R/experimentWPmethod.R
In ericdunipace/SLIMpaper: Interpretable Model Summaries Using the Wasserstein Distance
Defines functions
experimentWPMethod
Documented in
experimentWPMethod
#' Simulation study function
#'
#' @param target function that is the output of the get_binary_nonlinear, get_normal_linear, etc
#' @param hyperparameters hyperparameters for the Bayesian methodology
#' @param conditions conditions for the simulation
#'
#' @return
#' @export
experimentWPMethod <- function(target, hyperparameters, conditions) {
n <- conditions$n
p <- conditions$p
n.samps <- conditions$n.samps
penalty <- conditions$penalty
lambda.min.ratio <- conditions$lambda.min.ratio
n.lambda <- conditions$n.lambda
penalty_method <- conditions$penalty.factor
family <- conditions$family
solver <- conditions$solver
python.path <- conditions$python.path
recalc <- conditions$recalculate
if (is.null(solver) ) {
solver <- "mosek"
}
if (solver == "") {
solver <- "mosek"
}
solver <- match.arg(solver, choices = c("mosek", "gurobi",
"cplex", "cone", "lp"))
if(is.null(recalc)) recalc <- FALSE
if(recalc == "") recalc <- FALSE
epsilon <- 0.05
otmaxit <- 100
# pseudo.obs <- conditions$pseudo.obs
stan_dir <- conditions$stan_dir
calc_w2_post <- conditions$calc_w2_post
if(is.null(calc_w2_post)) calc_w2_post <- FALSE
# if(is.null(pseudo.obs)) pseudo.obs <- 0
pseudo.obs <- 0
posterior.method <- conditions$posterior.method
transport.method <- conditions$transport.method
if(is.null(transport.method)) transport.method <- "hilbert" #"univariate.approximation.pwr"
not.only.timing <- conditions$not.only.timing
if(is.null(not.only.timing)) not.only.timing <- FALSE
L0 <- conditions$L0
if(is.null(L0)) L0 <- FALSE
sa_seq <- sort(unique(c(2,5,floor(seq(ceiling(p/5),p,floor(p/5))))))
sa_max_time <- 64800
sa_prop <- "random"
# FSAiter <- 10*1:ceiling(p/2)
# RSAiter <- if( p %% 2) { rev(FSAiter)[-1] } else { rev(FSAiter) }
# SAiter <- c(FSAiter, RSAiter)
SAiter <- 10 * ceiling(p/2)
SAtemps <- 50
# SAiter <- 1
# SAtemps <- 1
#IP sequence
if( p < 200 ) {
ip_seq <- 1:p
} else {
ip_seq <- sa_seq
}
#w2 dist param
wp_alg <- conditions$wp_alg
if(is.null(wp_alg)) wp_alg <- "greenkhorn"
# MEAN FUNCTION FOR IMPORTANCE
pred.fun <- switch(family,
"gaussian" = target$sel.pred.fun("linpred"),
"binomial" = target$sel.pred.fun("linpred"),
"exponential" = function(x,theta) {
return(x[,-1,drop=FALSE] %*% theta[-1,,drop=FALSE])
})
# SETUP PARAMETERS
param <- target$rparam()
p_star <- if(family != "gaussian") {
min(length(param$theta),p)
} else {
min(length(param$theta),p + 4)
}
param$theta <- param$theta[1:p_star]
full_param <- c(param$theta, rep(0, max(p-p_star,0)))
#set up data
X <- target$X$rX(n, target$X$corr, p)
X_sing <- matrix(c(target$X$rX(1, target$X$corr, p)), nrow=1, ncol=p)
X_new <- target$X$rX(n, target$X$corr, p)
X_neighborhood <- cbind(1, SLIMpaper::rmvnorm(nsamples = p*10,
mean = X_sing[,-1,drop=FALSE],
covariance = cov(X[,-1,drop=FALSE])/n))
data <- target$rdata(n, X, c(param$theta),
param$sigma2, method = "modified.friedman", corr = target$X$corr)
single_data <- target$rdata(1, X_sing, c(param$theta),
param$sigma2, method = "modified.friedman", corr = target$X$corr)
new_data <- target$rdata(n, X_new, c(param$theta), param$sigma2, method = "modified.friedman", corr = target$X$corr)
neighb_data <- target$rdata(n, X_neighborhood, c(param$theta), param$sigma2, method = "modified.friedman", corr = target$X$corr)
Y <- data$Y
single_Y <- single_data$Y
new_Y_new_X <- new_data$Y
#True means
true_mu <- data$mu
new_mu <- new_data$mu
new_mu_sing <- single_data$mu
new_mu_neighb <- neighb_data$mu
# indices for different data
single_idx <- 1
new_idx <- 2:(n+1)
neighb_idx <- (n+2):(n+1 + p*10)
#derivative store
derivative.test <- NA
#sample theta
if(family != "binomial") {
X <- data$model_matrix(X,p_star)
X_sing <- data$model_matrix(X_sing,p_star)
X_new <- data$model_matrix(X_new, p_star)
X_neighborhood <- data$model_matrix(X_neighborhood, p_star)
hyperparameters$mu <- rep(0, p_star)
hyperparameters$Lambda <- matrix(1, p_star, p_star)
post_sample <- target$rpost(n.samps, X,
Y, hyperparameters,
method = posterior.method, stan_dir = stan_dir,
X.test = rbind(X_sing, X_new, X_neighborhood),
chains = 1, m0 = 20,
is.exponential = TRUE,
python.path = python.path)
post_interp <- post_sample
theta <- theta_new <- theta_sing <- post_interp$theta #regression coef
if(nrow(theta) != ncol(X)) theta <- t(theta)
if(!is.null(theta)) {
t_theta <- t(theta)
} else {
t_theta <- theta
}
sigma <- post_interp$sigma
derivative.test <- theta
pred.orig <- deriv.orig <- NULL
# X <- target$model_matrix(X)
# X_sing <- target$model_matrix(X_sing)
} else {
hyperparameters <- list(learning.rate = 1e-3,
lambda = 0.001,
batch.size = 128,
first.layer.width = as.integer(p*10),
hidden.layer.width = as.integer(2/3 * p + 1))
post_sample <- target$rpost(n.samps, X,
Y,
hyperparameters,
method = posterior.method,
stan_dir = stan_dir,
X.test = rbind(X_sing, X_new, X_neighborhood),
chains = 1, m0 = 20,
is.exponential = TRUE,
test.portion = 0,
learning.rate = 1e-3,
niter = 50,
python.path = python.path)
# post_interp <- target$rpost(n.samps, X, Y, NULL, method = "logistic", stan_dir = "exec/Stan/logistic_horseshoe_noQR.stan",
# X.test = rbind(X_sing, X_new, X_neighborhood),
# chains = 1, m0 = 20)
# add non-linearities if binomial
# if(family == "binomial") {
# cov_X <- cov(X[,-1,drop = FALSE])
# form <- formula("~.**2")
X <- data$model_matrix(X)
X_sing <- data$model_matrix(X_sing)
X_new <- data$model_matrix(X_new)
X_neighborhood <- data$model_matrix(X_neighborhood)
# }
theta <- lm.fit(X, post_sample$eta)$coefficients
theta_new <- lm.fit(X_new, post_sample$test$eta[new_idx,,drop=FALSE])$coefficients
theta_sing <- lm.fit(X_neighborhood, post_sample$test$eta[neighb_idx,,drop=FALSE])$coefficients
post_interp <- list(theta = theta,
eta = post_sample$eta, #X %*% theta,
mu = post_sample$mu, #data$invlink(X %*% theta),
test = list(eta = post_sample$test$eta,#rbind(X_sing %*% theta_sing, X_new %*% theta_new, X_neighborhood %*% theta_sing)
mu = post_sample$test$mu)
)
t_theta <- t(theta)
calc_w2_post <- FALSE
derivative.test <- sapply(post_sample$test$derivatives, function(d) d[1,])
pred.orig <- c(post_sample$yhat$test)[c(single_idx,neighb_idx)]
deriv.orig <- post_sample$yhat$derivatives[c(single_idx,neighb_idx),]
}
# if(family == "exponential" & posterior.method == "stan-cox") {
# log_dL0 <- rstan::extract(post_sample$model, pars= c("log_dL0"))$log_dL0
# intercept <- t(rowMeans(log_dL0))
# print(dim(post_sample$theta))
# post_sample$theta <- rbind(intercept, post_sample$theta)
# print(dim(post_sample$theta))
# post_sample$eta <- post_sample$eta + matrix(intercept, nrow = n, ncol=n.samps, byrow = TRUE)
# post_sample$test$eta <- post_sample$test$eta +
# matrix(intercept, nrow = n+1, ncol=n.samps, byrow = TRUE)
# }
#variance (if it exists for model)
#functions of theta
E_theta <- colMeans(theta)
# theta_norm <- rowSums(theta^2)
#conditional and marginal natural parameter means
cond_eta <- post_sample$eta
marg_eta <- rowMeans(cond_eta)
cond_eta_new <- post_sample$test$eta[new_idx,, drop=FALSE]
marg_eta_new <- rowMeans(cond_eta_new)
cond_eta_sing <- post_sample$test$eta[single_idx,,drop=FALSE]
marg_eta_sing <- rowMeans(cond_eta_sing)
cond_eta_neighb <- post_sample$test$eta[neighb_idx,,drop=FALSE]
marg_eta_neighb <- rowMeans(cond_eta_neighb)
#conditional and marginal means
# family != "exponential" &
if(!grepl("cox", posterior.method)) {
