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SED-ML / KiSAO

Ontology of algorithms for analyzing biological models, their parameters, and their outputs
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KISAO terms for parameter estimation / optimization #32

Closed jonrkarr closed 3 years ago

jonrkarr commented 5 years ago

Hello,

in order to be able to express parameter estimation tasks in SED-ML we need the capability of defining some optimization methods. Under:

KISAO_0000472: Simulated Annealing Random Search Particle Swarm Genetic Algorithm

and under KISAO_0000471: Truncated Newton Steepest Descent Praxis NL2SOL Nelder - Mead Levenberg - Marquardt Hooke & Jeeves

description of the methods i like here: http://copasi.org/Support/User_Manual/Methods/Optimization_Methods/

associated parameters would be nice as well, at the bare minimum we would need (full list of parameters listed on the site above):

Number of Generations: The parameter is a positive integer value to determine the number of generations the algorithm shall evolve the population.

Population Size: The parameter is a positive integer value to determine the size of the population

Iteration Limit: This parameter is positive integer determining the maximum number of iterations the algorithm shall perform.

Tolerance This parameter is a positive value determining the tolerance with which the solution shall be determined. If the improvement between two steps is less than the tolerance the algorithm stops.

Thank you so much,

best Frank

Reported by: *anonymous

jonrkarr commented 5 years ago

Hello Frank,

The requested terms should be available since KISAO version 2.5:

Simulated Annealing KISAO_0000503 Random Search KISAO_0000504 Particle Swarm KISAO_0000505 Genetic Algorithm KISAO_0000506

Truncated Newton KISAO_0000510 Steepest Descent KISAO_0000511 Praxis KISAO_0000512 NL2SOL KISAO_0000513 Nelder - Mead KISAO_0000514 Levenberg - Marquardt KISAO_0000515 Hooke & Jeeves KISAO_0000516

Number of Generations KISAO_0000517 Population Size KISAO_0000519 Iteration Limit -- I believe this exists already as maximum iterations KISAO_0000486 Tolerance -- we already had absolute tolerance KISAO_0000211 and relative tolerance KISAO_0000209

Kind regards, Anna

Original comment by: annazhukova

jonrkarr commented 5 years ago

Original comment by: annazhukova