fl-INPROCEEDINGS.bib
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@inproceedings{BLS11,
author = {Fran{\c{c}}ois Boulier and Fran{\c{c}}ois Lemaire
and Alexandre Sedoglavic},
title = {{On the Regularity Property of Differential Polynomials
Modulo Regular Differential Chains}},
booktitle = {{Proceedings of Computer Algebra in Scientific Computing, LNCS 6885}},
address = {Kassel, Germany},
note = {\url{http://hal.archives-ouvertes.fr/hal-00599440}},
pages = {61-72},
year = 2011
}
@inproceedings{BLPS11,
author = {Fran{\c{c}}ois Boulier and Fran{\c{c}}ois Lemaire
and Michel Petitot and Alexandre Sedoglavic},
title = {{Chemical Reaction Systems, Computer Algebra and
Systems Biology}},
booktitle = {{Proceedings of Computer Algebra in Scientific Computing, LNCS 6885}},
address = {Kassel, Germany},
editor = {Vladimir Gerdt et al.},
note = {\url{http://hal.archives-ouvertes.fr/hal-00603290}},
pages = {73-87},
year = 2011
}
@inproceedings{BKLPV10,
author = {Samuel Vidal and Michel Petitot and Fran{\c{c}}ois Boulier and Fran{\c{c}}ois Lemaire and C{\'e}line Kuttler},
title = {Models of Stochastic Gene Expression and Weyl Algebra},
booktitle = {Proceedings of ANB2010},
year = 2010,
abstract = {This paper presents a symbolic algorithm for computing the ODE systems which describe the evolution of the moments associated to a chemical reaction system, considered from a stochastic point of view. The algorithm, which is formulated in the Weyl algebra, seems more efficient than the corresponding method, based on partial derivatives. In particular, an efficient method for handling conservation laws is presented. The output of the algorithm can be used for a further investigation of the system behaviour, by numerical methods. Relevant examples are carried out.},
pdf = {pdfFiles/BKLPV-ANB2010.pdf}
}
@inproceedings{LU10b,
author = {Fran{\c{c}}ois Lemaire and Asl{\i{}} {\"U}rg{\"u}pl{\"u}},
title = {MABSys: Modeling and Analysis of Biological Systems},
booktitle = {Proceedings of ANB2010},
year = 2010,
abstract = {We present the MABSys package which gathers, as much as possible, some functions to carry out the modeling of biochemical reaction networks, their qualitative analysis and the exact simplification of systems of ordinary differential equations. Then we discuss Tyson's negative feedback oscillator model and the parameters values for which this system oscillates.},
pdf = {pdfFiles/LemaireUrguplu-ANB2010.pdf}
}
@inproceedings{LU2010,
author = {Fran{\c{c}}ois Lemaire and Asl{\i{}} {\"U}rg{\"u}pl{\"u}},
title = {A Method for semi-rectifying Algebraic and Differential Systems using Scaling type Lie Point Symmetries with Linear Algebra},
booktitle = {Proceedings of the International Symposium
on Symbolic and algebraic computation},
year = 2010,
editor = {ACM Press},
x-international-audience = {Yes},
abstract = {We present two new algorithms based on Lie symmetries
that respectively allow to semi-rectify algebraic
systems and reduce the number of parameters on which
the steady points of a differential system
depend. These algorithms facilitate the qualitative
analysis of algebraic and differential systems. They
are designed with a strong view towards
applications, such as modeling in biology. Their
implementation, already available in our MABSys
package, is of polynomial time complexity in the
input size.},
x-language = {EN}
}
@inproceedings{BCLM09,
title = {Real Root Isolation of Regular Chains},
author = {Fran{\c{c}}ois Boulier and Changbo Chen and
Fran{\c{c}}ois Lemaire and Marc {Moreno Maza}},
abstract = { We present an algorithm RealRootIsolate for
isolating the real roots of a system of multivariate
polynomials given by a zerodimensional squarefree
regular chain. The output of the algorithm is
guaranteed in the sense that all real roots are
obtained and are described by boxes of arbitrary
precision. Real roots are encoded with a hybrid
representation, combining a symbolic object, namely
a regular chain, and a numerical approximation given
by intervals. Our isolation algorithm is a
