inst/doc/MEIGOR-vignette.R

In MEIGOR: MEIGO - MEtaheuristics for bIoinformatics Global Optimization

## ----include=FALSE------------------------------------------------------------
library(knitr)
opts_chunk$set(
concordance=TRUE
)

## ----preliminaries, eval=TRUE, include=FALSE, echo=FALSE------------
options(width=70, useFancyQuotes=FALSE, prompt=" ", continue="  ")
set.seed(123L)

## ----installMEIGO2, eval=FALSE, pgf=TRUE, echo=TRUE-----------------
#  if (!requireNamespace("BiocManager", quietly=TRUE))
#      install.packages("BiocManager")
#  BiocManager::install("CellNOptR")

## ----load_package, eval=TRUE, pgf=TRUE, echo=FALSE,results='hide',warning=FALSE, message=FALSE----
library(MEIGOR)

## ----quickProblem, eval=FALSE, pgf=TRUE, echo=TRUE------------------
#  library(MEIGOR)
#  problem<-list(f=objective, x_L=rep(-1,2), x_U=rep(1,2))
#  opts<-list(maxeval=500, local_solver='DHC')

## ----quickProblemSolve, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'----
ex3<-function(x,k1,k2,k3,k4){
f=-x[4];
#Equality constraints (declare them before the inequality ones)
g<-rep(0,5);
g[1]=x[4]-x[3]+x[2]-x[1]+k4*x[4]*x[6];
g[2]=x[1]-1+k1*x[1]*x[5];
g[3]=x[2]-x[1]+k2*x[2]*x[6];
g[4]=x[3]+x[1]-1+k3*x[3]*x[5];

#Inequality constraint
g[5]=x[5]^0.5+x[6]^0.5;
return(list(f=f,g=g));
}

## ----multiStart, eval=FALSE, pgf=TRUE, echo=TRUE--------------------
#  Results_multistart<-MEIGO(problem,opts,algorithm="MULTISTART",p1,p2,...)

## ----unConstrainedF, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'----
ex1 <- function(x){
y<-4*x[1]*x[1]-2.1*x[1]^4+1/3*x[1]^6+x[1]*x[2]-4*x[2]*x[2]+4*x[2]^4;
return(y)
}

## ----unConstrainedSolve, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'----
#=========================
#PROBLEM SPECIFICATIONS
# =========================
problem<-list(f="ex1",x_L=rep(-1,2),x_U=rep(1,2))
opts<-list(maxeval=500, ndiverse=40, local_solver='DHC',
local_finish='LBFGSB', local_iterprint=1)
#=========================
# END OF PROBLEM SPECIFICATIONS
#=========================

Results<-MEIGO(problem,opts,algorithm="ESS");

## ----ex2F, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'------------
ex2<-function(x){
F=-x[1]-x[2];
g<-rep(0,2);
g[1]<-x[2]-2*x[1]^4+8*x[1]^3-8*x[1]^2;
g[2]<-x[2]-4*x[1]^4+32*x[1]^3-88*x[1]^2+96*x[1];
return(list(F=F,g=g))
}

## ----ex2Solve, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'--------
#=========================
#PROBLEM SPECIFICATIONS
#=========================
problem<-list(f="ex2",x_L=rep(0,2),x_U=c(3,4),
c_L=rep(-Inf,2), c_U=c(2,36))
opts<-list(maxeval=750, local_solver="DHC", local_n1=2, local_n2=3)
#========================
#END OF PROBLEM SPECIFICATIONS
# ========================

Results<-MEIGO(problem,opts,algorithm="ESS");

## ----ex3f, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'------------
ex3<-function(x,k1,k2,k3,k4){
f=-x[4];
#Equality constraints
	g<-rep(0,5);
	g[1]=x[4]-x[3]+x[2]-x[1]+k4*x[4]*x[6];
	g[2]=x[1]-1+k1*x[1]*x[5];
	g[3]=x[2]-x[1]+k2*x[2]*x[6];
	g[4]=x[3]+x[1]-1+k3*x[3]*x[5];