cond_mu <- post_sample$mu
marg_mu <- rowMeans(cond_mu)
cond_mu_new <- post_sample$test$mu[new_idx,, drop=FALSE]
marg_mu_new <- rowMeans(cond_mu_new)
cond_mu_sing <- post_sample$test$mu[single_idx,,drop=FALSE]
marg_mu_sing <- rowMeans(cond_mu_sing)
cond_mu_neighb <- post_sample$test$mu[neighb_idx,,drop=FALSE]
marg_mu_neighb <- rowMeans(cond_mu_neighb)
} else {
# cond_mu <- post_sample$mu$S$surv
# marg_mu <- apply(cond_mu, 2:3, mean)
#
# cond_mu_new <- post_sample$test$mu$S[,, -1,drop=FALSE]
# marg_mu_new <- apply(cond_mu_new, 2:3, mean)
#
# cond_mu_sing <- post_sample$test$mu$S[,,1,drop=FALSE]
# marg_mu_sing <- apply(cond_mu_sing, 2:3, mean)
# X <- X[,-1]
# X_new <- X_new[,-1]
# X_sing <- X_sing[,-1]
cond_mu <- data$invlink(post_sample$eta)
marg_mu <- rowMeans(cond_mu)
cond_mu_new <- data$invlink(post_sample$test$eta[new_idx,, drop=FALSE])
marg_mu_new <- rowMeans(cond_mu_new)
cond_mu_sing <- data$invlink(post_sample$test$eta[single_idx,,drop=FALSE])
marg_mu_sing <- rowMeans(cond_mu_sing)
cond_mu_neighb <- data$invlink(post_sample$test$eta[neighb_idx,,drop=FALSE])
marg_mu_neighb <- rowMeans(cond_mu_neighb)
}
#penalty terms
penalty_fact <- set_penalty_factor(theta = theta, method = penalty_method, intercept = TRUE,
x = X, y = cond_eta, transport.method = transport.method)
penalty_factN <- set_penalty_factor(theta = theta, method = penalty_method, intercept = TRUE,
x = X_new, y = cond_eta_new, transport.method = transport.method)
penalty_factO <- set_penalty_factor(theta = theta, method = penalty_method, intercept = TRUE,
x = X_sing, y = cond_eta_sing, transport.method = transport.method)
proj_penalty_fact <- set_penalty_factor(theta = theta, "distance", intercept = TRUE)
HC_penalty_fact <- set_penalty_factor(theta = theta, "expectation", intercept = TRUE)
#optional L0
if(L0){
cat(paste0("Running L0 methods only, same data: ", date(), "\n"))
L0list <- list(Selection = NULL,
Projection = NULL)
L0list$Selection <- WPL0(X = X, Y = cond_eta, theta = theta,
p = 2, ground_p = 2, method = "selection.variable",
transport.method = transport.method, epsilon = epsilon,
maxit = otmaxit)
L0list$Projection <- WPL0(X = X, Y = cond_eta, theta = theta,
p = 2, ground_p = 2, method = "projection",
transport.method = transport.method, epsilon = epsilon,
maxit = otmaxit)
cat("L0 Distance Calculations\n")
W2L0 <- distCompare(L0list,
target = list(posterior = NULL,
mean = cond_mu),
method = wp_alg,
quantity=c("mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
mseL0 <- distCompare(L0list,
target = list(posterior = NULL,
mean = true_mu),
method = "mse",
quantity="mean",
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
outList <- list (
W2_dist = W2L0,
mse = mseL0,
time = NULL,
order = list(selection = L0list$Selection$minCombPerActive,
projection = L0list$Projection$minCombPerActive)
)
return(outList)
}
time <- list(NULL)
PW2_insamp <- W2_insamp <-
PW2_newX <- W2_newX <-
PW2_single <- W2_single <-
mse_insamp <- mse_newX <- mse_single <-
Pmse_insamp <- Pmse_newX <- Pmse_single <- NULL
imp_insamp <- imp_newX <- imp_single <- NULL
w2_r2_single <- Pw2_r2_single <- NULL
if(not.only.timing) {
#### new method, single datapoint ####
# augDatO <- augPseudo(X_sing, cond_mu_sing, theta, theta_norm, pseudo.obs, n, same=TRUE)
# lambdas <- calc.lambdas(augDatO, lambda.min.ratio, penalty_fact, n.lambda)
cat(paste0("Running methods, single data point: ", date(),"\n"))
cat(" Selection: IP\n")
ipO <- W2IP(X = X_sing, Y = cond_eta_sing, theta = theta_sing,
display.progress=TRUE,
transport.method = transport.method,
model.size = ip_seq, maxit = 1e4,
infimum.maxit = 100, solution.method = solver,
parallel = NULL)
cat(" Lasso")
lassoSelO <- W2L1(X_sing, cond_eta_sing, theta_sing, family="gaussian", penalty=penalty,
penalty.factor=penalty_factO, nlambda = n.lambda,
lambda.min.ratio = lambda.min.ratio, infimum.maxit=100,
maxit=1e5, alpha = 0.99, gamma = 1.1,
transport.method = transport.method,
display.progress=TRUE, method = "selection.variable")
cat(" SW")
#stepwise
stepO <- WPSW(X_sing, cond_eta_sing, theta_sing, force=1, p=2,
direction = "backward",
method = "selection.variable",
transport.method = transport.method,
display.progress = TRUE)
cat(" SA")
#simulated annealing
annealO <- WPSA( X = X_sing, Y = cond_eta_sing, theta = theta_sing,
force = 1, p=2, model.size = sa_seq, iter = SAiter, temps = SAtemps,
options = list(method = "selection.variable",
energy.distribution = "boltzman",
transport.method = transport.method,
cooling.schedule="exponential",
proposal.method = sa_prop),
display.progress = TRUE , max.time = sa_max_time)
cat(paste0(annealO$message,"\n"))
cat("\n")
cat(" Projection: Lasso, ",date(),"\n")
#projection
lassoProjO <- W2L1(X_neighborhood, cond_eta_neighb, theta_sing, family="gaussian", penalty=penalty,
penalty.factor=proj_penalty_fact, nlambda = n.lambda,
lambda.min.ratio = lambda.min.ratio, infimum.maxit=1,
maxit=1e6, alpha = 0.99, gamma = 1.1,
transport.method = transport.method,
display.progress=TRUE, method = "projection")
cat(" SW, ",date(),"\n")
#stepwise
PstepO <- WPSW(X_neighborhood, cond_eta_neighb, theta_sing, force=1, p=2,
direction = "backward", method = "projection",
transport.method = transport.method,
display.progress = TRUE)
cat(" HC, ",date(),"\n")
#HC
PlassoHCO <- HC(X_neighborhood, cond_eta_neighb, theta = theta_sing, alpha = 0.99, gamma = 1.1,
family="gaussian", penalty=penalty, method = "projection",
penalty.factor=HC_penalty_fact, nlambda = n.lambda,
lambda.min.ratio = lambda.min.ratio, maxit = 1e5)
cat(" SA, ",date(),"\n")
# anneal
PannealO <- WPSA(X_neighborhood, cond_eta_neighb, theta=theta_sing,
force = 1, p=2, model.size = sa_seq, iter = SAiter,
temps = SAtemps,
options = list(method = "projection",
energy.distribution = "boltzman",
transport.method = transport.method,
cooling.schedule="exponential",
proposal.method = sa_prop),
display.progress = TRUE, max.time = sa_max_time)
# PL1O <- NULL
cat("\n L1, ",date(),"\n")
PL1O <- W1L1(X=X_neighborhood, Y=cond_eta_neighb,
solver = solver,
nlambda = n.lambda, penalty = penalty,
lambda.min.ratio = lambda.min.ratio, maxit = 1e5,
gamma = 1.1, display.progress = TRUE)
# cat("\n L3\n")
# PL3O <- WPL1(X=X_neighborhood, Y=cond_eta_neighb, p = 3,
# nlambda = n.lambda, penalty = penalty,
# lambda.min.ratio = lambda.min.ratio,
# gamma = 1.1,
# display.progress = TRUE)
# PLInfO <- NULL
cat("\n LInfinity, ",date(),"\n")
PLInfO <- WInfL1(X=X_neighborhood, Y=cond_eta_neighb,
nlambda = n.lambda, penalty = penalty,
lambda.min.ratio = lambda.min.ratio,
gamma = 1.1, solver = solver,
display.progress = TRUE)
cat("\n")
cat(paste0(PannealO$message))
cat("\n")
# }
# }
# trajAnnealN <- annealCoef(annealN, theta)
singleModels <- list("Binary Programming" = ipO,
"Lasso" = lassoSelO,
"Simulated Annealing" = annealO,
"Stepwise" = stepO#,
)
# rm("ipO", "lassoSelO", "annealO","stepO")
singleModelsP <- list("Lasso" = lassoProjO,
"Simulated Annealing" = PannealO,
"Stepwise" = PstepO,
"Hahn-Carvalho" = PlassoHCO
, "L1" = PL1O
# "L3" = PL3O,
, "LInf" = PLInfO
)
# rm("lassoProjO",
# "PannealO", "PstepO","PlassoHCO")
#recalculate values for single obs
if( recalc ) {
singleModelsP <- lapply(singleModelsP, function(x) {
x$eta <- lapply(x$theta, function(tt) X_sing %*% tt)
return(x)
})
cond_mu_calc <- cond_mu_sing
new_mu_calc <- new_mu_sing
} else {
cond_mu_calc <- cond_mu_neighb
new_mu_calc <- new_mu_neighb
}
cat("Calculating distances\n")
