Computational Methods in Systems Biology
Automated Property Synthesis of ODEs Based Bio-pathways Models 271 the formula below. This transformed data is then fed to the c ...
272 J. Zhou et al. In order to reduce the search complexity, we assume the BLTL based tem- plate is given as a conjunction of co ...
Automated Property Synthesis of ODEs Based Bio-pathways Models 273 of satisfaction. For the temporal variables we use the intuit ...
274 J. Zhou et al. We use the multiplicative form of the loss function since we found that the additive form performs badly. For ...
Automated Property Synthesis of ODEs Based Bio-pathways Models 275 template with most votes from all the trajectories is chosen ...
276 J. Zhou et al. Table 3.Properties synthesized for the six case studies. Simulationprofile Synthesized property (a) EGF-NGF P ...
Automated Property Synthesis of ODEs Based Bio-pathways Models 277 Table 3.Continued (d) Atorvastatin Pharmacokinetics Model p 1 ...
278 J. Zhou et al. Experimental findings [ 22 ] indicate that “dual serine/threonine phosphoryla- tion of SOS by Erk has been fo ...
Automated Property Synthesis of ODEs Based Bio-pathways Models 279 The properties synthesized in Table 3 (f) show the activation ...
280 J. Zhou et al. statistical model checking is then applied to this template to mine a concrete property. By checking the synt ...
Automated Property Synthesis of ODEs Based Bio-pathways Models 281 Bufo, S., Bartocci, E., Sanguinetti, G., Borelli, M., Lucang ...
282 J. Zhou et al. Le Novere, N., Bornstein, B., Broicher, A., Courtot, M., Donizelli, M., Dharuri, H., Li, L., Sauro, H., Schi ...
ToolPapers ...
TransferEntropyPT: An R Package to Assess Transfer Entropies via Permutation Tests Patrick Boba and Kay Hamacher(B) Technische U ...
286 P. Boba and K. Hamacher p(Z) of a random variableZfrom a sample spaceZto another distribution q(Z): KLDp|q= ∑ z∈Z p(z) log 2 ...
An R Package to Assess Transfer Entropies via Permutation Tests 287 It is inspired by the method proposed in [ 8 ] and facilitat ...
288 P. Boba and K. Hamacher Fig. 2.A network with two coupled feedback loops that eventually implement two (almost) independent ...
An R Package to Assess Transfer Entropies via Permutation Tests 289 Fig. 4.TE for the toy molecular system in Fig. 2 andkvy=0.00 ...
290 P. Boba and K. Hamacher Boba, P., Hamacher, K.: Accompanying supplemental material to this paper. https://www.cbs.tu-darmst ...
KADE: A Tool to Compile Kappa Rules into (Reduced) ODE Models Ferdinanda Camporesi1,2,J ́erˆome Feret1,2(B), and Kim Quyˆen L ́y ...
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