Mean clusters

Note: Repeatedly crashing my computer: SW should try
In[]:=
pcas=With[{ru={299459058088077823758143088095350287424,4,1}},PerturbedCellularAutomaton[ru,{{1},0},{120,{-30,50}},#,"ReturnPerturbations"->False]&/@allperts[CellularAutomaton[ru,{{1},0},{120,{-30,50}}]]];
In[]:=
SeedRandom[4445];​​out=FindClusters[PlotCA[pcas[[#]],"Trim"->{None,None}]->#&/@RandomSample[Range[Length[pcas]],3]]
Out[]=
{{3562},{4145},{1181}}
In[]:=
ArrayPlot[Map[Blend[Take[Last/@colorrules,4],BinCounts[#,{0,4,1}]]&,Transpose[pcas[[#]],{3,1,2}],{2}]]&/@out
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The Effect of Genetic Diversity

Modernized Histogram code to run
Overall effect on lifetime:
poplts=​​Module[​​{ru={299459058088077823758143088095350287424,4,1},init={{1},0},txspec={400,{-110,110}}},​​SeedRandom[5555];​​ParallelMap[Function[rule,TestCALifeTime[PerturbedCellularAutomaton[rule,init,txspec],#]&/@allperts[rule,init,txspec]]@@#&,RandomSample[quickneutral[ru],10]]]
Histogram[#,100,"Probability",AspectRatio->.4]&/@poplts//GraphicsGrid[Partition[#,5]]&
[[[ same analyses; different genomes ]]]
[[ Therapy that works on one genome doesn’t necessarily work on others .... show all 64 cases ]]

Biological Evolution and Our Model Organism

[[ Could be whole organism, or could be e.g. an organ ]]
In[]:=
rh=Reap[mh=Module[{ru,ca,lt,lts,pcas,fitness,initru={0,4,1},initfit={0}},SeedRandom[7899623];​​Sow[{initru,<||>,initfit}];​​NestList[CompoundExpression[​​ru=RandomRuleMutation[First[#]],​​ca=CellularAutomaton[ru,{{1},0},{200,{-200,200}}];​​lt=TestCALifeTime[ca];​​If[lt==-Infinity,Sow[{ru,<||>,{lt}}];#,​​pcas=Table[PerturbedCellularAutomaton[ru,{{1},0},{200,{-200,200}},1],Ceiling[lt/10]];​​fitness=Min[lts=Join[{lt},TestCALifeTime/@(First/@pcas)]];​​Sow[{ru,Last/@pcas,lts}];​​If[fitness>=Last[#],{ru,fitness},#]]]&,{initru,First[initfit]},2000]]][[2,1]];
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In[]:=
Show[ListStepPlot[mh[[All,2]]],ListPlot[Min/@rh[[All,3]],PlotHighlighting->None,PlotStyle->Red],Frame->True,AspectRatio->1/3]
Out[]=
In[]:=
Show[ListStepPlot[mh[[All,2]]],ListPlot[{Style[Catenate[MapIndexed[{First[#2],#1}&,rh[[All,3]],{2}]],Opacity[.5,Gray],PointSize[Large]],Style[MapIndexed[{First[#2],#}&,Min/@rh[[All,3]]],PointSize[Large],Red]},PlotHighlighting->None,Filling->Bottom],Frame->True,AspectRatio->1/3,PlotRange->{{0,50},{0,10}}]
Out[]=
In[]:=
Show[ListPlot[Style[Catenate[MapIndexed[{First[#2],#1}&,rh[[All,3]],{2}]],Opacity[.5,Gray],PointSize[Medium]],PlotHighlighting->None],ListPlot[Style[MapIndexed[{First[#2],#}&,Min/@rh[[All,3]]],PointSize[Medium],Red],PlotHighlighting->None,Filling->Bottom,FillingStyle->Lighter[Red]],ListStepPlot[mh[[All,2]],PlotHighlighting->None],Frame->True,AspectRatio->1/3,PlotRange->{{0,200},{0,12}}]
Out[]=
TODO: Run this for 400
In[]:=
allpertscands=Module[{init={{1},0},txspec={200,{-110,110}}},​​Map[​​Function[rule,allperts[rule,init,txspec]],cands]];
In[]:=
ltscands=Module[{init={{1},0},txspec={200,{-110,110}}},​​ParallelMap[​​Function[{rule,aps},TestCALifeTime[PerturbedCellularAutomaton[rule,init,txspec,#,"ReturnPerturbations"->False]]&/@aps]@@#&,Transpose[{cands,allpertscands}]]];
In[]:=
Histogram[#,100,"Probability",AspectRatio->.4]&/@ltscands//GraphicsGrid[Partition[#,6]]&
Out[]=

More honest therapy sensitivity

Clinical Trial Include?