if( calc_w2_post){
W2_single <- distCompare(singleModels, target = list(posterior = theta_sing,
mean = cond_mu_sing),
method = wp_alg,
quantity=c("posterior","mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
W1_single <- distCompare(singleModels, target = list(posterior = theta_sing,
mean = cond_mu_sing),
method = wp_alg,
quantity=c("posterior","mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit,
ground_p = 1,
p = 1)
# cat("W2 selection\n")
w2_r2_single <- WPR2(Y = cond_mu_sing, nu = W2_single, p = 2, method = wp_alg)
w1_r2_single <- WPR2(Y = cond_mu_sing, nu = W1_single, p = 1, method = wp_alg)
w2_r2_single_null <- WPR2(Y = NULL, nu = W2_single, p = 2, method = wp_alg)
w1_r2_single_null <- WPR2(Y = NULL, nu = W1_single, p = 1, method = wp_alg)
mse_single <- distCompare(singleModels, target = list(posterior = full_param,
mean = new_mu_sing),
method = "mse",
quantity=c("posterior", "mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
mse_single$mean$dist <- mse_single$mean$dist/mean((c(cond_mu_sing) - c(new_mu_sing))^2)
mse_single$post$dist <- mse_single$post$dist/mean((as.matrix(full_param) - c(theta))^2)
# cat("W2 projection\n")
PW2_single <- distCompare(singleModelsP, target = list(posterior = theta_sing,
mean = cond_mu_calc),
method = wp_alg,
quantity=c("posterior", "mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
PW1_single <- distCompare(singleModelsP, target = list(posterior = theta_sing,
mean = cond_mu_calc),
method = wp_alg,
quantity=c("posterior","mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit,
p = 1,
ground_p = 1)
Pw2_r2_single <- WPR2(Y = cond_mu_calc, nu = PW2_single, p = 2, method = wp_alg)
Pw1_r2_single <- WPR2(Y = cond_mu_calc, nu = PW1_single, p = 1, method = wp_alg)
if(recalc) {
Pw2_r2_single_null <- WPR2(Y = NULL, nu = PW2_single, p = 2, method = wp_alg)
Pw1_r2_single_null <- WPR2(Y = NULL, nu = PW1_single, p = 1, method = wp_alg)
} else {
Pw2_r2_single_null <- WPR2(Y = cond_mu_calc, nu = singleModelsP, p = 2, method = wp_alg)
Pw1_r2_single_null <- WPR2(Y = cond_mu_calc, nu = singleModelsP, p = 1, method = wp_alg)
}
Pmse_single <- distCompare(singleModelsP, target = list(posterior = full_param,
mean = new_mu_calc),
method = "mse",
quantity=c("posterior","mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
Pmse_single$mean$dist <- Pmse_single$mean$dist/mean((cond_mu_calc - c(new_mu_calc))^2)
Pmse_single$post$dist <- Pmse_single$post$dist/mean((as.matrix(full_param) - c(theta))^2)
}
else {
W2_single <- distCompare(singleModels, target = list(posterior = NULL,
mean = cond_mu_sing),
method = wp_alg,
quantity=c("mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
W1_single <- distCompare(singleModels, target = list(posterior = NULL,
mean = cond_mu_sing),
method = wp_alg,
quantity=c("mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit,
ground_p = 1,
p = 1)
# cat("W2 selection\n")
w2_r2_single <- WPR2(Y = cond_mu_sing, nu = W2_single, p = 2, method = wp_alg)
w1_r2_single <- WPR2(Y = cond_mu_sing, nu = W1_single, p = 1, method = wp_alg)
w2_r2_single_null <- WPR2(Y = cond_mu_sing, nu = singleModels, p = 2, method = wp_alg, base = data$invlink(colMeans(cond_eta)))
w1_r2_single_null <- WPR2(Y = cond_mu_sing, nu = singleModels, p = 1, method = wp_alg, base = data$invlink(colMeans(cond_eta)))
mse_single <- distCompare(singleModels, target = list(posterior = NULL,
mean = new_mu_sing),
method = "mse",
quantity="mean",
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
mse_single$mean$dist <- mse_single$mean$dist/mean((c(cond_mu_sing) - c(new_mu_sing))^2)
# mse_single$post$dist <- mse_single$post$dist/mean((as.matrix(full_param) - c(theta))^2)
# cat("W2 projection\n")
PW2_single <- distCompare(singleModelsP, target = list(posterior = NULL,
mean = cond_mu_calc),
method = wp_alg,
quantity=c("mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
PW1_single <- distCompare(singleModelsP, target = list(posterior = NULL,
mean = cond_mu_calc),
method = wp_alg,
quantity=c("mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit,
p = 1,
ground_p = 1)
Pw2_r2_single <- WPR2(Y = cond_mu_calc, nu = PW2_single, p = 2, method = wp_alg)
Pw1_r2_single <- WPR2(Y = cond_mu_calc, nu = PW1_single, p = 1, method = wp_alg)
if(recalc) {
Pw2_r2_single_null <- WPR2(Y = cond_mu_sing, nu = PW2_single, p = 2, method = wp_alg)
Pw1_r2_single_null <- WPR2(Y = cond_mu_sing, nu = PW1_single, p = 1, method = wp_alg)
} else {
Pw2_r2_single_null <- WPR2(Y = cond_mu_calc, nu = singleModelsP, p = 2, method = wp_alg)
Pw1_r2_single_null <- WPR2(Y = cond_mu_calc, nu = singleModelsP, p = 1, method = wp_alg)
}
Pmse_single <- distCompare(singleModelsP, target = list(posterior = NULL,
mean = new_mu_calc),
method = "mse",
quantity="mean",
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
Pmse_single$mean$dist <- Pmse_single$mean$dist/mean((cond_mu_calc - c(new_mu_calc))^2)
# Pmse_single$post$dist <- Pmse_single$post$dist/mean((as.matrix(full_param) - c(theta))^2)
}
# rm(singleModels)
#### Variable importance ####
cat(paste0("Running variable importance: ", date(),"\n"))
# pred.fun.theta <- switch(family,
# "gaussian" = theta,
# "binomial" = theta,
# "exponential" = list(baseline = post_sample$mu$S$base,
# param = theta))
# imp_newX <- WPVI(X = X_new, Y = NULL, theta = theta_new, pred.fun = pred.fun,
# p = 2, ground_p = 2, transport.method = "exact")
imp_single <- WPVI(X = X_sing, Y = NULL, theta = theta_sing, pred.fun = pred.fun,
p = 2, ground_p = 2, transport.method = "exact")
} else {
cat(paste0("Running methods, same data: ", date(),"\n"))
#### In sample ####
#IP
cat(" Selection: IP,\n")
time <- proc.time()
ip <- W2IP(X = X, Y = cond_eta, theta = theta,
display.progress=FALSE,
transport.method = transport.method,
model.size = ip_seq,
infimum.maxit = 100, solution.method = solver,
parallel = NULL)
ipTime <- proc.time() - time
# trajSel <- selDist$theta
cat(" Selection: IP, Lasso, ")
#selection variable
time <- proc.time()
lassoSel <- W2L1(X, cond_eta, theta, family="gaussian", penalty=penalty,
penalty.factor = penalty_fact, nlambda = n.lambda, alpha = 0.99,
gamma = 1.1,
lambda.min.ratio = lambda.min.ratio, infimum.maxit=1e2,
maxit = 1e6,
display.progress=FALSE,
transport.method = transport.method,
method = "selection.variable")
selTime <- proc.time() - time
# trajSel <- selDist$theta
cat(" HC, ")
#carvalho method
time <- proc.time()
lassoHC <- HC(X, cond_eta, theta = theta,
family="gaussian", penalty=penalty, method = "selection.variable",
penalty.factor=HC_penalty_fact, nlambda = n.lambda, alpha = 0.99, gamma = 1.1,
lambda.min.ratio = lambda.min.ratio, maxit = 1e5)
hcTime <- proc.time() - time
cat(" SW, ")
#stepwise
time <- proc.time()
step <- WPSW(X, Y = cond_eta, theta, force=1, p=2,
direction = "backward", method = "selection.variable",
transport.method = transport.method,
display.progress = FALSE)
stepTime <- proc.time() - time
# trajStep <- step$theta
cat(" SA\n")
#simulated annealing
annealTime <- NULL
# if(n > 512 | p > 11){
# anneal <- WPSA(X=X, Y=cond_eta, theta=theta,
# force = 1, p=2, model.size = 5, iter = SAiter, temps = SAtemps,
# options = list(method = "selection.variable",
# energy.distribution = "boltzman",
# transport.method = transport.method,
# cooling.schedule="exponential"),
# display.progress=TRUE)
# annealTime <- NULL
# }
# else {
time <- proc.time()
anneal <- WPSA(X=X, Y=cond_eta, theta=theta,
force = 1, p=2, model.size = sa_seq, iter = SAiter, temps = SAtemps,
