User:Alondra Vega/Notebook/Research/2010/05/28

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Today's Work

Image:Matlab practice changed parameters 2 3 and 6 AV 28052010.ppt

  • To begin practicing in Matlab, we created a test_data_file.xls. In this file my job was to change the parameter values, the weights.
  • Parameters 2 and 3 were to be changed simultaneously to show the greatest effect.
  • Separately, parameter 6 was to be changed to show how the fourth gene would be affected.
  • The network that we are working with has four genes.

Trial 1

  • To start things off, I left all parameter values both weights and thresholds equaling 1.
  • All genes have an equilibrium at 1 with different graph behaviors.

Trial 2

  • For the first trial I decided to make the parameter values of 2 and 3 smaller than 1. I made them equal 0.5. The gene that showed a difference in the way that it behaved was Gene 3.
  • All of the genes were at equilibrium at 1. Even though some of the parameters changed they still all went to 1.

Trial 3

  • For the second trial I decided to make both of the parameter values of 2 and 3 greater than 1. I made them equal 5.
  • Gene1's equilibrium point changed. It seems that it is now approaching 1.5.
  • Gene2's equilibrium also changed. It is now approaching 2. A value twice as big as the first equilibrium state.
  • Gene3's equilibrium changed to 1.7.
  • Gene4's equilibrium seems to be approaching a number less than 1.5.
  • All genes went to a different equilibrium value.

Trial 4

  • For this trial I changed the second parameter to a number greater than 1 and the third parameter value to a number less than 1. The second parameter value will stay as 5 and the third parameter value will change back to 0.5.
  • Gene1's equilibrium point seems to have shifted a little higher up from Trial 2. It seems to be arou8nd the value of 1.6.
  • Gene2's equilibrium value has shifted lower than in Trial 2. It now seems to be approaching the value of 1.6 or 1.7.
  • Gene3's equilibrium value has also lowered by 0.1. It is now 1.6.
  • Gene4's equilibrium value did not have a lot of variance.

Trial 5

  • For Trial 4 I switched the values of Trial 3. So now the second parameter has a value of 0.5 and the third parameter has a value of 5.
  • Gene1's equilibrium point had a very small variance. it may have been a 0.1 difference or less.
  • Gene2's equilibrium point decreased to 1.5.
  • Gene3's equilibrium point also decreased to 1.5.
  • Gene4's equilibrium point had a very small variance.

Trial 6

  • For Trial 5, both parameters 2 and 3 were changed to be -1. This is to observe the behavior that a negative weight has on the model.
  • Gene1's equilibrium point went back to 1, but before it went to 1 it had a small decrease in slope just below 1 and then it jumped back to 1.
  • Gene2's equilibrium also went back to one having the same behavior as Gene1 did. It just had a deeper steep in the decrease in slope.
  • Gene3's equilibrium also went back to 1. It went passed 1 to a little over 1.1 and then back down to about 0.82 before it went to equilibrium.
  • Gene4's equilibrium behaved as gene1. It had a little variance from the rest of the changes.

Trial 7

  • For Trial 6, the second parameter was left as negative and the third parameter was changed back to positive 1.
  • Gene1's equilibrium point did not change much from Trial 5.
  • Gene2's equilibrium is 1, but before it got there it had a dramatic change in slope. It went down from 0.6 back up to 1.
  • Gene3's equilibrium point changed the most in this trial. It went up to about 1.22 and created a peak in the graph. Then it decreased to have an equilibrium point at 1.
  • Gene4's equilibrium point showed minimal variance.

Trial 8

  • For Trial 7, the second parameter was changed to 1 and the third weight value was changed to -1.
  • Both Gene1 and Gene4 showed little variance.
  • Gene2's model behavior was similar to the behavior it had during Trial 6, just with less of a dramatic drop below 1. Its equilibrium is still 1.
  • Gene3's equilibrium point is still 1, but it went from about 1.56 to 1.


We notice that the equilibrium point for Gene4 did not have a lot of variance, thus we will look at the weight 
that affects this gene. It is weight 6.  For the following trials only the sixth parameter,weight, value
will be changed.

Trial 9

  • For this trial the value for parameter 6 was changed to 0.5.
  • For all graphs the equilibrium value did not go to 1, but the behavior of the graphs did no change.

Trial 10

  • For this trial, I changed the parameter value from 0.5 to 5.
  • Genes 1-3 did not show a lot of variance.
  • Gene4's equilibrium point changed to 2. Twice as much as the original. This is the first trial that shows Gene4 changing its equilibrium value with a great difference.

Trial 11

  • For this trial I changed the sixth weight into -1 to see how it would affect Gene 4.
  • Genes 1-3 still did not show a lot of variance in this trial.
  • Gene4's equilibrium went back to 1. The graph did show a slight decrease in slope before approaching 1, in comparison to all the previous trials.


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