Jérôme Feret Laboratoire d'Informatique de l'École Normale Supérieure

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SAS 2011 Formal model reduction Jérôme Feret Laboratoire d'Informatique de l'École Normale Supérieure INRIA, ÉNS, CNRS Friday, September the 16th

  • laboratoire d'informatique de l'ecole normale

  • abstract interpretation

  • formal model

  • msb4100014-e2 molecularsystemsbiology2005

  • abstract semantics


Publié le : mardi 19 juin 2012
Lecture(s) : 16
Source : di.ens.fr
Nombre de pages : 91
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SAS 2011
Formal model reduction
Jérôme Feret Laboratoire d’Informatique de l’École Normale Supérieure INRIA, ÉNS, CNRS
Friday, September the 16th
Joint-work with...
Walter Fontana Harvard Medical School
Jérôme Feret
Russ Harmer Harvard Medical School
Vincent Danos Edinburgh
2
Ferdinanda Camporesi Bologna / ÉNS
Jean Krivine Paris VII
Friday, September the 16th
Overview
1.Context and motivations 2. Handmade ODEs 3. Abstract interpretation framework 4. Kappa 5. Concrete semantics 6. Abstract semantics 7. Conclusion
Jérôme Feret
3
Friday, September the 16th
Jérôme Feret
Signalling
4
Pathways
Eikuch, 2007
Friday, September the 16th
Jérôme Feret
Pathway
maps
Oda, Matsuoka, Funahashi, Kitano, Molecular Systems Biology, 2005
5
Friday, September the 16th
Differential models
dtxd1= −k1x1x2+k1x3 ddxt2= −k1x1x2+k1x3 xddtxdtd43==kk12xx123x2k2xk41+pxv443+xx+552(kk32xx43x3k3kx52)x4 dx 5=∙ ∙ ∙ dt . ddxtn= −k1x1c2+k1x3
do not describe the structure of molecules; combinatorial explosion:forces choices that are not principled; a nightmare to modify.
Jérôme Feret
6
Friday, September the 16th
A gap between two worlds
Two levels of description: 1. Databases of proteins interactions in natural language + documented and detailed description + transparent description cannot be interpreted 2. ODE-based models + can be integrated opaque modelling process, models can hardly be modified there are also some scalability issues.
Jérôme Feret
7
Friday, September the 16th
Rule-based approach
We use site graph rewrite systems
1. The description level matches with both the observation level and the intervention level of the biologist.
We can tune the model easily. 2. Model description is very compact.
Jérôme Feret
8
Friday, September the 16th
Several
d
So
G
b
a
Y7
pi
semantics
E
R
Y68
r
l
Y48
r
Sh Interaction map
Jérôme Feret
Semantics
(qualititative
and/or
CTMC
9
quantitative)
can
be
dened.
= − ddxt1k1x1x2+k1x3 dx2 = −k1x1x2+k1x3 dt ddxt3=k1x1x2k1x3+2k2x3x3k2x4) dtdx4=k2x32k2x4+pv44+xx55− (k3x4k3x5) dx5= ∙ ∙ ∙ dt . dxdtn= −k1x1c2+k1x3 ODEs
Friday, September the 16th
Jérôme Feret
Complexity
10
walls
Friday, September the 16th
Jérôme Feret
A
breach
in
11
the
wall(s)
?
Friday, September the 16th
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