options = list(method = "selection.variable",
energy.distribution = "boltzman",
transport.method = transport.method,
cooling.schedule="exponential",
proposal.method = sa_prop),
display.progress=FALSE, max.time = sa_max_time)
annealTime <- proc.time() - time
cat(paste0(anneal$message,"\n"))
if(anneal$message != "completed") {
annealTime <- paste0(">", annealTime)
}
cat(" Projection: Lasso, ")
#projection
time <- proc.time()
lassoProj <- W2L1(X, cond_eta, theta, family="gaussian", penalty=penalty,
penalty.factor=proj_penalty_fact, nlambda = n.lambda,
lambda.min.ratio = lambda.min.ratio, infimum.maxit=1,
maxit = 1e6, alpha = 0.99, gamma = 1.1,
display.progress=FALSE,
transport.method = transport.method,
method = "projection")
projTime <- proc.time() - time
# trajProj <- projDist$theta
cat(" HC, ")
time <- proc.time()
PlassoHC <- HC(X, cond_eta, theta = theta,
family="gaussian", penalty=penalty, method = "projection",
alpha = 0.99, gamma = 1.1,
penalty.factor=HC_penalty_fact, nlambda = n.lambda,
lambda.min.ratio = lambda.min.ratio, maxit = 1e5)
PhcTime <- proc.time() - time
cat(" SW, ")
#stepwise
time <- proc.time()
Pstep <- WPSW(X, Y = cond_eta, theta, force=1, p=2,
direction = "backward", method = "projection",
transport.method = transport.method,
display.progress = FALSE)
PstepTime <- proc.time() - time
# trajStep <- step$theta
cat(" SA\n")
#simulated annealing
annealTime <- NULL
time <- proc.time()
Panneal <- WPSA(X=X, Y=cond_eta, theta=theta,
force = 1, p=2, model.size = sa_seq, iter = SAiter, temps = SAtemps,
options = list(method = "projection",
energy.distribution = "boltzman",
transport.method = transport.method,
cooling.schedule="exponential",
proposal.method = sa_prop),
display.progress=FALSE, max.time = sa_max_time)
PannealTime <- proc.time() - time
cat(paste0(Panneal$message,"\n"))
if(Panneal$message != "completed") {
PannealTime <- paste0(">", PannealTime)
}
time <- proc.time()
PL1 <- W1L1(X=X, Y=cond_eta, solver = solver,
nlambda = n.lambda, penalty = penalty,
lambda.min.ratio = lambda.min.ratio, maxit = 1e5,
gamma = 1.1)
PL1Time <- proc.time() - time
# time <- proc.time()
# PL3 <- WPL1(X=X, Y=cond_eta, p = 3,
# nlambda = n.lambda, penalty = penalty,
# lambda.min.ratio = lambda.min.ratio, maxit = 1e5,
# gamma = 1.1)
# PL3Time <- proc.time() - time
time <- proc.time()
PLInf <- WInfL1(X=X, Y=cond_eta,
nlambda = n.lambda, penalty = penalty,
lambda.min.ratio = lambda.min.ratio,
gamma = 1.1, solver = solver)
PLInfTime <- proc.time() - time
time <- list(selection = list(ip = ipTime[3], lasso = selTime[3],
HC = hcTime[3],
step = stepTime[3],
anneal = annealTime[3]),
projection = list(lasso = projTime[3],
L1 = PL1Time[3],
# L3 = PL3Time[3],
LInf = PLInfTime[3],
HC = PhcTime[3], step = PstepTime[3],
anneal = PannealTime[3]))
imp_insamp <- WPVI(X = X, Y = NULL, theta = theta, pred.fun = pred.fun,
p = 2, ground_p = 2, transport.method = "exact")
}
# augDat <- augPseudo(X, cond_eta, theta, theta_norm, pseudo.obs, n, same=TRUE)
# lambdas <- calc.lambdas(augDat, lambda.min.ratio, penalty_fact, n.lambda)
# }
# trajAnneal <- anneal$theta
# if (not.only.timing) {
# inSampModels <- list("Binary Programming" = ip,
# "L2" = lassoSel,
# "Simulated Annealing" = anneal,
# "Stepwise" = step,
# "Hahn-Carvalho" = lassoHC)
# inSampModelsProj <- list("L2" = lassoProj,
# "L1" = PL1,
# "LInf" = PLInf,
# "Simulated Annealing" = Panneal,
# "Stepwise" = Pstep,
# "Hahn-Carvalho" = PlassoHC)
# rm("ip","lassoSel", "anneal","step","lassoHC")
# rm("lassoProj","PL1", "PLInf", "Panneal","Pstep","PlassoHC")
#
# cat("Calculating distances\n")
# if( calc_w2_post){
# W2_insamp <- distCompare(inSampModels, target = list(posterior = theta,
# mean = cond_mu),
# method = wp_alg,
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# mse_insamp <- distCompare(inSampModels, target = list(posterior = full_param,
# mean = true_mu),
# method = "mse",
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# PW2_insamp <- distCompare(inSampModelsProj, target = list(posterior = theta,
# mean = cond_mu),
# method = wp_alg,
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# Pmse_insamp <- distCompare(inSampModelsProj, target = list(posterior = full_param,
# mean = true_mu),
# method = "mse",
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# }
# else {
# W2_insamp <- distCompare(inSampModels, target = list(posterior = NULL,
# mean = cond_mu),
# method = wp_alg,
# quantity=c("mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# mse_insamp <- distCompare(inSampModels, target = list(posterior = NULL,
# mean = true_mu),
# method = "mse",
# quantity="mean",
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# PW2_insamp <- distCompare(inSampModelsProj, target = list(posterior = NULL,
# mean = cond_mu),
# method = wp_alg,
# quantity=c("mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# Pmse_insamp <- distCompare(inSampModelsProj, target = list(posterior = NULL,
# mean = true_mu),
# method = "mse",
# quantity="mean",
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# }
#
# rm(inSampModels)
# rm(inSampModelsProj)
#
# #### new X variable ####
# #mse on new outcome data from same paramters and different X
# #new method
# # augDatN <- augPseudo(X_new, cond_mu_new, theta, theta_norm, pseudo.obs, n, same=TRUE)
# # lambdas <- calc.lambdas(augDatN, lambda.min.ratio, penalty_fact, n.lambda)
# cat(paste0("Running methods, new X variable: ", date(),"\n"))
# cat(" Selection: IP")
# ipN <- W2IP(X = X_new, Y = cond_eta_new, theta = theta_new,
# display.progress=TRUE,
# transport.method = transport.method,
# model.size = ip_seq,
# infimum.maxit = 100, solution.method = "cone",
# parallel = NULL)
#
# cat(" Lasso")
# lassoSelN <- W2L1(X_new, cond_eta_new, theta_new, family="gaussian",
# penalty=penalty, alpha = 0.99, gamma = 1.1,
# penalty.factor=penalty_factN, nlambda = n.lambda,
# lambda.min.ratio = lambda.min.ratio, infimum.maxit=100,
# maxit = 1e5,
# transport.method = transport.method,
# display.progress=TRUE, method = "selection.variable")
# # trajSelN <- extractCoef(lassoSelN)
#
# cat(" HC, ")
# #carvalho method
# lassoHCN <- HC(X_new, cond_eta_new, theta = theta_new,
# family="gaussian", penalty=penalty, alpha = 0.99, gamma = 1.1,
# penalty.factor=HC_penalty_fact, nlambda = n.lambda,
# lambda.min.ratio = lambda.min.ratio, maxit = 1e5)
#
# cat(" SW")
# #stepwise
# stepN <- WPSW(X_new, cond_eta_new, theta_new, force=1, p=2,
# direction = "backward", method = "selection.variable",
# transport.method = transport.method,
# display.progress = TRUE)
#
# cat(" SA")
# annealN <- WPSA(X=X_new, Y=cond_eta_new, theta=theta_new,
# force = 1, p=2, model.size = sa_seq, iter = SAiter,
# temps = SAtemps,
# options = list(method = "selection.variable",
# energy.distribution = "boltzman",
# transport.method = transport.method,
# cooling.schedule="exponential",
# proposal.method = sa_prop),
# display.progress = TRUE, max.time = sa_max_time)
# cat(paste0(annealN$message,"\n"))
# cat("\n")
#
# cat(" Projection: Lasso")
# #projection
# lassoProjN <- W2L1(X_new, cond_eta_new, theta_new, family="gaussian", penalty=penalty,
# penalty.factor=proj_penalty_fact, nlambda = n.lambda,
# lambda.min.ratio = lambda.min.ratio, infimum.maxit=1,
# maxit=1e5, alpha = 0.99, gamma = 1.1,
# transport.method = transport.method,
# display.progress=TRUE, method = "projection")
#
# cat(" SW")
# #stepwise
# PstepN <- WPSW(X_new, cond_eta_new, theta_new, force=1, p=2,
