DZAP1 L-curve analysis KH

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L-curve analysis

Github issue

Github issue 172

Purpose

We are attempting to determine which alpha value we should use when running the model.

Parameters

For all input sheets the optimization parameters were set:

  • alpha : 1.00E-02
  • kk_max : 1
  • MaxIter : 1.00E+08
  • TolFun : 1.00E-10
  • MaxFunEval : 1.00E+08
  • TolX : 1.00E-10
  • production_function : Sigmoid
  • L_curve : 1.00E+00
  • estimate_params : 1.00E+00
  • make_graphs : 0.00E+00
  • fix_P : 0
  • fix_b : 0

Running the L-curve

  • with_deletions_ONLY_DNA_binding_dZAP1_15_Genes_2_1_2016
    • Computer: Run on Seaver 120-12
    • Code Version: GRNmap beta 6:32 pm 2/1/2016
    • Has 27 edges
    • Run started: 6:31 pm 2/1/2016
    • The program finished running at 8:37 am 2/2/2016
    • There were 16 input xlsx, output xlsx, and output.mat files created
    • The input sheets (and thus the output sheets) were saved in a folder called “KristenHorstmann” in the thaw space. A file called KristenHorstmannwith_deletions_ONLY_DNA_binding_dZAP1_15_Genes_2_1_2016LCurveLCurveData was output and saved in the thaw space (not in the “KristenHorstmann” folder
    • There is only one optimization_diagnostic.jpg, meaning that likely it is overwriting after every run.
  • with_deletions_ONLY_DNA_binding_dZAP1_15_Genes_2_1_2016
    • Computer: Run on Seaver 120-13
    • Code Version: GRNmap beta 6:38 pm 2/1/2016
    • Run started: 6:40 pm 2/1/2016
    • The program computer 6 alphas and crashed on the 7th alpha.
    • The error was:

Attempted to access strain_x1(2,:); index out of bounds because numel(strain_x1)=1. Error in lse (line 104) x1 = strain_x1(i,:); Error in GRNLCurve (line 66) GRNstruct = lse(GRNstruct); Error in GRNmodel (line 32) GRNstruct = GRNLCurve(GRNstruct);

    • Accidentally was the same sheet run on computer 12, ran new one as stated below:
  • with_deletions_ONLY_DNA_34_Genes_2_1
    • Computer: Run on SEA 120-13
    • Code Version: GRNmap beta 6:38 pm 2/1/2016
    • Run started: 5:42 pm 2/2/2016
    • By the wa7, has 98 edges, likely why taking so long.
    • The program was still running at 4:13 PM 2/3/16 and was on the 5th alpha, which started at 2:58 AM.
    • The program was still running at 6:26 PM 2/4/16 and was on the 7th alpha, which started at 7:05 AM.
    • Program was still running at 2:40 PM 2/5/16 and was on the 8th alpha.
  • ONLY_DNA_binding_dZAP1_28_genes_2_1_16
    • Computer: Run on Seaver 120-14
    • Code Version: GRNmap beta 6:35 pm 2/1/2016
    • Has 43 edges
    • Run started: 7:38 pm 2/1/2016
    • The program was still running at 8:56 am 2/2/2016. At this time it was on the 8th alpha.
    • Program was sitll running at 4:15 PM 2/3/16. At this time it was on the 12th alpha, which started at 12:38 AM.
    • The program was still running at 6:27 PM 2/4/16 and was on the 14th alpha, which started at 9:59 AM.
    • Program was still running at 2:43 PM on 2/5 and was on the 16th alpha.
  • ONLY_DNA_binding_dZAP1_14_genes_2_1
    • Has 15 edges
    • Computer: Run on Seaver 120-15
    • Code Version: GRNmap beta 6:34 pm 2/1/2016
    • Run started: 7:45 pm 2/1/2016
    • The program finished running at 3:11 am 2/2/2016
    • There were 16 input xlsx, output xlsx, and output.mat files created
    • The input sheets (and thus the output sheets) were saved in a folder called “KHorstmann” in the thaw space. A file called KHorstmannONLY_DNA_binding_dZAP1_14_genes_2_1LCurveLCurveData was output and saved in the thaw space (not in the “KHorstmann” folder.
    • There is only one optimization_diagnostic.jpg, meaning that likely it is overwriting after every run.

Output of L-Curve Analysis

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