Deriche
Fractality in the neuron axonal topography of the human brain based on 3-D diffusion MRI. The European
Physical Journal B - Condensed Matter and Complex Systems, vol 85:5, pages 150–157, 2012.
9.
A. Ghosh, T. Megherbi, F. O. Boumghar and R. Deriche
Fiber Orientation Distribution from Non-Negative Sparse Recovery. In 2013 IEEE International Symposium
on Biomedical Imaging: From Nano to Macro, April 2013, San Fransisco.
A. Ghosh, T. Papadopoulo and R. Deriche
Generalized Invariants of a 4th order tensor: Building blocks for new biomarkers in dMRI? In Proceedings of
Workshop on Computational Diffusion MRI, MICCAI, pages: 165–173, 2012.
A. Ghosh, T. Papadopoulo and R. Deriche
Biomarkers for HARDI : 2nd and 4th Order Tensor Invariants. In 2012 IEEE International Symposium on
Biomedical Imaging: From Nano to Macro (ISBI), Barcelona, May 2012.
T. Milne, A. Ghosh and R. Deriche
Constrained Diffusion Kurtosis Imaging Using Ternary Quartics & MLE. In Proceedings of Workshop on
Computational Diffusion MRI, MICCAI, pages: 153–-164, 2012.
J. Cheng, S. Merlet, E. Caruyer, A. Ghosh, T. Jiang and R. Deriche
Compressive Sensing Ensemble Average Propagator Estimation via L1 Spherical Polar Fourier Imaging. In
Proceedings of Workshop on Computational Diffusion MRI, MICCAI, 2011.
A. Ghosh and R. Deriche
A Polynomial Approach for Maxima Extraction and its Application to Tractography in HARDI. In Information
Processing in Medical Imaging (IPMI) 2011, July 2011.
A. Ghosh and R. Deriche
Extracting geometrical features & peak fractional anisotropy from the ODF for white matter characterization.
In 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, April 2011.
J. Cheng, A. Ghosh, T. Jiang and R. Deriche
Diffeomorphism Invariant Riemannian Framework for Ensemble Average Propagator Computing. Medical
Image Computing and Computer-Assisted Intervention - MICCAI, volume 6892 of Lecture Notes in Computer
Science, pages 98-106, 2011.
A. Ghosh and R. Deriche
Fast and closed-form ensemble-average-propagator approximation from the 4th- order diffusion tensor. In
IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pages 1105–1108. April 2010.
2010
2009
2008
2006
2014
10. J. Cheng, A. Ghosh, T. Jiang, and R. Deriche
Model-free and analytical EAP reconstruction via spherical polar fourier diffusion MRI. In Medical Image
Computing and Computer-Assisted Intervention - MICCAI, volume 6361, pages 590-597, 2010.
11. J. Cheng, A. Ghosh, R. Deriche, and T. Jiang
Model-free, regularized, fast, and robust analytical orientation distribution function estimation. In Medical
Image Computing and Computer-Assisted Intervention - MICCAI, volume 6361 of Lecture Notes in Computer
Science, pages 648- 656, 2010.
12. A. Ghosh, M. Moakher, and R. Deriche
Ternay quartic approach for positive 4th order diffusion tensors revisited. In 2009 IEEE International
Symposium on Biomedical Imaging: From Nano to Macro, pages 618-621, June 2009.
13. J. Cheng, A. Ghosh, T. Jiang, and R. Deriche
A Riemannian framework for orientation distribution function computing. In Medical Image Computing and
Computer Assisted Intervention (MICCAI), pages 911-918, September 2009.
14. A. Ghosh, M. Descoteaux, and R. Deriche
Riemannian Framework for estimating Symmetric Positive Definite 4th Order Diffusion Tensors. In Medical
image computing and computer-assisted intervention – MICCAI, pages 858-865, 2008.