# direction = "backward", method = "projection",
# transport.method = transport.method,
# display.progress = TRUE)
# cat(" HC, ")
# #HC
# PlassoHCN <- HC(X_new, cond_eta_new, theta = theta_new, alpha = 0.99, gamma = 1.1,
# family="gaussian", penalty=penalty, method = "projection",
# penalty.factor=HC_penalty_fact, nlambda = n.lambda,
# lambda.min.ratio = lambda.min.ratio, maxit = 1e5)
# cat(" SA")
# # anneal
# PannealN <- WPSA(X=X_new, Y=cond_eta_new, theta=theta_new,
# force = 1, p=2, model.size = sa_seq, iter = SAiter,
# temps = SAtemps,
# options = list(method = "projection",
# energy.distribution = "boltzman",
# transport.method = transport.method,
# cooling.schedule="exponential",
# proposal.method = sa_prop),
# display.progress = TRUE, max.time = sa_max_time)
# cat(paste0(PannealN$message,"\n"))
# cat("\n")
# # }
# # trajAnnealN <- annealCoef(annealN, theta)
# newXModels <- list("Binary Programming" = ipN,
# "Lasso" = lassoSelN,
# "Simulated Annealing" = annealN,
# "Stepwise" = stepN,
# "Hahn-Carvalho" = lassoHCN)
# rm("ipN","lassoSelN", "annealN","stepN","lassoHCN")
# newXModelsP <- list("Lasso" = lassoProjN,
# "Simulated Annealing" = PannealN,
# "Stepwise" = PstepN,
# "Hahn-Carvalho" = PlassoHCN)
# rm("lassoProjN",
# "PannealN", "PstepN","PlassoHCN")
#
# cat("Calculating distances\n")
# if( calc_w2_post){
# W2_newX <- distCompare(newXModels, target = list(posterior = theta_new,
# mean = cond_mu_new),
# method = wp_alg,
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# mse_newX <- distCompare(newXModels, target = list(posterior = full_param,
# mean = new_mu),
# method = "mse",
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# PW2_newX <- distCompare(newXModelsP, target = list(posterior = theta_new,
# mean = cond_mu_new),
# method = wp_alg,
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# Pmse_newX <- distCompare(newXModelsP, target = list(posterior = full_param,
# mean = new_mu),
# method = "mse",
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# }
# else {
# W2_newX <- distCompare(newXModels, target = list(posterior = NULL,
# mean = cond_mu_new),
# method = wp_alg,
# quantity=c("mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# mse_newX <- distCompare(newXModels, target = list(posterior = NULL,
# mean = new_mu),
# method = "mse",
# quantity="mean",
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# PW2_newX <- distCompare(newXModelsP, target = list(posterior = NULL,
# mean = cond_mu_new),
# method = wp_alg,
# quantity=c("mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# Pmse_newX <- distCompare(newXModelsP, target = list(posterior = NULL,
# mean = new_mu),
# method = "mse",
# quantity="mean",
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# }
#
#
# rm(newXModels, newXModelsP)
#### generate output list ####
outList <- list (
W2_dist = list(inSamp = list(selection = W2_insamp,
projection = PW2_insamp),
# newX = list(selection = W2_newX,
# projection = PW2_newX),
single = list(selection = W2_single,
projection = PW2_single) ),
mse = list(inSamp = list(selection = mse_insamp,
projection = Pmse_insamp),
# newX = list(selection = mse_newX,
# projection = Pmse_newX),
single = list(selection = mse_single,
projection = Pmse_single) ),
importance = list(inSamp = imp_insamp,
# newX = imp_newX,
single = imp_single),
W2_r2 = list(expectation = list(
inSamp = list(selection = NULL,
projection = NULL),
single = list(selection = w2_r2_single,
projection = Pw2_r2_single) ),
null = list(
inSamp = list(selection = NULL,
projection = NULL),
single = list(selection = w2_r2_single_null,
projection = Pw2_r2_single_null) )
),
W1_r2 = list(expectation = list(
inSamp = list(selection = NULL,
projection = NULL),
single = list(selection = w1_r2_single,
projection = Pw1_r2_single) ),
null = list(
inSamp = list(selection = NULL,
projection = NULL),
single = list(selection = w1_r2_single_null,
projection = Pw1_r2_single_null) )
),
time = time, #,
data = list(test = list(
X = X_sing,
mean = new_mu_sing),
neighborhood = list(X = X_neighborhood,
mean = new_mu_neighb)
),
models = list(
selection = lapply(singleModels, function(s) s$theta),
projection = lapply(singleModelsP, function(s) s$theta),
estimation = list(boot = post_sample$test$eta[c(single_idx,neighb_idx),],
original = list(prediction = pred.orig,
derivatives = deriv.orig)
),
derivatives = derivative.test
))
return(outList)
}
ericdunipace/SLIMpaper documentation built on May 5, 2024, 3:43 p.m.
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Defines functions experimentWPMethod
Documented in experimentWPMethod
#' Simulation study function
#'
#' @param target function that is the output of the get_binary_nonlinear, get_normal_linear, etc
#' @param hyperparameters hyperparameters for the Bayesian methodology
#' @param conditions conditions for the simulation
#'
#' @return
#' @export
experimentWPMethod <- function(target, hyperparameters, conditions) {
n <- conditions$n
p <- conditions$p
n.samps <- conditions$n.samps
penalty <- conditions$penalty
lambda.min.ratio <- conditions$lambda.min.ratio
n.lambda <- conditions$n.lambda
penalty_method <- conditions$penalty.factor
family <- conditions$family
solver <- conditions$solver
python.path <- conditions$python.path
recalc <- conditions$recalculate
if (is.null(solver) ) {
solver <- "mosek"
}
if (solver == "") {
solver <- "mosek"
}
solver <- match.arg(solver, choices = c("mosek", "gurobi",
"cplex", "cone", "lp"))
if(is.null(recalc)) recalc <- FALSE
if(recalc == "") recalc <- FALSE
epsilon <- 0.05
otmaxit <- 100
# pseudo.obs <- conditions$pseudo.obs
stan_dir <- conditions$stan_dir
calc_w2_post <- conditions$calc_w2_post
if(is.null(calc_w2_post)) calc_w2_post <- FALSE
# if(is.null(pseudo.obs)) pseudo.obs <- 0
pseudo.obs <- 0
posterior.method <- conditions$posterior.method
transport.method <- conditions$transport.method
if(is.null(transport.method)) transport.method <- "hilbert" #"univariate.approximation.pwr"
not.only.timing <- conditions$not.only.timing
if(is.null(not.only.timing)) not.only.timing <- FALSE
L0 <- conditions$L0
if(is.null(L0)) L0 <- FALSE
sa_seq <- sort(unique(c(2,5,floor(seq(ceiling(p/5),p,floor(p/5))))))
sa_max_time <- 64800
sa_prop <- "random"
# FSAiter <- 10*1:ceiling(p/2)
# RSAiter <- if( p %% 2) { rev(FSAiter)[-1] } else { rev(FSAiter) }
# SAiter <- c(FSAiter, RSAiter)
SAiter <- 10 * ceiling(p/2)
SAtemps <- 50
# SAiter <- 1
# SAtemps <- 1
#IP sequence
if( p < 200 ) {
ip_seq <- 1:p
} else {
ip_seq <- sa_seq
}
#w2 dist param
wp_alg <- conditions$wp_alg
if(is.null(wp_alg)) wp_alg <- "greenkhorn"
# MEAN FUNCTION FOR IMPORTANCE
pred.fun <- switch(family,
"gaussian" = target$sel.pred.fun("linpred"),
"binomial" = target$sel.pred.fun("linpred"),
"exponential" = function(x,theta) {
return(x[,-1,drop=FALSE] %*% theta[-1,,drop=FALSE])
})
# SETUP PARAMETERS
param <- target$rparam()
p_star <- if(family != "gaussian") {
min(length(param$theta),p)
} else {
min(length(param$theta),p + 4)
}
param$theta <- param$theta[1:p_star]
full_param <- c(param$theta, rep(0, max(p-p_star,0)))
#set up data
X <- target$X$rX(n, target$X$corr, p)
X_sing <- matrix(c(target$X$rX(1, target$X$corr, p)), nrow=1, ncol=p)
X_new <- target$X$rX(n, target$X$corr, p)
X_neighborhood <- cbind(1, SLIMpaper::rmvnorm(nsamples = p*10,
mean = X_sing[,-1,drop=FALSE],
covariance = cov(X[,-1,drop=FALSE])/n))
data <- target$rdata(n, X, c(param$theta),
param$sigma2, method = "modified.friedman", corr = target$X$corr)
