PMC:2654804 / 20952-24520 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/2654804","sourcedb":"PMC","sourceid":"2654804","source_url":"https://www.ncbi.nlm.nih.gov/pmc/2654804","text":"In Table 2 we report the best known solutions for all benchmark problems, and we will now describe the detailed information in the table. The solutions have been found using our own identification algorithm (Gennemark and Wedelin, 2007). All solution models as well as source models are available in SBML on our web site.\nTable 2. Best known solutions to the benchmark problems\nProblem Error of source model −L+λK Best known solutiona Solution of original problem (if available)\nError −L+λK Residual −L Structure FP/FN/LD Stability between runs Average time (s) (1 GHz) Structure FP/FN/LD Time (s) (1 GHz)\nsimpleLin1 8 8 0 0/0/0 5/5 17\nsimpleLin2 187.4 140.2 132.2 0/0/– 5/5 86\nsimpleFb1 7 7 0 0/0/0 5/5 14\nsimpleFb2 45.46 42.14 34.14 1/1/– 3/5 36\nsimpleFb3 7 7 0 0/0/0 3/5 41\nsimpleFb4 18.39 7.071 0.0713 0/0/– 2/5 47 0/0/– –\nosc1 6 6.149 0.1491 0/0/0 5/5 18\nosc2 122.1 87.34 57.34 0/0/0 4/5 24 – –\nmetabol1 30 30 0 0/0/0 3/3 5400\nmetabol2 1214 751.6 601.6 0/0/– 2/3 11 000\nmetabol3 1442 861.1 696.1 2/1/– 1/5b 13 000\n3genes1 39 39 0 0/0/0 3/3 35 000\nss_cascade1 14 14 0 0/0/0 5/5 180 0/0/300 8900\nss_cascade2 14 14 0 0/0/0 4/5 130\nss_cascade3 498.9 476.7 462.7 1/1/– 1/5b 860\nss_branch1 17 17 0 0/0/0 5/5 68 0/0/15 2200\nss_branch2 17 17 0 0/0/0 5/5 110 0/0/5 35 000\nss_branch3 17 17 0 0/0/0 5/5 150 0/0/2 15 000\nss_branch4 17 17 0 0/0/0 5/5 71 0/0/0 25 000\nss_branch5 211.3 142.1 122.1 4/1/– 3/5 300 – –\nss_branch6 18 18 0 0/0/0 5/5 90 0/0/5 1100\nss_5genes1 23 23 0 0/0/0 5/5 600 1/0/– 2.4E+8\nss_5genes2 300.3 211.0 183.0 5/0/– 2/5b 2100\nss_5genes3 23 23 0 0/0/0 5/5 380\nss_5genes4 23 23 0 0/0/0 5/5 640 37/0/– 40 000\nss_5genes5 23 23.00 1.14E−3 0/0/0.02 5/5 400 4/2/– 7200\nss_5genes6 23 23 0 0/0/0 5/5 130 0/0/50 56 000\nss_5genes7 23 23 0 0/0/0 5/5 190 0/0/0.2 15 000\nss_5genes8 28 28 0 0/0/0 5/5 440 0/0/5 26 000\n0/0/2.5 7000\nss_15genes1 62 62 0 0/0/0 5/5 1500\nss_15genes2 2010 1783 1478 3/4/– 2/5b 18 000\nss_30genes1 128 128 0 0/0/0 5/5 7900\nss_30genes2 4098 3628 2993 6/7/– 1/3b 94 000 242/10/– 6.2E+6\nss_30genes3 128 128 0 0/0/0 3/3 18 000 0/0/25 8.6E+6\ncytokine1 25.92 17.92 1/5c 11 – –\ncytokine2 42.17 32.17 1/5c 23\nss_ethanolferm1 127.4 110.4 1/5c 190 err\u003e127.4d –\nss_ethanolferm2 1308 1292 1/5c 360\nss_sosrepair1 2642 2611 1/5c 510 err\u003e2642d 2.7E+5\nss_sosrepair2 2823 2789 1/5c 470\nss_cadBA1 750.6 726.6 1/5c 250 err\u003e750.6d \u003e540\nss_cadBA2 709.1 687.1 1/5c 260\nss_clock1 928.4 803.4 1/5c 360 – 15 000\nss_clock2 814.5 649.5 1/5c 440\naBest known solutions, based on comparsion to the solutions of the original problems. For ss_30genes2, the similarity with the source model strongly indicates that our solution is the best, but since we do not have access to the solution of the original problem this is not confirmed.\nb The majority of runs have an error below the error of the source model, but differ slightly in structure.\ncReal datasets with relatively few experiments and/or data-points making many similar models reasonable, increasing the variability in found solutions.\ndSince no source model is available, we have evaluated the original solution with our error function, and it has an error higher than our solution.\nThe error of the source model refers to the error of the model from which data was simulated. The best result is taken from several runs with various random seeds. The error, the negative log-likelihood and the number of false positives and negative (FP/FN) reactions are reported. Stability measures the frequency of runs for which the best structure is obtained. Computation time in seconds is given as the average of several 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