#Inequality constraint
	g[5]=x[5]^0.5+x[6]^0.5;
	return(list(f=f,g=g));
}

## ----ex2Solve3, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'-------
#=========================
#PROBLEM SPECIFICATIONS
#=========================
problem<-list(f="ex3",x_L=rep(0,6),x_U=c(rep(1,4),16,16),
neq=4, c_L=-Inf, c_U=4)
opts<-list(maxtime=5, local_solver='solnp')
#=========================
#END OF PROBLEM SPECIFICATIONS
#=========================
k1=0.09755988;
k3=0.0391908;
k2=0.99*k1;
k4=0.9*k3;
Results<-MEIGO(problem,opts,algorithm="ESS",k1,k2,k3,k4);

## ----ex4f, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'------------
	ex4<-function(x){
		F = x[2]^2 + x[3]^2 + 2.0*x[1]^2 + x[4]^2 - 5.0*x[2] - 5.0*x[3] - 21.0*x[1] + 7.0*x[4];
		g<-rep(0,3);
		g[1] = x[2]^2 + x[3]^2 + x[1]^2 + x[4]^2 + x[2] - x[3] + x[1] - x[4];
		g[2] = x[2]^2 + 2.0*x[3]^2 + x[1]^2 + 2.0*x[4]^2 - x[2] - x[4];
		g[3] = 2.0*x[2]^2 + x[3]^2 + x[1]^2 + 2.0*x[2] - x[3] - x[4];
		return(list(F=F, g=g));
	}

## ----ex4main, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'---------
#========================= PROBLEM SPECIFICATIONS ===========================
problem<-list(f="ex4", x_L=rep(0,4), x_U=rep(10,4), x_0=c(3,4,5,1),
int_var=3, c_L=rep(-Inf,3), c_U=c(8,10,5))
opts<-list(maxtime=2)
#========================= END OF PROBLEM SPECIFICATIONS =====================
Results<-MEIGO(problem,opts,algorithm="ESS");

## ----ex5f, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'------------
	ex5<-function(x,texp,yexp){
		yini<-c(100, 0, 0, 0 ,0);
		times<-texp;
		out   <- lsodes(yini, times, ex5_dynamics, parms = x)

		tout<-out[,1];
		yout<-out[,-1];
		J <- sum((yout-yexp)^2);
		g<-0;
		residuals<-(yout-yexp);

		return(list(J,g,residuals))
	}
	#***************************************************
	#Function of the dynamic system
	ex5_dynamics<-function(t,y,p){
	  dy<-rep(0,5)

	  dy[1]<--(p[1]+p[2])*y[1];
	  dy[2]<-p[1]*y[1];
	  dy[3]<-p[2]*y[1]-(p[3]+p[4])*y[3]+p[5]*y[5];
	  dy[4]<-p[3]*y[3];
	  dy[5]<-p[4]*y[3]-p[5]*y[5];
	  return(list(dy))
	}
	#***************************************************

## ----ex5Solve, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide', warning=FALSE, message=FALSE----
	#=======================
	#PROBLEM SPECIFICATIONS
	#=======================
	problem<-list(f="ex5", x_L=rep(0.01,5), x_U=rep(1,5), x_0=rep(0.1,5))
	opts<-list(maxeval=1000, log_var=1:5,
	local_solver='NL2SOL', inter_save=1)
	#========================
	#END OF PROBLEM SPECIFICATIONS
	#=======================
#time intervals

texp<-c(0, 1230, 3060, 4920, 7800,
	10680, 15030, 22620, 36420)

#Distribution of species concentration
#	     y(1)    y(2)    y(3)    y(4)    y(5)

yexp<-rbind(c(100.0, 0.0, 0.0, 0.0, 0.0),
	c(88.35, 7.3, 2.3, 0.4, 1.75),
	c( 76.4  , 15.6,    4.5 ,   0.7 ,   2.8),
	c(65.1 ,   23.1  ,   5.3 ,    1.1 ,    5.8),
	c(50.4  ,  32.9   ,  6.0   ,  1.5   ,  9.3),
	c(37.5  ,  42.7 ,    6.0 ,    1.9  ,  12.0),
	c(25.9  ,  49.1  ,   5.9  ,   2.2 ,   17.0),
	c( 14.0  ,  57.4    , 5.1  ,   2.6   , 21.0),
	c(4.5 ,   63.1  ,   3.8   ,  2.9  ,  25.7));