single_data <- target$rdata(1, X_sing, c(param$theta),
param$sigma2, method = "modified.friedman", corr = target$X$corr)
new_data <- target$rdata(n, X_new, c(param$theta), param$sigma2, method = "modified.friedman", corr = target$X$corr)
neighb_data <- target$rdata(n, X_neighborhood, c(param$theta), param$sigma2, method = "modified.friedman", corr = target$X$corr)
Y <- data$Y
single_Y <- single_data$Y
new_Y_new_X <- new_data$Y
#True means
true_mu <- data$mu
new_mu <- new_data$mu
new_mu_sing <- single_data$mu
new_mu_neighb <- neighb_data$mu
# indices for different data
single_idx <- 1
new_idx <- 2:(n+1)
neighb_idx <- (n+2):(n+1 + p*10)
#derivative store
derivative.test <- NA
#sample theta
if(family != "binomial") {
X <- data$model_matrix(X,p_star)
X_sing <- data$model_matrix(X_sing,p_star)
X_new <- data$model_matrix(X_new, p_star)
X_neighborhood <- data$model_matrix(X_neighborhood, p_star)
hyperparameters$mu <- rep(0, p_star)
hyperparameters$Lambda <- matrix(1, p_star, p_star)
post_sample <- target$rpost(n.samps, X,
Y, hyperparameters,
method = posterior.method, stan_dir = stan_dir,
X.test = rbind(X_sing, X_new, X_neighborhood),
chains = 1, m0 = 20,
is.exponential = TRUE,
python.path = python.path)
post_interp <- post_sample
theta <- theta_new <- theta_sing <- post_interp$theta #regression coef
if(nrow(theta) != ncol(X)) theta <- t(theta)
if(!is.null(theta)) {
t_theta <- t(theta)
} else {
t_theta <- theta
}
sigma <- post_interp$sigma
derivative.test <- theta
pred.orig <- deriv.orig <- NULL
# X <- target$model_matrix(X)
# X_sing <- target$model_matrix(X_sing)
} else {
hyperparameters <- list(learning.rate = 1e-3,
lambda = 0.001,
batch.size = 128,
first.layer.width = as.integer(p*10),
hidden.layer.width = as.integer(2/3 * p + 1))
post_sample <- target$rpost(n.samps, X,
Y,
hyperparameters,
method = posterior.method,
stan_dir = stan_dir,
X.test = rbind(X_sing, X_new, X_neighborhood),
chains = 1, m0 = 20,
is.exponential = TRUE,
test.portion = 0,
learning.rate = 1e-3,
niter = 50,
python.path = python.path)
# post_interp <- target$rpost(n.samps, X, Y, NULL, method = "logistic", stan_dir = "exec/Stan/logistic_horseshoe_noQR.stan",
# X.test = rbind(X_sing, X_new, X_neighborhood),
# chains = 1, m0 = 20)
# add non-linearities if binomial
# if(family == "binomial") {
# cov_X <- cov(X[,-1,drop = FALSE])
# form <- formula("~.**2")
X <- data$model_matrix(X)
X_sing <- data$model_matrix(X_sing)
X_new <- data$model_matrix(X_new)
X_neighborhood <- data$model_matrix(X_neighborhood)
# }
theta <- lm.fit(X, post_sample$eta)$coefficients
theta_new <- lm.fit(X_new, post_sample$test$eta[new_idx,,drop=FALSE])$coefficients
theta_sing <- lm.fit(X_neighborhood, post_sample$test$eta[neighb_idx,,drop=FALSE])$coefficients
post_interp <- list(theta = theta,
eta = post_sample$eta, #X %*% theta,
mu = post_sample$mu, #data$invlink(X %*% theta),
test = list(eta = post_sample$test$eta,#rbind(X_sing %*% theta_sing, X_new %*% theta_new, X_neighborhood %*% theta_sing)
mu = post_sample$test$mu)
)
t_theta <- t(theta)
calc_w2_post <- FALSE
derivative.test <- sapply(post_sample$test$derivatives, function(d) d[1,])
pred.orig <- c(post_sample$yhat$test)[c(single_idx,neighb_idx)]
deriv.orig <- post_sample$yhat$derivatives[c(single_idx,neighb_idx),]
}
# if(family == "exponential" & posterior.method == "stan-cox") {
# log_dL0 <- rstan::extract(post_sample$model, pars= c("log_dL0"))$log_dL0
# intercept <- t(rowMeans(log_dL0))
# print(dim(post_sample$theta))
# post_sample$theta <- rbind(intercept, post_sample$theta)
# print(dim(post_sample$theta))
# post_sample$eta <- post_sample$eta + matrix(intercept, nrow = n, ncol=n.samps, byrow = TRUE)
# post_sample$test$eta <- post_sample$test$eta +
# matrix(intercept, nrow = n+1, ncol=n.samps, byrow = TRUE)
# }
#variance (if it exists for model)
#functions of theta
E_theta <- colMeans(theta)
# theta_norm <- rowSums(theta^2)
#conditional and marginal natural parameter means
cond_eta <- post_sample$eta
marg_eta <- rowMeans(cond_eta)
cond_eta_new <- post_sample$test$eta[new_idx,, drop=FALSE]
marg_eta_new <- rowMeans(cond_eta_new)
cond_eta_sing <- post_sample$test$eta[single_idx,,drop=FALSE]
marg_eta_sing <- rowMeans(cond_eta_sing)
cond_eta_neighb <- post_sample$test$eta[neighb_idx,,drop=FALSE]
marg_eta_neighb <- rowMeans(cond_eta_neighb)
#conditional and marginal means
# family != "exponential" &
if(!grepl("cox", posterior.method)) {
cond_mu <- post_sample$mu
marg_mu <- rowMeans(cond_mu)
cond_mu_new <- post_sample$test$mu[new_idx,, drop=FALSE]
marg_mu_new <- rowMeans(cond_mu_new)
cond_mu_sing <- post_sample$test$mu[single_idx,,drop=FALSE]
marg_mu_sing <- rowMeans(cond_mu_sing)
cond_mu_neighb <- post_sample$test$mu[neighb_idx,,drop=FALSE]
marg_mu_neighb <- rowMeans(cond_mu_neighb)
} else {
# cond_mu <- post_sample$mu$S$surv
# marg_mu <- apply(cond_mu, 2:3, mean)
#
# cond_mu_new <- post_sample$test$mu$S[,, -1,drop=FALSE]
# marg_mu_new <- apply(cond_mu_new, 2:3, mean)
#
# cond_mu_sing <- post_sample$test$mu$S[,,1,drop=FALSE]
# marg_mu_sing <- apply(cond_mu_sing, 2:3, mean)
# X <- X[,-1]
# X_new <- X_new[,-1]
# X_sing <- X_sing[,-1]
cond_mu <- data$invlink(post_sample$eta)
marg_mu <- rowMeans(cond_mu)
cond_mu_new <- data$invlink(post_sample$test$eta[new_idx,, drop=FALSE])
marg_mu_new <- rowMeans(cond_mu_new)
cond_mu_sing <- data$invlink(post_sample$test$eta[single_idx,,drop=FALSE])
marg_mu_sing <- rowMeans(cond_mu_sing)
cond_mu_neighb <- data$invlink(post_sample$test$eta[neighb_idx,,drop=FALSE])
marg_mu_neighb <- rowMeans(cond_mu_neighb)
}
#penalty terms
penalty_fact <- set_penalty_factor(theta = theta, method = penalty_method, intercept = TRUE,
x = X, y = cond_eta, transport.method = transport.method)
penalty_factN <- set_penalty_factor(theta = theta, method = penalty_method, intercept = TRUE,
x = X_new, y = cond_eta_new, transport.method = transport.method)
penalty_factO <- set_penalty_factor(theta = theta, method = penalty_method, intercept = TRUE,
x = X_sing, y = cond_eta_sing, transport.method = transport.method)
proj_penalty_fact <- set_penalty_factor(theta = theta, "distance", intercept = TRUE)
HC_penalty_fact <- set_penalty_factor(theta = theta, "expectation", intercept = TRUE)
#optional L0
if(L0){
cat(paste0("Running L0 methods only, same data: ", date(), "\n"))
L0list <- list(Selection = NULL,
Projection = NULL)
L0list$Selection <- WPL0(X = X, Y = cond_eta, theta = theta,
p = 2, ground_p = 2, method = "selection.variable",
transport.method = transport.method, epsilon = epsilon,
maxit = otmaxit)
L0list$Projection <- WPL0(X = X, Y = cond_eta, theta = theta,
p = 2, ground_p = 2, method = "projection",
transport.method = transport.method, epsilon = epsilon,
maxit = otmaxit)
cat("L0 Distance Calculations\n")
W2L0 <- distCompare(L0list,
target = list(posterior = NULL,
mean = cond_mu),
method = wp_alg,
quantity=c("mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
mseL0 <- distCompare(L0list,
target = list(posterior = NULL,
mean = true_mu),
method = "mse",
quantity="mean",
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
outList <- list (
W2_dist = W2L0,
mse = mseL0,
time = NULL,
order = list(selection = L0list$Selection$minCombPerActive,
projection = L0list$Projection$minCombPerActive)
)
return(outList)
}
time <- list(NULL)
PW2_insamp <- W2_insamp <-
PW2_newX <- W2_newX <-
PW2_single <- W2_single <-
mse_insamp <- mse_newX <- mse_single <-
Pmse_insamp <- Pmse_newX <- Pmse_single <- NULL
