{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T10:16:57Z","timestamp":1768817817867,"version":"3.49.0"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1161,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation:\u2003Biological systems are understood through iterations of modeling and experimentation. Not all experiments, however, are equally valuable for predictive modeling. This study introduces an efficient method for experimental design aimed at selecting dynamical models from data. Motivated by biological applications, the method enables the design of crucial experiments: it determines a highly informative selection of measurement readouts and time points.<\/jats:p><jats:p>Results:\u2003We demonstrate formal guarantees of design efficiency on the basis of previous results. By reducing our task to the setting of graphical models, we prove that the method finds a near-optimal design selection with a polynomial number of evaluations. Moreover, the method exhibits the best polynomial-complexity constant approximation factor, unless P = NP. We measure the performance of the method in comparison with established alternatives, such as ensemble non-centrality, on example models of different complexity. Efficient design accelerates the loop between modeling and experimentation: it enables the inference of complex mechanisms, such as those controlling central metabolic operation.<\/jats:p><jats:p>Availability:\u2003Toolbox \u2018NearOED\u2019 available with source code under GPL on the Machine Learning Open Source Software Web site (mloss.org).<\/jats:p><jats:p>Contact:\u2003busettoa@inf.ethz.ch<\/jats:p><jats:p>Supplementary information:\u2003Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt436","type":"journal-article","created":{"date-parts":[[2013,7,31]],"date-time":"2013-07-31T00:34:28Z","timestamp":1375230868000},"page":"2625-2632","source":"Crossref","is-referenced-by-count":38,"title":["Near-optimal experimental design for model selection in systems biology"],"prefix":"10.1093","volume":"29","author":[{"given":"Alberto Giovanni","family":"Busetto","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, Australia"},{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alain","family":"Hauser","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriel","family":"Krummenacher","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikael","family":"Sunn\u00e5ker","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, Australia"},{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, Australia"},{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sotiris","family":"Dimopoulos","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, Australia"},{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, Australia"},{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheng Soon","family":"Ong","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00f6rg","family":"Stelling","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, Australia"},{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joachim M.","family":"Buhmann","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, Australia"},{"name":"1 Department of Computer Science, ETH Zurich, 2Competence Center for Systems Physiology and Metabolic Diseases, 3Department of Mathematics, ETH Zurich, 4Department of Biosystems Science and Engineering, ETH Zurich, 5Swiss Institute of Bioinformatics, Zurich, Switzerland and 6National ICT Australia, Melbourne, 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