	Results<-MEIGO(problem,opts,algorithm="ESS",texp,yexp);

## ----ex3solve, eval=FALSE, pgf=TRUE, echo=TRUE,results='hide'-------
#  #=========================
#  #PROBLEM SPECIFICATIONS
#  #=========================
#  problem<-list(f="ex3",x_L=rep(0,6),x_U=c(rep(1,4),16,16),
#   neq=4, c_L=-Inf, c_U=4)
#  opts<-list(ndiverse=10, local_solver='SOLNP', local_tol=3)
#  #=========================
#  #END OF PROBLEM SPECIFICATIONS
#  #=========================
#  k1=0.09755988;
#  k3=0.0391908;
#  k2=0.99*k1;
#  k4=0.9*k3;
#  Results<-MEIGO(problem,opts,algorithm="multistart",k1,k2,k3,k4);

## ----sourceRosen10, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'----
rosen10<-function(x){
		f<-0;
		n=length(x);
		for (i in 1:(n-1)){
			f <- f + 100*(x[i]^2 - x[i+1])^2 + (x[i]-1)^2;
		}
		return(f)
	}

	nvar<-10;


## ----rosen10settings, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'----
problem<-list(f="rosen10", x_L=rep(-5,nvar), x_U=rep(1,nvar))


## ----algVNS, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'----------
algorithm="VNS";

## ----vnsOPts, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'---------
opts<-list(maxeval=2000, maxtime=3600*69, use_local=1,
	 aggr=0, local_search_type=1, decomp=1, maxdist=0.5)

## ----vnsCallMEIGO, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'----
			Results<-MEIGO(problem,opts,algorithm)

## ----options, eval=FALSE, pgf=TRUE, echo=TRUE-----------------------
#  
#  opts=list();
#  opts[[1]]$maxeval<-value1
#  opts[[2]]$maxeval<-value2
#  opts[[3]]$maxeval<-value3

## ----ceSSexample, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide', warning=FALSE, message=FALSE----

rosen10<-function(x){
	f<-0;
	n=length(x);
	for (i in 1:(n-1)){
		 f <- f + 100*(x[i]^2 - x[i+1])^2 + (x[i]-1)^2;
	}
	return(f)
}

nvar=20;
problem<-list(f=rosen10, x_L=rep(-1000,nvar), x_U=rep(1000,nvar));

#Set 1 nodes and 2 cpu's per node
n_nodes=1;
n_cpus_per_node=3;

#Set different values for dim_refset, bal and n2
#for each of the 10 cpu's to be used
dim1 = 23;     bal1 = 0;     n2_1 = 0;
dim2 = 33;     bal2 = 0;     n2_2 = 0;
dim3 = 46;     bal3 = 0;     n2_3 = 2;
dim4 = 56;     bal4 = 0;     n2_4 = 4;
dim5 = 72;     bal5 = 0.25;  n2_5 = 7;
dim6 = 72;     bal6 = 0.25;  n2_6 = 10;
dim7 = 88;     bal7 = 0.25;  n2_7 = 15;
dim8 = 101;    bal8 = 0.5;   n2_8 = 20;
dim9 = 111;    bal9 = 0.25;  n2_9 = 50;
dim10 = 123;   bal10 = 0.25; n2_10 = 100;

opts_dim=c(dim1,dim2,dim3,dim4,dim5,dim6,dim7,dim8,dim9,dim10);
opts_bal=c(bal1,bal2,bal3,bal4,bal5,bal6,bal7,bal8,bal9,bal10);
opts_n2=c(n2_1,n2_2,n2_3,n2_4,n2_5,n2_6,n2_7,n2_8,n2_9,n2_10);
D=10;

#Initialize counter and options
counter=0;
opts=list();
hosts=c();

for(i in 1:n_nodes){
  for(j in 1:n_cpus_per_node){

    counter=counter+1;

    #Set the name of every thread
    if(i<10)hosts=c(hosts,paste('node0',i,sep=""));
    if(i>=10 && i<100)hosts=c(hosts,paste('node',i,sep=""));

    opts[[counter]]=list();

