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What and Who
Title:From Tarski to Tropical Geometry: Towards Symbolic Analysis of Biological Networks
Speaker:Andreas Weber
coming from:University of Bonn
Speakers Bio:
Event Type:Talk
Visibility:D1, D2, D3, D4, D5, SWS, RG1, MMCI
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Level:Public Audience
Language:English
Date, Time and Location
Date:Tuesday, 21 August 2018
Time:14:00
Duration:60 Minutes
Location:Saarbrücken
Building:E1 4
Room:024
Abstract
Symbolic Methods bear the promise to cope with the high parameter
uncertainty commonly found in biological networks. Using logical and
algebraic tools for satisfiability checking in the first-order theory of
the reals qualitative questions such as the ones asking for
multi-stationarity or existence of oscillations can be answered by
providing logical formulae describing the corresponding fulfilling
parameter regions. We provide a case study involving models of the MAPK
cascade, an important signalling pathway.
On the one hand the promise comes at the cost of high worst case
complexity of the symbolic methods (used in the case study). On the
other hand approximation techniques using ideas from Tropical Geometry
can be applied, which have a sound theoretic foundation and also deal
with parameter uncertainty. Identification of "slow" parameters, an
essential prerequisite for many model reduction techniques, and even
candidates for metastable regimes can be obtained by analyzing the
solution polytopes of certain Tropical Equilibration problems. Whereas
the Tropical Equilibration problem is NP-hard in its generic form,
computation results obtained on the BIOMOD database indicate that its
restriction to instances arising from biochemical networks might be
tractable.
Contact
Name(s):Jennifer Müller
Phone:2900
EMail:--email address not disclosed on the web
Video Broadcast
Video Broadcast:NoTo Location:
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Created:
Jennifer Müller/MPI-INF, 08/14/2018 09:55 AM
Last modified:
Uwe Brahm/MPII/DE, 08/21/2018 07:01 AM
  • Jennifer Müller, 08/14/2018 10:16 AM -- Created document.