imp_insamp <- imp_newX <- imp_single <- NULL
w2_r2_single <- Pw2_r2_single <- NULL
if(not.only.timing) {
#### new method, single datapoint ####
# augDatO <- augPseudo(X_sing, cond_mu_sing, theta, theta_norm, pseudo.obs, n, same=TRUE)
# lambdas <- calc.lambdas(augDatO, lambda.min.ratio, penalty_fact, n.lambda)
cat(paste0("Running methods, single data point: ", date(),"\n"))
cat(" Selection: IP\n")
ipO <- W2IP(X = X_sing, Y = cond_eta_sing, theta = theta_sing,
display.progress=TRUE,
transport.method = transport.method,
model.size = ip_seq, maxit = 1e4,
infimum.maxit = 100, solution.method = solver,
parallel = NULL)
cat(" Lasso")
lassoSelO <- W2L1(X_sing, cond_eta_sing, theta_sing, family="gaussian", penalty=penalty,
penalty.factor=penalty_factO, nlambda = n.lambda,
lambda.min.ratio = lambda.min.ratio, infimum.maxit=100,
maxit=1e5, alpha = 0.99, gamma = 1.1,
transport.method = transport.method,
display.progress=TRUE, method = "selection.variable")
cat(" SW")
#stepwise
stepO <- WPSW(X_sing, cond_eta_sing, theta_sing, force=1, p=2,
direction = "backward",
method = "selection.variable",
transport.method = transport.method,
display.progress = TRUE)
cat(" SA")
#simulated annealing
annealO <- WPSA( X = X_sing, Y = cond_eta_sing, theta = theta_sing,
force = 1, p=2, model.size = sa_seq, iter = SAiter, temps = SAtemps,
options = list(method = "selection.variable",
energy.distribution = "boltzman",
transport.method = transport.method,
cooling.schedule="exponential",
proposal.method = sa_prop),
display.progress = TRUE , max.time = sa_max_time)
cat(paste0(annealO$message,"\n"))
cat("\n")
cat(" Projection: Lasso, ",date(),"\n")
#projection
lassoProjO <- W2L1(X_neighborhood, cond_eta_neighb, theta_sing, family="gaussian", penalty=penalty,
penalty.factor=proj_penalty_fact, nlambda = n.lambda,
lambda.min.ratio = lambda.min.ratio, infimum.maxit=1,
maxit=1e6, alpha = 0.99, gamma = 1.1,
transport.method = transport.method,
display.progress=TRUE, method = "projection")
cat(" SW, ",date(),"\n")
#stepwise
PstepO <- WPSW(X_neighborhood, cond_eta_neighb, theta_sing, force=1, p=2,
direction = "backward", method = "projection",
transport.method = transport.method,
display.progress = TRUE)
cat(" HC, ",date(),"\n")
#HC
PlassoHCO <- HC(X_neighborhood, cond_eta_neighb, theta = theta_sing, alpha = 0.99, gamma = 1.1,
family="gaussian", penalty=penalty, method = "projection",
penalty.factor=HC_penalty_fact, nlambda = n.lambda,
lambda.min.ratio = lambda.min.ratio, maxit = 1e5)
cat(" SA, ",date(),"\n")
# anneal
PannealO <- WPSA(X_neighborhood, cond_eta_neighb, theta=theta_sing,
force = 1, p=2, model.size = sa_seq, iter = SAiter,
temps = SAtemps,
options = list(method = "projection",
energy.distribution = "boltzman",
transport.method = transport.method,
cooling.schedule="exponential",
proposal.method = sa_prop),
display.progress = TRUE, max.time = sa_max_time)
# PL1O <- NULL
cat("\n L1, ",date(),"\n")
PL1O <- W1L1(X=X_neighborhood, Y=cond_eta_neighb,
solver = solver,
nlambda = n.lambda, penalty = penalty,
lambda.min.ratio = lambda.min.ratio, maxit = 1e5,
gamma = 1.1, display.progress = TRUE)
# cat("\n L3\n")
# PL3O <- WPL1(X=X_neighborhood, Y=cond_eta_neighb, p = 3,
# nlambda = n.lambda, penalty = penalty,
# lambda.min.ratio = lambda.min.ratio,
# gamma = 1.1,
# display.progress = TRUE)
# PLInfO <- NULL
cat("\n LInfinity, ",date(),"\n")
PLInfO <- WInfL1(X=X_neighborhood, Y=cond_eta_neighb,
nlambda = n.lambda, penalty = penalty,
lambda.min.ratio = lambda.min.ratio,
gamma = 1.1, solver = solver,
display.progress = TRUE)
cat("\n")
cat(paste0(PannealO$message))
cat("\n")
# }
# }
# trajAnnealN <- annealCoef(annealN, theta)
singleModels <- list("Binary Programming" = ipO,
"Lasso" = lassoSelO,
"Simulated Annealing" = annealO,
"Stepwise" = stepO#,
)
# rm("ipO", "lassoSelO", "annealO","stepO")
singleModelsP <- list("Lasso" = lassoProjO,
"Simulated Annealing" = PannealO,
"Stepwise" = PstepO,
"Hahn-Carvalho" = PlassoHCO
, "L1" = PL1O
# "L3" = PL3O,
, "LInf" = PLInfO
)
# rm("lassoProjO",
# "PannealO", "PstepO","PlassoHCO")
#recalculate values for single obs
if( recalc ) {
singleModelsP <- lapply(singleModelsP, function(x) {
x$eta <- lapply(x$theta, function(tt) X_sing %*% tt)
return(x)
})
cond_mu_calc <- cond_mu_sing
new_mu_calc <- new_mu_sing
} else {
cond_mu_calc <- cond_mu_neighb
new_mu_calc <- new_mu_neighb
}
cat("Calculating distances\n")
if( calc_w2_post){
W2_single <- distCompare(singleModels, target = list(posterior = theta_sing,
mean = cond_mu_sing),
method = wp_alg,
quantity=c("posterior","mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
W1_single <- distCompare(singleModels, target = list(posterior = theta_sing,
mean = cond_mu_sing),
method = wp_alg,
quantity=c("posterior","mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit,
ground_p = 1,
p = 1)
# cat("W2 selection\n")
w2_r2_single <- WPR2(Y = cond_mu_sing, nu = W2_single, p = 2, method = wp_alg)
w1_r2_single <- WPR2(Y = cond_mu_sing, nu = W1_single, p = 1, method = wp_alg)
w2_r2_single_null <- WPR2(Y = NULL, nu = W2_single, p = 2, method = wp_alg)
w1_r2_single_null <- WPR2(Y = NULL, nu = W1_single, p = 1, method = wp_alg)
mse_single <- distCompare(singleModels, target = list(posterior = full_param,
mean = new_mu_sing),
method = "mse",
quantity=c("posterior", "mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
mse_single$mean$dist <- mse_single$mean$dist/mean((c(cond_mu_sing) - c(new_mu_sing))^2)
mse_single$post$dist <- mse_single$post$dist/mean((as.matrix(full_param) - c(theta))^2)
# cat("W2 projection\n")
PW2_single <- distCompare(singleModelsP, target = list(posterior = theta_sing,
mean = cond_mu_calc),
method = wp_alg,
quantity=c("posterior", "mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
PW1_single <- distCompare(singleModelsP, target = list(posterior = theta_sing,
mean = cond_mu_calc),
method = wp_alg,
quantity=c("posterior","mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit,
p = 1,
ground_p = 1)
Pw2_r2_single <- WPR2(Y = cond_mu_calc, nu = PW2_single, p = 2, method = wp_alg)
Pw1_r2_single <- WPR2(Y = cond_mu_calc, nu = PW1_single, p = 1, method = wp_alg)
if(recalc) {
Pw2_r2_single_null <- WPR2(Y = NULL, nu = PW2_single, p = 2, method = wp_alg)
Pw1_r2_single_null <- WPR2(Y = NULL, nu = PW1_single, p = 1, method = wp_alg)
} else {
Pw2_r2_single_null <- WPR2(Y = cond_mu_calc, nu = singleModelsP, p = 2, method = wp_alg)
Pw1_r2_single_null <- WPR2(Y = cond_mu_calc, nu = singleModelsP, p = 1, method = wp_alg)
}
Pmse_single <- distCompare(singleModelsP, target = list(posterior = full_param,
mean = new_mu_calc),
method = "mse",
quantity=c("posterior","mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
Pmse_single$mean$dist <- Pmse_single$mean$dist/mean((cond_mu_calc - c(new_mu_calc))^2)
Pmse_single$post$dist <- Pmse_single$post$dist/mean((as.matrix(full_param) - c(theta))^2)
}
else {
W2_single <- distCompare(singleModels, target = list(posterior = NULL,
mean = cond_mu_sing),
method = wp_alg,
quantity=c("mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
W1_single <- distCompare(singleModels, target = list(posterior = NULL,
mean = cond_mu_sing),
method = wp_alg,
quantity=c("mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit,
ground_p = 1,
p = 1)
# cat("W2 selection\n")
w2_r2_single <- WPR2(Y = cond_mu_sing, nu = W2_single, p = 2, method = wp_alg)
w1_r2_single <- WPR2(Y = cond_mu_sing, nu = W1_single, p = 1, method = wp_alg)