generalization, for regular chains, of the algorithm
proposed by Collins and Akritas. We have
implemented RealRootIsolate as a command of the
module SemiAlgebraicSetTools of the RegularChains
library in Maple. Benchmarks are reported. },
booktitle = {Asian Symposium on Computer Mathematics},
year = 2009,
x-international-audience = {Yes},
x-language = {EN},
pdf = {pdfFiles/Boulier.Chen.Lemaire.Moreno-Maza.VCA.2009.pdf}
}
@inproceedings{BL08b,
author = {Fran{\c{c}}ois Boulier and Fran{\c{c}}ois Lemaire},
title = {{Differential algebra and system modeling in
cellular biology}},
note = {{Tutorial}},
booktitle = {Proceedings of Algebraic Biology 2008},
series = {LNCS},
volume = 5147,
editor = {K. Horimoto, G. Regensburger, M. Rosenkranz and
T. Kutsia},
year = 2008,
pages = {22-39},
publisher = {Springer Verlag Berlin Heidelberg},
url = {http://hal.archives-ouvertes.fr/hal-00274689/fr},
year = 2008,
abstract = {Among all the modeling approaches dedicated to
cellular biology, differential algebra is
particularly related to the well-established one
based on nonlinear differential equations. In this
paper, it is shown that differential algebra makes
both simple and algorithmic one of the model
reduction methods, the quasi-steady state
approximation theory, in the particular setting of
generalized chemical reactions systems. This recent
breakthrough may suggest some evolution of modeling
techniques based on nonlinear differential
equations, by incorporating the reduction hypotheses
in the models. Potential improvements of parameters
fitting methods are discussed too.},
x-international-audience = {Yes},
x-language = {EN}
}
@inproceedings{LMPX08,
author = {Fran{\c{c}}ois Lemaire and Marc {Moreno Maza} and
Wei Pan and Yuzhen Xie},
title = {When does (T) equal sat(T)?},
booktitle = {Proceedings of the International Symposium on
Symbolic and algebraic computation},
publisher = {ACM Press},
year = 2008,
pages = {207-214},
x-international-audience = {Yes},
x-language = {EN}
}
@inproceedings{BLLM08,
author = {Fran{\c{c}}ois Boulier and Marc Lefranc and
Fran{\c{c}}ois Lemaire and Pierre-Emmanuel Morant},
title = {Applying a rigorous quasi-steady state approximation
method for proving the absence of oscillations in
models of genetic circuits},
booktitle = {Proceedings of Algebraic Biology 2008},
series = {LNCS},
volume = 5147,
editor = {K. Horimoto, G. Regensburger, M. Rosenkranz and
T. Kutsia},
pages = {56-65},
publisher = {Springer Verlag Berlin Heidelberg},
url = {http://hal.archives-ouvertes.fr/hal-00213327},
year = 2008,
x-international-audience = {Yes},
x-language = {EN}
}
@inproceedings{BLLM08b,
author = {Fran{\c{c}}ois Boulier and Marc Lefranc and
Fran{\c{c}}ois Lemaire and Pierre-Emmanuel Morant},
title = {Applying a rigorous quasi-steady state approximation
method for proving the absence of oscillations in
models of genetic circuits},
booktitle = {Proceedings of Journ\'{e}es Ouvertes Biologie
Informatique Mathématiques},
year = 2008,
pages = {77-82},
url = {http://www.lifl.fr/jobim2008/actes/jobim08-boulier.pdf},
x-international-audience = {Yes},
x-language = {EN}
}
@inproceedings{BLLMU07,
author = {Fran{\c{c}}ois Boulier and Marc Lefranc and
Fran{\c{c}}ois Lemaire and Pierre--Emmanuel Morant
and Asl{\i{}} {\"U}rg{\"u}pl{\"u}},
title = {{On proving the absence of oscillations in models of
genetic circuits}},
booktitle = {Proceedings of Algebraic Biology 2007},
series = {LNCS},
volume = 4545,
editor = {H. Anai, K. Horimoto and T. Kutsia},
year = 2007,
pages = {66--80},
location = {RISC, Castle Hagenberg, Austria},
url = {http://hal.archives-ouvertes.fr/hal-00139667},
publisher = {Springer Verlag Berlin Heidelberg},
x-international-audience = {Yes},
x-language = {EN}
}
@inproceedings{MVTPLCSBL07,
author = {Pierre--Emmanuel Morant and Constant Vandermoere and
Benjamin Parent and Fran{\c{c}}ois Lemaire and
Florence Corellou and Christian Schwartz and
Fran{\c{c}}ois--Yves Bouget and Marc Lefranc},
title = {{Oscillateurs g\'en\'etiques simples. Applications
\`a l'horloge circadienne d'une algue
unicellulaire}},
