DGLN3 L-curve analysis TM

L-curve analysis

Github issue

Github issue 172

Purpose

We are attempting to determine which alpha value we should use when running the model. For dGLN3 we are running 6 different input sheets from 3 different families of networks:

1. dGLN3_35-gene_120-edges_add_input_TM_2016-01-20_delete-genes
   • CIN5, GLN3, HAP4, HMO1, SWI4, and ZAP1 were added to the network even if they were not deemed significant by Yeastract
   • The genes CRZ1 and FLO11are deleted because they do not have any data for any of the 4 replicates in the 15 and 30 time points for the log2expression for HMO1 and HAP4
2. dGLN3_35-gene_120-edges_add_input_TM_2016-01-21_delete-expression-data
   • CIN5, GLN3, HAP4, HMO1, SWI4, and ZAP1 were added to the network even if they were not deemed significant by Yeastract
   • The log2expression sheets for HMO1 and HAP4 are deleted because there is no data in these sheets for any of the 4 replicates in the 15 and 30 time points for CRZ1 and FLO11.
3. dGLN3_35-gene_120-edges_disregard_input_TM_2015-01-21
   • CIN5, GLN3, HAP4, HMO1, SWI4, and ZAP1 were not added to network if they were not deemed significant by Yeastract

L-curve Analysis Graphs

GLN3_L-curve Analysis

• 15_gene_33_edges_add_17_delete-expression-data
  • "Elbow" of graph appears to be between 0.01 and 0.005
• 16_gene_24_edges_disregard_16
  • "Elbow" of graph appears to be between 0.005 and 0.001

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

• 15_gene_33_edges_add_17_delete-expression-data
  • Computer: Run on Seaver 120-07
  • Code Version: GRNmap beta 1:05 pm 2/1/2016
  • Run started: 1:35 pm 2/1/2016
  • The program finished running at 9:53 pm 2/1/2016 (~9.5 hours to run)
  • 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 “TM_GRNMAP_02-01-2016” in the thaw space. A file called TM_GRNMAP_02-01-2016dGLN3_15_gene_33_edges_add_17_input_TM_2016-01-21_delete-expression-dataLCurveLCurveData was output and saved in the thaw space (not in the “TM_GRNMAP_02-01-2016” folder.
  • There is only one optimization_diagnostic.jpg, meaning that likely it is overwriting after every run.

• 35_gene_120_edges_add_1_delete-expression-data
  • Computer: Run on Seaver 120-06
  • Code Version: GRNmap beta 1:15 pm 2/1/2016
  • Run started: 1:41 pm 2/1/2016
  • The program was still running at 8:32 am 2/2/2016. At this time it was on the 6th alpha.
  • Update: The program was still running at 12:26 pm 2/3/2016. At this time it was on the 9th alpha.
  • Update: The program was still running at 6:40 PM 2/4/16. At this time it was on the 14th alpha.
• The program was finished by 1:21 on 2/5/16 and was saved into a folder called "TM_GRNMAP_02-01-2016" in the thaw space.
  • There is only one optimization_diagnostic.jpg, meaning that likely it is overwriting after every run.

• 14_gene_26_edges_add_17_delete-genes
  • Computer: Run on Seaver 120-05
  • Code Version: GRNmap beta 1:15 pm 2/1/2016
  • Run started: 1:31 pm 2/1/2016
  • The program was still running at 8:36 am 2/2/2016. At this time it was on the 13th alpha.
  • Update: The program was still running at 12:28 pm 2/3/2016. At this time it was on the 13th alpha.
  • Update: The program was still running at 6:38 PM 2/4/16. At this time it was on the 13th alpha (4,588,400 iteration).

• 33_gene_110_edges_add_1_delete-genes
  • Computer: Run on Seaver 120-04
  • Code Version: GRNmap beta 1:24 pm 2/1/2016
  • Run started: 1:32 pm 2/1/2016
  • The program was still running at 8:37 am 2/2/2016. At this time it was on the 5th alpha.
  • Update: The program was still running at 12:28 pm 2/2/2016. At this time it was on the 8th alpha.
  • Update: The program was still running at 6:41 PM 2/4/16. At this time it was on the 10th alpha (319,300 iteration)

• 16_gene_24_edges_disregard_16
  • Computer: Run on Seaver 120-03
  • Code Version: GRNmap beta 1:51 pm 2/1/2016
  • L-curve was set to 0 rather than 1, meaning that L-curve analysis was not performed.
  • Run started: 8:40 am 2/2/2016
  • The program finished running at 1:27 pm 2/2/2016 (~5 hours to run)
  • 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 “TM_GRNMAP_02-01-2016” in the thaw space. A file called TM_GRNMAP_02-01-2016dGLN3_16_gene_24_edges_desregard_16_input_TM_2016-01-21LCurveLCurveData was output and saved in the thaw space (not in the “TM_GRNMAP_02-01-2016” folder.
  • There is only one optimization_diagnostic.jpg, meaning that likely it is overwriting after every run.

• 33_gene_110_edges_add_1_delete-genes
  • Computer: Run on Seaver 120-02
  • Code Version: GRNmap beta 1:54 pm 2/1/2016
  • Run started: 1:59 pm 2/1/2016
  • The program was still running at 8:42 am 2/2/2016. At this time it was on the 9th alpha.
  • Update: The program was still running at 12:35 am 2/3/2016. At this time it was on the 14th alpha.
• The program was finished at 6:49 on 2/4.

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