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annotate m-toolbox/classes/+utils/@math/mhsample_td.m @ 52:daf4eab1a51e database-connection-manager tip

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Fix. Default password should be [] not an empty string
author Daniele Nicolodi <nicolodi@science.unitn.it>
date Wed, 07 Dec 2011 17:29:47 +0100
parents f0afece42f48
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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2 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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3 % Metropolis algorithm
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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4 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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5 % M Nofrarias 15-06-09
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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6 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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7 % $Id: mhsample_td.m,v 1.1 2010/11/26 13:48:48 luigi Exp $
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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8 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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9 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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10
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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11
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
12 function smpl = mhsample_td(model,in,out,cov,number,limit,parnames,Tc,xi,xo,search,jumps,parplot,dbg_info,inNames,outNames,Noise,cutbefore,cutafter)
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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13
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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14 import utils.const.*
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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15
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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16 % compute mean and range
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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17 mn = mean(limit);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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18 range = diff(limit);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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19 % initialize
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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20 acc = [];
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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21 nacc = 1;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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22 nrej = 1;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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23 loop = 0;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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24 oldacc = 0;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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25 oldrej = 0;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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26 chgsc = 0;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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27 nparnames = length(parnames);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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28
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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29
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
30 % switch depending on model class (initial likelihood)
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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31 switch class(model)
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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32 case 'matrix'
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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33 % loglk1 = utils.math.loglikehood_matrix(xo,in,out,nse,model,parnames);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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34 % loglk1 = utils.math.loglikehood_matrix(xo,in,out,nse,model,parnames,inModel,outModel);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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35 case 'smodel'
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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36 % loglk1 = utils.math.loglikehood(xo,in,out,nse,model,parnames);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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37 case 'ssm'
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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38 loglk1 = utils.math.loglikehood_ssm_td(xo,in,out,parnames,model,inNames,outNames,Noise,'cutbefore',cutbefore,'cutafter',cutafter);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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39 otherwise
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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40 error('### Model must be either from the ''smodel'' or the ''ssm'' class. Please check the inputs')
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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41 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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42
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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43 % accept the first sample if no search active
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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44 if ~search
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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45 smpl(1,:) = xo;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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46 nacc = 1;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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47 else
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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48 smpl = [];
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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49 nacc = 0;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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50 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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51 nrej = 0;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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52
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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53 utils.helper.msg(msg.IMPORTANT, 'Starting Monte Carlo sampling', mfilename('class'), mfilename);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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54
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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55
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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56 hjump = 0;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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57 % main loop
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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58 while(nacc<number)
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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59 % jumping criterion during search phase
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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60 % - 2-sigma by default
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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61 % - 10-sigma jumps at mod(10) samples
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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62 % - 100-sigma jumps at mod(25) samples
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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63 % - 1000-sigma jumps at mod(100) samples
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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64 if search
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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65 if nacc <= Tc(1)
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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66 if(mod(nacc,10) == 0 && mod(nacc,25) ~= 0 && mod(nacc,100) ~= 0 && hjump ~= 1)
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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67 hjump = 1;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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68 xn = mvnrnd(xo,jumps(2)^2*cov);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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69 elseif(mod(nacc,25) == 0 && mod(nacc,100) ~= 0 && hjump ~= 1)
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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70 hjump = 1;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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71 xn = mvnrnd(xo,jumps(3)^2*cov);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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72 elseif(mod(nacc,100) == 0 && hjump ~= 1)
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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73 hjump = 1;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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74 xn = mvnrnd(xo,jumps(4)^2*cov);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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75 % xn = xo + range/2+rand(size(xo));
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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76 else
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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77 hjump = 0;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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78 xn = mvnrnd(xo,jumps(1)^2*cov);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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79 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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80 else
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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81 xn = mvnrnd(xo,cov);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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82 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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83 else
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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84 xn = mvnrnd(xo,cov);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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85 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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86
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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87 % check if out of limits
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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88 if( any(xn < limit(1,:)) || any(xn > limit(2,:)))
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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89 logprior = inf;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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90 loglk2 = inf;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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91 betta = inf;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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92 else
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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93 % compute annealing
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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94 if ~isempty(Tc)
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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95 if nacc <= Tc(1)
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
96 betta = 1/2 * 10^(-xi*(1-Tc(1)/Tc(2)));
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
97 elseif Tc(1) < nacc && nacc <= Tc(2)
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
98 betta = 1/2 * 10^(-xi*(1-nacc/Tc(2)));
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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99 else
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
100 betta = 1/2;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
101 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
102 else
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
103 betta = 1/2;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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104 end
f0afece42f48 Import.
Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
105 % switch depending on model class (new likelihood)
f0afece42f48 Import.
Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
106 switch class(model)
f0afece42f48 Import.
Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
107 case 'matrix'
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
108 % loglk2 = utils.math.loglikehood_matrix(xn,in,out,nse,model,parnames,inModel,outModel);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
109 case 'smodel'
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
110 % loglk2 = utils.math.loglikehood(xn,in,out,nse,model,parnames);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
111 case 'ssm'
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
112 loglk2 = utils.math.loglikehood_ssm_td(xn,in,out,parnames,model,inNames,outNames,Noise,'cutbefore',cutbefore,'cutafter',cutafter);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
113 otherwise
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
114 error('### Model must be either from the ''smodel'' or the ''ssm'' class. Please check the inputs')
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
115 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
116 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
117
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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118 % likelihood ratio
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
119 logr = betta*(loglk2 - loglk1) ;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
120 % decide if sample is accepted or not
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
121 if logr < 0
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
122 xo = xn;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
123 nacc = nacc+1;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
124 smpl(nacc,:) = xn;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
125 loglk1 =loglk2;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
126 if dbg_info
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
127 utils.helper.msg(msg.IMPORTANT, sprintf('acc.\t loglik: %d -> %d betta: %d ratio: %d',loglk1,loglk2,betta,logr), mfilename('class'), mfilename);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
128 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
129 elseif rand(1) > (1 - exp(-logr))
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
130 xo = xn;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
131 nacc = nacc+1;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
132 smpl(nacc,:) = xn;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
133 loglk1 =loglk2;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
134 if dbg_info
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
135 utils.helper.msg(msg.IMPORTANT, sprintf('acc.\t loglik: %d -> %d betta: %d ratio: %d',loglk1,loglk2,betta,logr), mfilename('class'), mfilename);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
136 end
f0afece42f48 Import.
Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
137 else
f0afece42f48 Import.
Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
138 nrej = nrej+1;
f0afece42f48 Import.
Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
139 if dbg_info
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
140 utils.helper.msg(msg.IMPORTANT, sprintf('rej.\t loglik: %d -> %d betta: %d ratio: %d',loglk1,loglk2,betta,logr), mfilename('class'), mfilename);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
141 end
f0afece42f48 Import.
Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
142 end
f0afece42f48 Import.
Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
143
f0afece42f48 Import.
Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
144 % display and save
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
145 if(mod(nacc,100) == 0 && nacc ~= oldacc)
f0afece42f48 Import.
Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
146 updacc = nacc-oldacc;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
147 updrej = nrej-oldrej;
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
148 ratio(nacc/10,:) = updacc/(updacc+updrej);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
149 utils.helper.msg(msg.IMPORTANT, sprintf('accepted: %d rejected : %d acc. rate: %4.2f',nacc,updrej,ratio(end)), mfilename('class'), mfilename);
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
150 for i = 1:numel(parnames)
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
151 fprintf('### Parameters: %s = %d \n',parnames{i},xn(i))
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
152 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
153 oldacc = nacc;
f0afece42f48 Import.
Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
154 oldrej = nrej;
f0afece42f48 Import.
Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
diff changeset
155 save('chain.txt','smpl','-ASCII')
f0afece42f48 Import.
Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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156 save('acceptance.txt','ratio','-ASCII')
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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157 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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158
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Daniele Nicolodi <nicolodi@science.unitn.it>
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159 % plot
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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160 if ((mod(nacc,100) == 0) && (nacc ~= 0) && ~isempty(parplot))
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Daniele Nicolodi <nicolodi@science.unitn.it>
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161 for i = 1:numel(parplot)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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162 figure(parplot(i))
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Daniele Nicolodi <nicolodi@science.unitn.it>
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163 plot(smpl(:,parplot(i)))
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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164 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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165 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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166
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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167 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
parents:
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168 end