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GENETIS

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Entry time:	Fri Jul 10 16:35:26 2020
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<table border="1" cellpadding="1" cellspacing="1" style="width:500px"> <tbody> <tr> <td>Name</td> <td>Update</td> <td>Plans for Monday</td> </tr> <tr> <td>Alex M</td> <td> <p>Yesterday we started a run of the database version of the loop. The goal was to use it to replicate the results from the run we finished yesterday using the same parameters (NPOP=8, SEEDS=10, bicone separation = 0.05 cm). We initially ran into problems with the databse which we fixed this morning. We successfully completed the 0th generation, but then the .uan files for the next generation weren't created properly. Alex and I will try to resolve this. Amy suggested we only need to run 6-7 generations to confirm that we get the same results as from the previous run. The 0th generation agreed with the 0th generation of the previous run (in terms of DNA; the effective volume/fitness score plots looked similar, but there is slight room for noise in AraSim so the exact values are slightly different; but overall they look very similar). I also confirmed that the generation DNA is the same in generation 1 of the current database run as in the previous run.</p> <p>The name of this run is Data_Base_Test_7_10.</p> <p>The name of the previous run we are comparing against is Length_Cutoff_Test_3.</p> </td> <td> <p>The top priority right now needs to be with fixing the error in the database version that is causing the uan files to be made incorrectly. Once that is fixed, we can continue the run and confirm that we get the same results After that, we'll have Eliot and Leo run their version using the same parameters to confirm that they get the same results as the previous two runs. From there, we'll merge the branches and begin a real run.</p> <p>The first real run will use NPOP=8, 3 dimensions (LRT), a separation distance of 3 cm, and will run for up to 15 generations. We'll also fix the issue of the mutation standard deviation (see yesterday's update for the three differences between our current runs and the future real runs). </p> <p>Our goal is to get as much real data as possible next week. I'm confident that we can have at least one with 3 dimensions (LRT) done by next Friday (we'll shoot for 15 generations, but if it seems to converge between 10-15 we can stop it). </p> <p>If we can finish that run, we can start another run using 4 dimensions, where we add an option to make the bicone assymetric in length (L1L2RT). These are the runs we're hoping to use in the paper.</p> </td> </tr> <tr> <td>Alex P</td> <td> </td> <td> </td> </tr> <tr> <td>Eliot</td> <td> </td> <td> </td> </tr> <tr> <td>Leo</td> <td>Today we looked at the results of our last run. This run consisted of 8 individuals and was set at 20 generations, but we just wanted to see how far it would evolve. We noticed that the error came from LRTS.py when we need to reshape the arrays from gensData.py in order to plot them. The error said that the array couldn't be reshaped because the new array's dimensions were too small. After digging around and rerunning with past save states, we were thinking that the issue wasn't with the code, but was actually an issue with generation the loop said it was on. For instance if we were on gen 5, LRTS thought we were on 4. Eliot was pretty sure this was because we had been interupted during part of our run, so Leo gave him the benefit of the doubt and decided to run again. This time we only ran 3 individuals up to the 1st generation, just to make sure the plots were working. Leo was running, making sure not to have any interuptions, and indeed all the plotting softwares worked. So, to the best of our knowledge our version of the loop is ready to go.</td> <td>Next week we are just waiting for the Alexs to finish up with their testing so we can start merging. We didn't have any plans to work on outside of that.</td> </tr> <tr> <td>Evelyn</td> <td> </td> <td> </td> </tr> <tr> <td>Ryan</td> <td>Finished the crossover function for Paperclips and ran a few tests for the roulette + crossover. Tests seem to show that the paperclips quickly (between 3-5 generations ) converge to become the same paperclip and fitness scores (determined by z-curl) dropped off after the second generation. This is most likely due to the fact that currently there is no form of gene mutations written into the crossover function for repopulation and so the angles the segments can have are locked from the first selection. However, I am not 100% certain on this and there could just be a hidden error somewhere as at times in some (not all ) of the tests I did there were times where the roulette function passed many of the same paperclip to the next generation, therefore decreasing the size of the gene pool. I need to do further tests to be certain of one or the other but otherwise, everything seems to be working as intended.   </td> <td>The next step I plan on taking is creating a mutation function in effort to make the gene pool larger. It is likely that I will look at the bicone's roulette program to model this mutation but I am considering writing a simple one first just to run tests on the effect on the diversity. After this step is complete, I will move on to creating a function that is able to send certain amounts of the population to the tournament and the rest to roulette to see what mix gives the best results. I also as a pre-step to this may take the existing algorithms in paperclips and re-write them as functions rather than loops in main to make the passing of different parts easier and faster. </td> </tr> <tr> <td>Ben</td> <td> </td> <td> </td> </tr> <tr> <td>Ethan</td> <td>Continued documenting AREA project in google doc. Worked with Ben on getting AraSim running and fixing errors.</td> <td>Meeting with Ben to continue on AREA project. We may try to get AraSim run the children in parallel to make it go faster as it takes a very large amount of time currently.</td> </tr> </tbody> </table> <p> </p> Encoding: HTML ELCode plain Suppress Email notification Resubmit as new entry

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