DGLN3 L-curve analysis TM

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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. 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 2/1/2016

  • 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.
    • Resulted in an "S curve."
  • 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 iterations).
    • Update: Still running at 2:36 PM 2/5/16. At this time it was still on the 13th alpha (5,868,600 iterations).
    • Update: Still running at 2:47 pm 2/19/2016. At this time it was still on the 13th alpha (27,304,800 iterations).
    • Program was forced to quit. The data up to the 13th alpha was used to make an L-curve.
  • 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)
    • Update: Still running at at 2:37 PM 2/5/16. At this time it was on the 11th alpha.
    • The program was finished by 1:24 am on 2/11/16 and was saved into a folder called "TM_GRNMAP_02-01-2016" in the thaw space.
    • Resulted in an "S curve."
  • 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 by 6:49 on 2/4/16.
    • Resulted in an "S curve."

Running the L-curve 2/19/2016

There was a formatting issue that created "s" curves rather than "l" curves. Add the title "threshold_b" in the second column of the "threshold_b" sheet. Set makeGraphs = 1 because beta will now make L-curve graphs for the second two.

  • 35-gene_100-edges_TM_dgln3-fam_no-strains-added_Sigmoid_estimation
    • Computer: Run on Seaver 120-0# (all the way on the right in the first row)
    • Code Version: GRNmap beta 5:05 pm 2/19/2016
    • Run started: 5:07 pm 2/19/2016
    • The program was finished by 7:04 am on 2/22/16.
    • Resulted in an "S curve."
  • 33-gene_110-edges_TM_dgln3-fam_strains-added_Sigmoid_estimation_delete-genes
    • Computer: Run on Seaver 120-0# (one over from all the way on the right in the first row)
    • Code Version: GRNmap beta 4:50 pm 2/19/2016
    • Run started: 4:51 pm 2/19/2016
    • Update: The program was still running at 1:31 pm 2/26/16. At this time it was on the 12th alpha.
  • 35-gene_120-edges_TM_dgln3-fam_strains-added_Sigmoid_estimation_delete-expression-data
    • Computer: Run on Seaver 120-0# (all the way on the right in the second row)
    • Code Version: GRNmap beta 4:55 pm 2/19/2016
    • Run started: 5:03 pm 2/19/2016
    • Update: Someone edited the program before the 13th alpha could be completed.

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