From e692fafd30782ba783d6c3a194fd7f72f31eaa18 Mon Sep 17 00:00:00 2001 From: Stephan Grein Date: Wed, 19 Jan 2022 10:18:45 +0100 Subject: [PATCH] Adding suggestion of optimizers for benchmark models. --- README.md | 32 +++++++++++++++++++++++++++++++- 1 file changed, 31 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 6ede877..b403a16 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,37 @@ A collection of mathematical models with experimental data in the [PEtab](https://github.com/PEtab-dev) format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling. The publication for the introduction and analysis of the benchmark problem collection is available at https://academic.oup.com/bioinformatics/article/35/17/3073/5280731. Contributions to the collection are very welcome. For this, please create a new branch, add your model and test your files with the provided functions, and start a pull request. We will then check your model and merge it into the collection. We are continuously working on the extension of the collection. - +a +# Optimizer efficiency for benchmark models +|Model name|Optimizer|Overall efficiency|Number of starts| +|:---| :---:| ---:|---:| +|Alkan_SciSignal2018|L-BFGS-B|0.5873002343726723|250 +|Bachmann_MSB2011|cg|0.8535095423511391|250 +|Beer_MolBioSystems2014|nlopt_11|0.3021393820412641|250 +|Bertozzi_PNAS2020|nlopt_42|0.0625368965225103|250 +|Blasi_CellSystems2016|nlopt_42|0.062619053603697|250 +|Boehm_JProteomeRes2014|nlopt_42|0.0625503158813442|250 +|Borghans_BiophysChem1997|nlopt_42|0.0625090423025281|250 +|Brannmark_JBC2010|Nelder-Mead|0.0300288309625841|250 +|Bruno_JExpBot2016|nlopt_42|0.0624973327924617|250 +|Crauste_CellSystems2017|nlopt_42|0.0625128653808899|250 +|Elowitz_Nature2000|nlopt_42|0.06251683093855|250 +|Fiedler_BMC2016|nlopt_42|0.0625210244076697|250 +|Fujita_SciSignal2010|newton-cg|0.2861550080202327|250 +|Giordano_Nature2020|Nelder-Mead|0.0782034592682471|250 +|Isensee_JCB2018|COBYLA|0.648030745923714|250 +|Lucarelli_CellSystems2018|tnc|0.2908116422868182|250 +|Okuonghae_ChaosSolitonsFractals2020|nlopt_42|0.0624754021054171|250 +|Oliveira_NatCommun2021|L-BFGS-B|0.0125610504744164|250 +|Perelson_Science1996|nlopt_42|0.062476295984509|250 +|Rahman_MBS2016|SLSQP|0.0361244345719155|250 +|Raimundez_PCB2020|fides|0.3226217261103182|250 +|SalazarCavazos_MBoC2020|SLSQP|0.3506103769454492|250 +|Schwen_PONE2014|newton-cg|0.1201887849471576|250 +|Sneyd_PNAS2002|SLSQP|0.1393394787410767|250 +|Weber_BMC2015|Nelder-Mead|0.0771565221791643|250 +|Zhao_QuantBiol2020|Nelder-Mead|0.0357648294805615|250 +|Zheng_PNAS2012|Nelder-Mead|0.0757800686116193|250 ## License