booktitle = {{proceedings of the {\em Rencontre du non
lin\'eaire}}},
address = {Paris},
url = {http://nonlineaire.univ-lille1.fr},
year = 2007,
x-international-audience = {no},
x-language = {fr}
}
@inproceedings{CLMPX07,
title = {Efficient Computations of Irredundant Triangular
Decompositions with the RegularChains Library.},
author = {Changbo Chen and François Lemaire and Marc {Moreno
Maza} and Wei Pan and Yuzhen Xie},
editor = {Yong Shi and G. Dick van Albada and Jack Dongarra
and Peter M. A. Sloot},
series = {Lecture Notes in Computer Science},
url = {http://dblp.uni-trier.de/db/conf/iccS/iccS2007-2.html#ChenLMPX07},
volume = 4488,
booktitle = {ICCS '07: Proceedings of the 7th international
conference on Computational Science, Part II},
year = 2007,
pages = {268--271},
location = {Beijing, China},
publisher = {Springer-Verlag},
x-international-audience = {Yes},
x-language = {EN},
abstract = {We present new functionalities that we have added to the
RegularChains library in Maple to efficiently compute irredundant
triangular decompositions. We report on the implementation of different
strategies. Our experiments show that, for difficult input systems, the
computing time for removing redundant components can be reduced to
a small portion of the total time needed for solving these systems.}
}
@inproceedings{CGLMP07,
author = {Changbo Chen and Oleg Golubitsky and Fran{\c{c}}ois
Lemaire and Marc {Moreno Maza} and Wei Pan},
title = {Comprehensive Triangular Decomposition},
booktitle = {Computer Algebra in Scientific Computing},
series = {Lecture Notes in Computer Science},
volume = 4770,
publisher = {Springer},
year = 2007,
pages = {73-101},
x-international-audience = {Yes},
x-language = {EN},
url = {http://www.csd.uwo.ca/~moreno/Publications/ChenLemaireGolubitskyMorenoMazaPan-CASC-07.pdf}
}
@inproceedings{BLM06,
author = {Fran{\c{c}}ois Boulier and Fran{\c{c}}ois Lemaire
and Marc {Moreno Maza}},
title = {{Well known theorems on triangular systems and the
$D^5$ principle}},
booktitle = {{Proceedings of Transgressive Computing 2006}},
address = {{Granada, Spain}},
pages = {79--91},
url = {http://hal.archives-ouvertes.fr/hal-00137158},
year = 2006,
x-international-audience = {Yes},
x-language = {EN}
}
@inproceedings{LMX06,
author = {Fran{\c{c}}ois Lemaire and Marc {Moreno Maza} and
Yuzhen Xie},
title = {{Making a sophisticated symbolic solver available to
different communities of users}},
booktitle = {{Asian Technology Conference in Mathematics'06}},
year = 2006,
abstract = {Triangular decompositions have become one of the major
tools for solving systems of non-linear algebraic or
differential equations symbolically. These
decompositions display more geometrical information
than other symbolic descriptions of polynomial
systems. However, their specifications and the
algorithms computing them are quite sophisticated.
Their implementation in mathematical software, their
accessibility, and ease of use for non-expert users
are challenges that we discuss in this paper. We
discuss our solutions and illustrate them with the
implementation of an algorithm for triangular
decompositions, called Triade, in three computer
algebra systems: AXIOM, ALDOR, and MAPLE, targeting
different communities of users. We believe that
these implementations of the same sophisticated
mathematical algorithm for different communities of
experts, advanced users, and non-experts is a unique
experience in the area of symbolic computations
which could benefit other algorithms in this field.},
address = {Hong Kong, China},
x-international-audience = {Yes},
x-language = {EN}
}
@inproceedings{LMX05,
author = {Fran{\c{c}}ois Lemaire and Marc {Moreno Maza} and
Yuzhen Xie},
title = {{The RegularChains library in MAPLE 10}},
booktitle = {{The MAPLE conference}},
address = {Waterloo, Canada},
pages = {355--368},
editor = {Ilias S. Kotsireas},
year = 2005,
abstract = {The RegularChains library provide facilities for symbolic
computations with systems of polynomial equations. In particular,
it allows to compute modulo a set of algebraic relations.
