Research

Software Design :


The main purposes of my researches address the software design with the object oriented methods. These methods are powerful tools to model complex systems.The first systems that I have studied are medical computer diagnosis aided systems. Today, I work on modelisation of metabolic networks.

Metabolic networks modelisation.

Significant overhangs can be obtained if the computers in biology are not only used to traduce calculation (simple or complex) but also to build structured models of the biologic data. In this way, some international projects like E-Cell, Virtual Cell and so on, want to make this for the entire cell. To model biologic descriptions, object oriented methods allows to introduce semantic information about manipulated data inside softwares. We work with these methods to model metabolic networks (static information) and specially mitochondrial data, and to design mitochondrial activity (dynamic information). At this time, many description languages exist to build structured descriptions, like XML family languages which allows to describe used data like text files, outside programs. For the needs of our project MitoScoP (Mitochondria in Silico Project), we have looked forward SBML language which is specially dedicate to metabolic networks coding. It is an evidence that if we conformed us to the domain standards the visibily of the project in the biologist community, will be improved. However, we have noted some lacks in this language when we have used to describe mitochondria. So we plan to propose some adds like the entity ``Enzyme'' which is not explicited in the current version of SBML, and the modification of the general arborescence to integrate the multiplicity of calculating procedures. At the stack of concern of the modelisation process implied by the mitochondrial activity, our system will contain procedures like "differential equations" (when they are known), and modelisation from multi-agent behaviours. Such system known as hybrid because being able to infer with the same data model several kinds of procedures, might be evolutive and flexible simulated tool to test different hypothesese proposed by biologists about mitochondrial pathologies which they study.

References :

Object oriented methods and Design Patterns

Architecture of software is a major point of interest today and the use of structuring methods to develop systems become widespread. For an inflammatory rheumatology application, we have worked on the design of a computer-aided diagnostic system including several methods of reasoning. To define such system an Object-Oriented analysis was managed, but the problem to identify the ``good'' objects is not always solved by this analysis. Some tools, called patterns, can help developers to solve this problem. Patterns give an assistance to refine existing objects and to discover new ones. Catalogs have been published as ``Design Patterns'' by E. Gamma. We have built a software called LADRI (Logiciel d'Aide au Diagnostic en Rhumatologie Inflammatoire) which integrates 4 of these patterns. The patterns Composite and State are used for knowledge representation; Strategy models the diagnostic algorithms and Iterator performs generic task encountered in diagnosis making system.

the complete paper about patterns in a medical diagnostic system.

Genetic epidemidelogy

The weighted pairwise correlation (WPC) approach provides simple and flexible tests for genetic linkage which may be adapted to qualitative, quantitative or age-dependent traits. These tests also seem to have good power. However, when working with large pedigrees, a disease susceptibility gene not linked to the marker studied induces correlations of the trait values, leading to inflated type-one errors for these tests. We propose a new approach for inference based on the randomisation of the alleles following the mendelian laws and conditioning on the alleles of the founders. This approach is applied to the analysis of the quantitative traits in a set of simulated pedigrees. The {\em a posteriori} comparison of the findings to the true model indicates directions for future work.

Publications

Metabolic networks design

Virtual Mitochondria : Metabolic Modelling And Control
Marie Aimar, Stéphane Ludinard, Bernard Korzeniewski, Jean-Pierre Mazat and Christine Nazaret.
International Journal on Molecular and Cellular Biology(Kluwer Academic Publishers), vol 29:1-2, p227-232, 2002..

Virtual mitochondria and their control
Marie Aimar, Bernard Korzeniewski, Jean-Pierre Mazat and Christine Nazaret.
Modelling and simulation of biological processes in the context of genomics, Autrans (France), March 18 - 21, 2002.

Object oriented methods, Design Patterns and Medical computer-aided diagnosis systems

PaLaDeM : a Pattern Language for a Decision Making System in Medicine (ps abstract).
M. Beurton-Aimar et B. Le Blanc. IPMU2000, 8th Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems, Madrid (Espagne), July 3 - 7, 2000.

A Decision Making System in Inflammatory Rheumatology using Different Reasoning Methods (ps abstract).
M. Beurton-Aimar, B. Le Blanc. International Journal of Computers and their Applications, 6 (2): 73-77, 1999.

Medical KBS Design with Patterns (ps).
M. Beurton-Aimar. 9th Workshop for PhD Students in Object Oriented Systems. Object-Oriented Technology, ECOOP'99 Workshops, Panels, and Posters, Lisbonne (Portugal), 14-18 juin 1999.
Lecture Notes in Computer Science 1743.

Using Patterns into the Conception of a Medical KBS: LADRI, a Software for Diagnosis in Rheumatology. (ps)
M. Beurton-Aimar et B. Le Blanc. Object-Oriented Technology, ECOOP'99 Workshops, Panels, and Posters, Lisbonne (Portugal), 14-18 juin. Lecture Notes in Computer Science 1743, (à paraître).

Designing Medical Knowledge-based System from Patterns. (ps abstract)
M. Beurton-Aimar et B. Le Blanc. Proceed. of the 14th Int. Conference on Computers And Their Applications, pp 218-221, Cancun (Mexique), 7-9 avril, 1999.

LADRI: a Decision Making System in Inflammatory Rheumatology. (ps abstract)
M. Beurton-Aimar, B. Le Blanc et J.P. Vernhes. Proceed. of the 7th Int. Conference on
Intelligent Systems, pp 51-56, Paris, 1-2 juillet, 1998.

Création d'une base de connaissances objet pour l'aide au diagnostic en rhumatologie (1) (ps abstract).
M. Beurton-Aimar, J.P. Vernhes, B. Le Blanc, J. Dehais et R. Salamon. 10ème congrès français de rhumatologie. Rev. du rhumatisme, 11 : 762, 1997.

Logiciel d'aide au diagnostic en rhumatologie inflammatoire (2) (ps abstract).
J.P. Vernhes, M. Beurton-Aimar, B. Le Blanc, J. Dehais et R. Salamon. 10ème congrès français
de rhumatologie. Rev. du rhumatisme, 11 : 763, 1997.

Modélisation Objet et Aide au Diagnostic : Application à la Rhumatologie Inflammatoire (ps abstract).
M. Beurton-Aimar, J.P. Vernhes, B. Le Blanc, J. Dehais, 2ème Colloque de Sciences Cognitives façade atlantique, COGNITIQUES/Cognitics, série des sciences cognitives appliquées, 2 : 175, 1996.

Genetics


Multipoint linkage analysis using the WPC statistic (ps abstract).
D. Commenges, M. Beurton-Aimar. Genetic Epidemiology, 17 : 515-519, 1999.


WPC Test based on randomization for analyzing quantitative traits on simulated pedigrees (ps abstract).
D. Commenges, M. Beurton-Aimar. Genetic Epidemiology, 14 : 971-4, 1997.

Analysis of MRI images

Towards computer-aided diagnosis for white matter abnormalities
Laurent Vallet, Marie Beurton-Aimar Pascal Desbarats, Colette Fabrigoule, Michèle Allard
International Conference on Computer Vision and GraphicsSeptember 22-24, 2004 Warsaw, Poland.