    #Set specific options for each thread
    opts[[counter]]$local_balance  	=	opts_bal[counter];
    opts[[counter]]$dim_refset     	= 	opts_dim[counter];
    opts[[counter]]$local_n2		=	opts_n2[counter];

    #Set common options for each thread

    opts[[counter]]$maxeval			=	10000;
    opts[[counter]]$local_solver	=	"dhc";

    #Options not set will take default values for every thread

  }
}

#Set the address of each machine, defined inside the 'for' loop
opts$hosts=c('localhost','localhost','localhost');

#Do not define the additional options for cooperative methods (e.g., ce_maxtime, ce_isparallel, etc..)
#They will take their default values
opts$ce_niter=5;
opts$ce_type="SOCKS";
opts$ce_isparallel=TRUE;

#Call the solver
Results<-MEIGO(problem,opts,algorithm="CeSSR")

## ----ceVNSexample, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide', warning=FALSE, message=FALSE----
rosen10<-function(x){
		f<-0;
		n=length(x);
		for (i in 1:(n-1)){
			f <- f + 100*(x[i]^2 - x[i+1])^2 + (x[i]-1)^2;
		}
		return(f)
	}

nvar=20;

problem<-list(f=rosen10, x_L=rep(-1000,nvar), x_U=rep(1000,nvar))

opts=list();
opts[[1]]=list(use_local=1,aggr=1,local_search=1,decomp=1,maxdist=0.8,maxeval=2000);
opts[[2]]=list(use_local=1,aggr=0,local_search=2,decomp=0,maxdist=0.5,maxeval=2000);
opts[[3]]=list(use_local=1,aggr=0,local_search=2,decomp=0,maxdist=0.5,maxeval=2000);
opts[[4]]=list(use_local=1,aggr=0,local_search=2,decomp=0,maxdist=0.5,maxeval=2000);

opts$hosts=c('localhost','localhost','localhost','localhost');

opts$ce_niter=10;
opts$ce_type="SOCKS";
opts$ce_isparallel= TRUE;

Results=MEIGO(problem,opts, algorithm="CeVNSR");

## ----label=CNORodeExample_fig, eval=FALSE, echo=TRUE,results='hide'----
#  library(MEIGOR);
#  library(CNORode);
#  data("CNORodeExample",package="MEIGOR");
#  plotCNOlist(cnolist);

## ----label=CNORodeExample_fig_plot,include=TRUE,echo=FALSE,results='hide'----
library(MEIGOR);
library(CNORode);
data("CNORodeExample",package="MEIGOR");
plotCNOlist(cnolist);

## ----label=CNORodeExample_fig_model, eval=FALSE, pgf=TRUE, echo=TRUE,results='hide'----
#  plotModel(model, cnolist);

## ----label=CNORodeExample_fig_model_plot,include=TRUE,echo=FALSE,results='hide'----
plotModel(model, cnolist);

## ----label=CNORodeExample_initial, eval=FALSE, pgf=FALSE, echo=TRUE,results='hide'----
#  
#  initial_pars=createLBodeContPars(model, LB_n = 1, LB_k = 0.09,
#  	LB_tau = 0.1, UB_n = 5, UB_k = 0.95, UB_tau = 10, random = TRUE);
#  
#  simData=plotLBodeFitness(cnolist, model,initial_pars,
#  		reltol = 1e-05, atol = 1e-03, maxStepSize = 0.01);

## ----label=CNORodeExample_initial_plot,include=TRUE,echo=FALSE,results='hide'----

initial_pars=createLBodeContPars(model, LB_n = 1, LB_k = 0.09,
	LB_tau = 0.1, UB_n = 5, UB_k = 0.95, UB_tau = 10, random = TRUE);

simData=plotLBodeFitness(cnolist, model,initial_pars,
		reltol = 1e-05, atol = 1e-03, maxStepSize = 0.01);

## ----label=CNORodeExample_optimize, eval=TRUE,echo=TRUE,results='hide'----
f_hepato<-getLBodeContObjFunction(cnolist, model, initial_pars, indices=NULL,
 time = 1, verbose = 0, transfer_function = 3, reltol = 1e-04, atol = 1e-03,
maxStepSize =Inf, maxNumSteps = 1e4, maxErrTestsFails = 50, nan_fac = 5)

