Difference between revisions of "Optimization examples"

Revision as of 14:06, 15 March 2019

Here we give some examples of the BioUML usage for solving the problem of parameter estimation applied to the models of biochemical pathways. For details about creation your oun optimization document in BioUML, see the chapter Optimization document. All information about the optimization methods implemented in BioUML is done in the chapter Optimization problem.

Testing the convergence rate of the optimization methods

• Optimization document: data > Examples > Optimization > Data > Documents > test_case_1A
• Model: data > Examples > Optimization > Data > Diagrams > diagram_1A
• Experimental data: data > Examples > Optimization > Data > Experiments > exp_data_1

To analyze a convergence rate of the optimization methods implemented in BioUML [1], we considered a reaction chain extracted from the model by Neumann et al. [2] and representing activation of caspase-8 triggered by the receptor CD95 (APO-1/Fas).

The test model of caspase-8 activation

ID Reactions Reaction rates Initial values r1 CD95L + FADD:CD95R → DISC k1 ⋅ [CD95L] ⋅ [CD95R:FADD] [CD95L]0 = 113.220, [CD95R:FADD]0 = 91.266 r2 DISC + pro8 → DISC:pro8 k2 ⋅ [DISC] ⋅ [pro8] [pro8]0 = 64.477, [DISC]0 = 0.0 r3 DISC:pro8 + pro8 → 2 · p43/p41 k3 ⋅ [DISC:pro8] ⋅ [pro8] [pro8]0 = 64.477, [DISC:pro8]0 = 0.0 r4 2 · p43/p41 → casp8 k4 ⋅ [p43/p41]2 [p43/p41]0 = 0.0 r5 casp8 → k5 ⋅ [casp8] [casp8]0 = 0.0

We performed estimation of parameters using the search space defined as:

where upper bounds were chosen based on the order of magnitude of parameter values proposed in [2].

Estimation was based on the experimental data obtained by Neumann et al. [2] for procaspase-8 and its cleaved products p43/p41 and caspase-8.

We reviewed solutions obtained by all optimization methods for 100 runs. Each run was based on the generation of 10⁷ different guesses. The best result was obtained by the particle swarm optimization (PSO) and the cellular genetic algorithm (MOCell). Methods SRES, MOCell and PSO found similar solutions. Methods ASA and glbSolve found other values for parameters k₁ and k₂ showing lower efficiency.

The objective function mean values dynamics for 100 runs. The best value obtained by PSO is marked by the red line.

The best guesses obtained by optimization methods for 100 runs Parameters SRES MOCell PSO ASA glbSolve k1 0.0004691 0.0004611 0.0004277 0.0001028 0.0020576 k2 0.0002059 0.0002046 0.0002155 0.0007875 0.0001228 k3 0.0009999 0.0010000 0.0009984 0.0009930 0.0009527 k4 0.0007915 0.0008225 0.0008419 0.0008117 0.0007790 k5 0.0325900 0.0336720 0.0334167 0.0334118 0.0313443

Values of the objective function for 100 runs Methods The best value The mean value The worst value PSO 11.787 13.164 14.703 MOCell 12.082 13.484 14.771 SRES 12.466 14.987 18.283 ASA 13.728 15.794 16.610 glbSolve 16.614 16.614 16.614

Testing computation speed of the methods for models with the different number of parameters

• Optimization documents: data > Examples > Optimization > Data > Documents
  (test cases 1A, 1B, 1C, 2, 3)
• Models: data > Examples > Optimization > Data > Diagrams
  (diagrams 1A, 1B, 1C, 2, 3 for the corresponding test cases)
• Experimental data: data > Examples > Optimization > Data > Experiments
  (exp_data_1 for the test cases 1A, 1B, 1C; exp_data_2 for the test case 2; exp_data_3 for the test case 3)

To test a computation speed of the optimization methods in BioUML for models with the different number of parameters and species, we considered the following test cases. Firstly, we derived three models of CD95-induced activation of caspase-8 from the model by Neumann et al. [2] with varying degrees of detail (the test cases 1A, 1B and 1C). Secondly, we took the test case proposed by Mendes et al. [3] for the MAP kinase cascade model developed by Kholodenko et al. [4] (the test case 2). Finally, we tested the model by Bagci et al. [5] representing the mitochondria-depended apoptosis (the test case 3).

• 

  Test case 1A: 7 species and 5 reaction rate parameters.

• 

  Test case 1B: 13 species and 10 reaction rate parameters.

• 

  Test case 1C: 18 species and 12 reaction rate parameters.

• 

  Test case 2: 8 species and 22 reaction rate parameters.

• 

  Test case 3: 32 species and 57 reaction rate parameters.

• 

  The number of objective function evaluations per second for the different test cases in BioUML.

References

1. Kutumova E., Ryabova A., Valeev T., Kolpakov F. BioUML plug-in for nonlinear parameter estimation using multiple experimental data. Virtual Biology. 2013. 1:47-58.
2. Neumann L., Pforr C., Beaudouin J., Pappa A., Fricker N., Krammer P.H., Lavrik I.N., Eils R. Dynamics within the CD95 death-inducing signaling complex decide life and death of cells. Molecular Systems Biology. 2010. 6:352.
3. Mendes P., Hoops S., Sahle S., Gauges R., Dada J., Kummer U. Computational modeling of biochemical networks using COPASI. Methods in Molecular Biology. 2009. 500:17–59.
4. Kholodenko B.N. Negative feedback and ultrasensitivity can bring about oscillations in the mitogenactivated protein kinase cascades. European Journal of Biochemistry. 2000. 267(6):1583–1588.
5. Bagci E.Z., Vodovotz Y., Billiar T.R., Ermentrout G.B., Bahar I. Bistability in apoptosis: roles of bax, bcl-2, and mitochondrial permeability transition pores. Biophysical Journal. 2006. 90(5):1546–1559.