Automatic case discussion (and recombination) handles
zero-divisors and parameters. This permits triangular decomposition
of polynomial equations},
x-international-audience = {Yes},
x-language = {EN}
}
@inproceedings{BDVHL04,
author = {Fran{\c{c}}ois Boulier and Lilianne Denis--Vidal and
Thibaut Henin and Fran{\c{c}}ois Lemaire},
title = {{L{\'{E}}PISME}},
booktitle = {proceedings of the ICPSS conference},
note = {Submitted to the Journal of Symbolic Computation},
url = {http://hal.archives-ouvertes.fr/hal-00140368},
year = 2004,
x-international-audience = {Yes},
x-language = {EN}
}
@inproceedings{BLRZ03,
author = { Joe Bonasia and Fran{\c{c}}ois Lemaire and Greg
Reid and Lihong Zhi},
title = { Determination of approximate symmetries of
differential equations },
booktitle = {CRM proceedings and Lectures Notes},
editor = {David Gomez-Ullate},
year = 2004,
volume = 39,
pages = {233-249},
publisher = {American Mathematical Society},
abstract = {
There has been considerable progress in the theory and computer
implementation of symbolic computation algorithms to automatically determine
and exploit exact symmetries of exact differential equations. Such programs
usually apply a finite number of exact differentiations and eliminations
to the overdetermined linearized equations for the unknown symmetries (the
symmetry defining equations), to complete them to certain involutive or standard
forms. The symmetry properties can be determined from these involutive
forms.
In many applications, however, the differential equations describing a
model are only known approximately. For example they may contain parameters
that are only known approximately. Symbolic methods are unstable if
applied to the symmetry defining equations directly, and indirect techniques
(e.g. replacing approximate parameters by symbolic ones) might not be practical
in cases with many parameters. Discussion and examples are given of
such difficulties.
A new generation of symbolic-numeric methods is described and applied
to the problem of determining symmetries of differential equations.
We introduce a class of differential-elimination methods which uses Numerical
Linear Algebra, and in particular the Singular Value Decomposition,
to perform the elimination process on the symmetry defining equations. Our
approach uses symbolic differentiations but not symbolic eliminations. Substitution
of an appropriate random point in the independent variables, followed
by numerical projection is used to test for the conditions of completion to a
projective involutive form. We prove that this form is equivalent to the involutive
form of the Cartan-Kuranishi theory of partial differential equations.
Our method is applied to determining symmetry properties of 50 ode
from the collection in Kamke's book.
},
x-international-audience = {Yes},
x-language = {EN}
}
@inproceedings{Lemaire02b,
author = {Fran{\c{c}}ois Lemaire},
title = {{Les classements les plus g{\'e}n{\'e}raux assurant
l'analycit{\'e} des syst{\`e}mes orthonomes pour des
conditions initiales analytiques}},
booktitle = {proceedings of Computer Algebra in Scientific
computation 2002},
address = {Yalta, Ukraine},
editor = {{Victor G. Ganzha} and {Ernst W. Mayr} and {Evgenii
V. Vorozhtsov}},
publisher = {{Instit{\"u}t f{\"u}r Informatik, Technische
Universit{\"a}t M{\"u}nchen}},
pages = {207--219},
year = 2002
}
@inproceedings{BLM01b,
author = {Fran{\c{c}}ois Boulier and Fran{\c{c}}ois Lemaire
and Marc {Moreno Maza}},
title = {{PARDI!}},
booktitle = {ISSAC'01: Proceedings of the 2001 international
symposium on Symbolic and algebraic computation},
year = 2001,
isbn = {1-58113-417-7},
pages = {38--47},
location = {London, Ontario, Canada},
url = {http://hal.archives-ouvertes.fr/hal-00139354},
publisher = {ACM Press},
address = {New York, NY, USA}
}
@inproceedings{BL00,
author = {Fran{\c{c}}ois Boulier and Fran{\c{c}}ois Lemaire},
title = {{Computing canonical representatives of regular
differential ideals}},
booktitle = {ISSAC'00: Proceedings of the 2000 International
Symposium on Symbolic and algebraic computation},
year = 2000,
isbn = {1-58113-218-2},
pages = {38--47},
location = {St. Andrews, Scotland},
url = {http://hal.archives-ouvertes.fr/hal-00139177},
publisher = {ACM Press},
address = {New York, NY, USA}
}