Merge MCMC parameter estimation toolbox #42
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added 30 commits
August 27, 2017 20:59
…nding second step parameters differently.
… 40 iterations, parallel, thinning 10, step size 1.3
…ion points, apr 2, 3 pm
… need to do a commit every time.
…anges of the tx elongation, agtp regeneration system turnoff time, AA_F, UTRKd parameters. Going to initialize with the previous distributions and rerun at a much larger step size, and a much higher standard deviation (so that there is more mixing. only doing 20 iterations. going to analyze results. then rerun on new step sizes and standard deviations. eventually want to have a small SD and a small SS. This is the cooling effect. Simulated annealing. it should not violate detailed balance since eventually we will still to one set of conditioned, and this initial phase can just be thought of as a randomization phase where we try to find some initial distribution of points. This randomization is not totally random, indeed we are messily searching a distribution of parameters that fit the data, albeit poorly. " git commit -m "first set of nessa and lambda runs done. Now extended the parameter ranges of the tx elongation, agtp regeneration system turnoff time, AA_F, UTRKd parameters. Going to initialize with the previous distributions and rerun at a much larger step size, and a much higher standard deviation. so that there is more mixing. only doing 20 iterations. going to analyze results. then rerun on new step sizes and standard deviations. eventually want to have a small SD and a small SS. This is the cooling effect. Simulated annealing. it should not violate detailed balance since eventually we will still to one set of conditioned, and this initial phase can just be thought of as a randomization phase where we try to find some initial distribution of points. This randomization is not totally random, indeed we are messily searching a distribution of parameters that fit the data, albeit poorly. " "
…l are fixed from values found from training D. Note that in training D, we found the ktx and ktl to be exactly inversely proportional.
…. has not been run yet. will run.
…into minmcmcv5a
…ameter ranges, as described in the evernote note "035 APR 2020 VNPRL F2 (->F3)+ IFFL training E(->F)"
…into minmcmcv5a
…into minmcmcv5a # Conflicts: # generate_paper_figs/Core_characterization_plots.m
…ithub happened that caused it to be deleted: Take note. my dropbox folder is available on both my mac (com1) and desktop (com2). This repo is available on dropbox, and therefore, on both com1 and com2. But really, this dropbox version should be thought of as the working copy for com1, NOT com2. We will call this working copy WC1. Now, this repo also has a local non-dropbox working copy on com2. We will call this working copy WC2. The problem occured when i edited a file (runsummareis.m) that was in WC1 on com2. but then from com2, i committed and pushed WC2 (which had the unedited file), and pulled this change onto com1's working copy, WC1. In this process, i overwrote all my changes to the file. So really, word of advice: 1. whenever you make a change, puch it to the repo immediately, while it is still fresh. 2. Never change anything from com2 on the dropbox folder, and then expect that change to still be there when you push WC2 onto the remote repo. Actually I think this problem occurred because I created the file on both WC1 and WC2, but did not commit either. I made changes to the one in WC1, but not WC2, and then committed the one in WC2, and then pulled this to overwrite the one in WC1, losing that copy in WC1.
…e files to tbe build a cell repo
…into minmcmcv5a
…ich had the parameter values incorporated, and some small changes to a couple of component m files.
…sion throws an error where the rawdata_ACSDSG2014.m is not found.
…orrection files. More changes coming before this will be working. (this commit is to transfer the code between machines)
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Vipul has now finished his PhD and so I'm assuming we can merge this code into the master repository on BuildACell.
@vipulsinghal02 Is this ready to go? If not, can you post here what needs to be added/fixed?