## ----label=CNORodeExample_define_prob, eval=TRUE,echo=TRUE,results='hide'----
n_pars=length(initial_pars$LB);
problem<-list(f=f_hepato, x_L=initial_pars$LB[initial_pars$index_opt_pars],
	x_U=initial_pars$UB[initial_pars$index_opt_pars],x_0=initial_pars$LB[initial_pars$index_opt_pars]);

## ----label=CNORodeExample_define_opts, eval=TRUE,echo=TRUE,results='hide'----
opts<-list(maxeval=100, local_solver=0,ndiverse=10,dim_refset=6);

## ----label=CNORodeExample_2, eval=TRUE,echo=TRUE,results='hide'-----
Results<-MEIGO(problem,opts,algorithm="ESS")

## ----label=CNORodeExample_opt, eval=FALSE, pgf=FALSE,echo=TRUE,results='hide'----
#  opt_pars=initial_pars;
#  opt_pars$parValues=Results$xbest;
#  simData=plotLBodeFitness(cnolist, model,opt_pars,
#  	reltol = 1e-05, atol = 1e-03, maxStepSize = 0.01);

## ----label=CNORodeExample_opt_plot,include=TRUE,echo=FALSE,results='hide'----
opt_pars=initial_pars;
opt_pars$parValues=Results$xbest;
simData=plotLBodeFitness(cnolist, model,opt_pars,
	reltol = 1e-05, atol = 1e-03, maxStepSize = 0.01);

## ----label=CellNOptR_example_cnolist_fig, eval=FALSE, pgf=TRUE, echo=TRUE, results='hide'----
#  library(MEIGOR);
#  library(CellNOptR);
#  data("CellNOptR_example",package="MEIGOR");
#  cnolist=CNOlist(cnolist);
#  plotCNOlist(cnolist)

## ----label=CellNOptR_example_cnolist,include=TRUE,echo=FALSE,results='hide'----
library(MEIGOR);
library(CellNOptR);
data("CellNOptR_example",package="MEIGOR");
cnolist=CNOlist(cnolist);
plotCNOlist(cnolist);

## ----label=CellNOptR_example_fig_model, eval=FALSE, pgf=TRUE, echo=TRUE,results='hide'----
#  model <- preprocessing(cnolist, model,
#  	 expansion=TRUE, compression=TRUE, verbose=FALSE);
#  plotModel(model, cnolist);

## ----label=CellNOptR_example_fig_model_plot,include=TRUE,echo=FALSE,results='hide', warning=FALSE----
model <- preprocessing(cnolist, model, expansion=TRUE, compression=TRUE, verbose=FALSE);
plotModel(model, cnolist);

## ----label=CellNOptR_prep_fig_model, eval=TRUE, pgf=TRUE, echo=TRUE, results='hide'----
get_fobj<- function(cnolist,model){

	f<-function(x,model1=model,cnolist1=cnolist){
		simlist=prep4sim(model1)
		score=computeScoreT1(cnolist1, model1, x)
		return(score)
	}
}
fobj=get_fobj(cnolist,model)

## ----label=CellNOptR_prep_3, eval=TRUE, pgf=TRUE, echo=TRUE, results='hide'----
nvar=16;

problem<-list(f=fobj, x_L=rep(0,nvar), x_U=rep(1,nvar))
opts<-list(maxeval=2000, maxtime=30, use_local=1,
	aggr=0, local_search_type=1, decomp=1, maxdist=0.5)

## ----label=CellNOptR_4, eval=TRUE, pgf=TRUE, echo=TRUE, results='hide'----
Results<-MEIGO(problem,opts,"VNS")

## ----label=CellNOptR_example_plot_optModel,echo=TRUE,eval=FALSE,results='hide'----
#  optModel=cutModel(model,Results$xbest);
#  plotModel(optModel,cnolist);

## ----label=CellNOptR_example_plot_optModel_fig,include=TRUE,echo=FALSE,results='hide'----
optModel=cutModel(model,Results$xbest);
plotModel(optModel,cnolist);