15. A. Ghosh, E. Tsigaridas, M. Descoteaux, P. Comon, B. Mourrain, and R. Deriche
A polynomial based approach to extract the maxima of an antipodally symmetric spherical function and its
application to extract fiber directions from the orientation distribution function in diffusion MRI. In
Proceedings of Workshop on Computational Diffusion MRI, MICCAI, 2008.
16. V. Rakesh, A. Ghosh, B. Dasgupta and K. V. Kasiviswanathan
Integrated Resource Development for Design and Analysis of Kinematically Redundant Manipulators. 14th
International Conference on CAD/CAM and Factories of the Future (CARS and FOF), Coimbatore, India,
pages: 614–620, 19-22 July 2006.
Conference Abstracts (peer reviewed)
1.
2012
2.
2011
3.
4.
2010
5.
6.
7.
8.
9.
2009
10.
11.
12.
2008
13.
A. Ghosh and R. Deriche
Greedy NNLS: Fiber Orientation Distribution From Non-Negatively Constrained Sparse Recovery. In
Proceedings of ISMRM 2014, Milan, Italy, May 2014. Accepted.
S. Merlet, E. Caruyer, A. Ghosh and R. Deriche
Parametric Dictionary Learning in Diffusion MRI, HARDI Contest. In 2012 IEEE International Symposium on
Biomedical Imaging: From Nano to Macro (ISBI), Barcelona, May 2012.
J. Cheng, A. Ghosh, T. Jiang, and R. Deriche
A Riemannian Framework for Ensemble Average Propagator Computing. ISMRM Montreal Canada, 2011.
J. Cheng, S. Merlet, A. Ghosh, E. Caruyer, T. Jiang, and R. Deriche
Compressive Sensing Ensemble Average Propagator Estimation via L1 Spherical Polar Fourier Imaging. 19th
ISMRM Montreal Canada, 2011.
A. Ghosh and R. Deriche
Unraveling the ODF: Extracting its maxima & other geometric characteristics for bio-markers & tractography
in diffusion MRI. In Proceedings 2010: Medical Imaging: Perspectives on Perception and Diagnostics, IIT
Delhi, India, December 2010.
J. Cheng, A. Ghosh, T. Jiang, and R. Deriche
Riemannian median and its applications for orientation distribution function computing. In Proceedings
ISMRM, 2010.
J. Cheng, A. Ghosh, T. Jiang, and R. Deriche
Fast, model-free, analytical diffusion PDF profile estimation from the DWI signals. In 16th Annual Meeting of
the Organization for Human Brain Mapping, Barcelona, June 2010.
J. Cheng, A. Ghosh, T. Jiang, and R. Deriche
Fast, model-free , analytical ODF reconstruction from the q-space signal. In 16th Annual Meeting of the
Organization for Human Brain Mapping, Barcelona, June 2010.
A. Ghosh, E. Ozarslan, and R. Deriche
Challenges in reconstructing the propagator via a cumulant expansion of the one-dimensional q-space MR
signal. In Proceedings of ISMRM, May 2010.
A. Ghosh, E. Tsigaridas, M. Descoteaux, and R. Deriche
A polynomial based approach to extract fiber directions from the ODF and its experimental validation. In
Proceedings ISMRM, volume 17, page 1389, 2009.
J. Cohen-Adad, A. Ghosh, H. Leblond, M. Descoteaux, R. Deriche, H. Benali, and S. Rossignol
Comparison of DTI and Q-Ball imaging metrics in a cat model of spinal cord injury. In 14th Annual Meeting
of the Organization for Human Brain Mapping (HBM), San Fransisco, USA, July 2009.
J. Cohen-Adad, H. Leblond, A. Ghosh, M. Descoteaux, R. Deriche, H. Benali, and S. Rossignol
Evaluation of Q-Ball metrics for assessing the integrity of the injured spinal cord. In Proceedings ISMRM,
volume 17, page 639, 2009.
A. Ghosh, M. Descoteaux, and R. Deriche
4th order diffusion tensor estimation and application. In Proceedings ISMRM, volume 16, page 3321, 2008.

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