Revision modifications

Graound truth for the simrank

• read d3plot displacements

• one time step, last

  • calcualte the diff
  • all time steps
  • just 5 parts

• Make the todo tasks

• Compare 3001

  • Simrank matrix value
    • argsort issue with small value, numpy.array([1., 0.5, 1.]).argsort(kind="heapsort")
  • Simrank loop
  • make feature graph
  • Pe vs IE weight
    • why from single to all paired sim differ
    • Have two different weight
    • Correct kg01 loading

• Similarity from RMSE

• How is it with component graph

• Diagnoal value not 1 > effect of spread

  • Look in paper
  • Move the test functions

• Run simrank for each simulation and ref seprately

• What does SimRank do

• Change the spread function

Extended data debug

• get top color
• decrease number of simulation range

Write result

• update displacements
• update text
• write extended result

SimRank issue

• spread normalization differ from simrank weighted normalization. spread normalize vs source edges where simRank normalizes vs target edges

• recalculate spread

• why sim > 1

  • check sim for test_epread > not bigger than 1
  • check combining sprd and evd

• change simRankpp function to simrank_pp_similarity_numpy in nrg_simRank/inv_simRnk_extnd.py

• clean sprd, evd, C option in nrg_simRank/inv_simRnk_extnd.py

• run the extnd result

• check simrank result with github functions > wrong result on the simple example

• transfer result to the plot_nrg_extnd

• spread only for PID nodes

• change weight manipulation to weight subtraction

Make new result

• Pe plot with selecting only closest

update cevt result

• run the result
• change the method
• verify the result
  • whey there is similarities close to zero, is it 0 or sth else> tehre are smaller than 0.11 but not zero
  • why hh-ll doen't pick small HH anymore > errList is active
  • check the KDE if the smlll similarities belong to pid than sims > the errList was empty

scatter plot comparison

• the color code, L sim to be red

• legend order

• save four plot

• add four pic in tex

• legend inside

• fix the bolt for plot_report.py

• section 6.2, 4 pid -> components

• split the paper

• cite the conf paper modeling

Graph visualization

• make same vis as paper
  • check the error list > it was ok, the issue was that initital plot was without weight - one des is missing in curre
• show loop with removing high distance nodes
  • why network2tikzi doesn't plot > issue with latex, set the style with plotly
• show visualization with more releases / several rls together

SimRank with grouping

• add grouping to the database
• load the features
• simrank query to set graph for groping-des COG - make new design based on box grouping - add the weights to the edge of box design - add intiger name of the box to the graph