w2_r2_single_null <- WPR2(Y = cond_mu_sing, nu = singleModels, p = 2, method = wp_alg, base = data$invlink(colMeans(cond_eta)))
w1_r2_single_null <- WPR2(Y = cond_mu_sing, nu = singleModels, p = 1, method = wp_alg, base = data$invlink(colMeans(cond_eta)))
mse_single <- distCompare(singleModels, target = list(posterior = NULL,
mean = new_mu_sing),
method = "mse",
quantity="mean",
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
mse_single$mean$dist <- mse_single$mean$dist/mean((c(cond_mu_sing) - c(new_mu_sing))^2)
# mse_single$post$dist <- mse_single$post$dist/mean((as.matrix(full_param) - c(theta))^2)
# cat("W2 projection\n")
PW2_single <- distCompare(singleModelsP, target = list(posterior = NULL,
mean = cond_mu_calc),
method = wp_alg,
quantity=c("mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
PW1_single <- distCompare(singleModelsP, target = list(posterior = NULL,
mean = cond_mu_calc),
method = wp_alg,
quantity=c("mean"),
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit,
p = 1,
ground_p = 1)
Pw2_r2_single <- WPR2(Y = cond_mu_calc, nu = PW2_single, p = 2, method = wp_alg)
Pw1_r2_single <- WPR2(Y = cond_mu_calc, nu = PW1_single, p = 1, method = wp_alg)
if(recalc) {
Pw2_r2_single_null <- WPR2(Y = cond_mu_sing, nu = PW2_single, p = 2, method = wp_alg)
Pw1_r2_single_null <- WPR2(Y = cond_mu_sing, nu = PW1_single, p = 1, method = wp_alg)
} else {
Pw2_r2_single_null <- WPR2(Y = cond_mu_calc, nu = singleModelsP, p = 2, method = wp_alg)
Pw1_r2_single_null <- WPR2(Y = cond_mu_calc, nu = singleModelsP, p = 1, method = wp_alg)
}
Pmse_single <- distCompare(singleModelsP, target = list(posterior = NULL,
mean = new_mu_calc),
method = "mse",
quantity="mean",
parallel=NULL,
transform = data$invlink,
epsilon = epsilon,
niter = otmaxit)
Pmse_single$mean$dist <- Pmse_single$mean$dist/mean((cond_mu_calc - c(new_mu_calc))^2)
# Pmse_single$post$dist <- Pmse_single$post$dist/mean((as.matrix(full_param) - c(theta))^2)
}
# rm(singleModels)
#### Variable importance ####
cat(paste0("Running variable importance: ", date(),"\n"))
# pred.fun.theta <- switch(family,
# "gaussian" = theta,
# "binomial" = theta,
# "exponential" = list(baseline = post_sample$mu$S$base,
# param = theta))
# imp_newX <- WPVI(X = X_new, Y = NULL, theta = theta_new, pred.fun = pred.fun,
# p = 2, ground_p = 2, transport.method = "exact")
imp_single <- WPVI(X = X_sing, Y = NULL, theta = theta_sing, pred.fun = pred.fun,
p = 2, ground_p = 2, transport.method = "exact")
} else {
cat(paste0("Running methods, same data: ", date(),"\n"))
#### In sample ####
#IP
cat(" Selection: IP,\n")
time <- proc.time()
ip <- W2IP(X = X, Y = cond_eta, theta = theta,
display.progress=FALSE,
transport.method = transport.method,
model.size = ip_seq,
infimum.maxit = 100, solution.method = solver,
parallel = NULL)
ipTime <- proc.time() - time
# trajSel <- selDist$theta
cat(" Selection: IP, Lasso, ")
#selection variable
time <- proc.time()
lassoSel <- W2L1(X, cond_eta, theta, family="gaussian", penalty=penalty,
penalty.factor = penalty_fact, nlambda = n.lambda, alpha = 0.99,
gamma = 1.1,
lambda.min.ratio = lambda.min.ratio, infimum.maxit=1e2,
maxit = 1e6,
display.progress=FALSE,
transport.method = transport.method,
method = "selection.variable")
selTime <- proc.time() - time
# trajSel <- selDist$theta
cat(" HC, ")
#carvalho method
time <- proc.time()
lassoHC <- HC(X, cond_eta, theta = theta,
family="gaussian", penalty=penalty, method = "selection.variable",
penalty.factor=HC_penalty_fact, nlambda = n.lambda, alpha = 0.99, gamma = 1.1,
lambda.min.ratio = lambda.min.ratio, maxit = 1e5)
hcTime <- proc.time() - time
cat(" SW, ")
#stepwise
time <- proc.time()
step <- WPSW(X, Y = cond_eta, theta, force=1, p=2,
direction = "backward", method = "selection.variable",
transport.method = transport.method,
display.progress = FALSE)
stepTime <- proc.time() - time
# trajStep <- step$theta
cat(" SA\n")
#simulated annealing
annealTime <- NULL
# if(n > 512 | p > 11){
# anneal <- WPSA(X=X, Y=cond_eta, theta=theta,
# force = 1, p=2, model.size = 5, iter = SAiter, temps = SAtemps,
# options = list(method = "selection.variable",
# energy.distribution = "boltzman",
# transport.method = transport.method,
# cooling.schedule="exponential"),
# display.progress=TRUE)
# annealTime <- NULL
# }
# else {
time <- proc.time()
anneal <- WPSA(X=X, Y=cond_eta, theta=theta,
force = 1, p=2, model.size = sa_seq, iter = SAiter, temps = SAtemps,
options = list(method = "selection.variable",
energy.distribution = "boltzman",
transport.method = transport.method,
cooling.schedule="exponential",
proposal.method = sa_prop),
display.progress=FALSE, max.time = sa_max_time)
annealTime <- proc.time() - time
cat(paste0(anneal$message,"\n"))
if(anneal$message != "completed") {
annealTime <- paste0(">", annealTime)
}
cat(" Projection: Lasso, ")
#projection
time <- proc.time()
lassoProj <- W2L1(X, cond_eta, theta, family="gaussian", penalty=penalty,
penalty.factor=proj_penalty_fact, nlambda = n.lambda,
lambda.min.ratio = lambda.min.ratio, infimum.maxit=1,
maxit = 1e6, alpha = 0.99, gamma = 1.1,
display.progress=FALSE,
transport.method = transport.method,
method = "projection")
projTime <- proc.time() - time
# trajProj <- projDist$theta
cat(" HC, ")
time <- proc.time()
PlassoHC <- HC(X, cond_eta, theta = theta,
family="gaussian", penalty=penalty, method = "projection",
alpha = 0.99, gamma = 1.1,
penalty.factor=HC_penalty_fact, nlambda = n.lambda,
lambda.min.ratio = lambda.min.ratio, maxit = 1e5)
PhcTime <- proc.time() - time
cat(" SW, ")
#stepwise
time <- proc.time()
Pstep <- WPSW(X, Y = cond_eta, theta, force=1, p=2,
direction = "backward", method = "projection",
transport.method = transport.method,
display.progress = FALSE)
PstepTime <- proc.time() - time
# trajStep <- step$theta
cat(" SA\n")
#simulated annealing
annealTime <- NULL
time <- proc.time()
Panneal <- WPSA(X=X, Y=cond_eta, theta=theta,
force = 1, p=2, model.size = sa_seq, iter = SAiter, temps = SAtemps,
options = list(method = "projection",
energy.distribution = "boltzman",
transport.method = transport.method,
cooling.schedule="exponential",
proposal.method = sa_prop),
display.progress=FALSE, max.time = sa_max_time)
PannealTime <- proc.time() - time
cat(paste0(Panneal$message,"\n"))
if(Panneal$message != "completed") {
PannealTime <- paste0(">", PannealTime)
}
time <- proc.time()
PL1 <- W1L1(X=X, Y=cond_eta, solver = solver,
nlambda = n.lambda, penalty = penalty,
lambda.min.ratio = lambda.min.ratio, maxit = 1e5,
gamma = 1.1)
PL1Time <- proc.time() - time
# time <- proc.time()
# PL3 <- WPL1(X=X, Y=cond_eta, p = 3,
# nlambda = n.lambda, penalty = penalty,
# lambda.min.ratio = lambda.min.ratio, maxit = 1e5,
# gamma = 1.1)
# PL3Time <- proc.time() - time
time <- proc.time()
PLInf <- WInfL1(X=X, Y=cond_eta,
nlambda = n.lambda, penalty = penalty,
lambda.min.ratio = lambda.min.ratio,
gamma = 1.1, solver = solver)
PLInfTime <- proc.time() - time
time <- list(selection = list(ip = ipTime[3], lasso = selTime[3],
HC = hcTime[3],
step = stepTime[3],
anneal = annealTime[3]),
projection = list(lasso = projTime[3],
L1 = PL1Time[3],
# L3 = PL3Time[3],
LInf = PLInfTime[3],
HC = PhcTime[3], step = PstepTime[3],
anneal = PannealTime[3]))
imp_insamp <- WPVI(X = X, Y = NULL, theta = theta, pred.fun = pred.fun,
p = 2, ground_p = 2, transport.method = "exact")
}
# augDat <- augPseudo(X, cond_eta, theta, theta_norm, pseudo.obs, n, same=TRUE)
# lambdas <- calc.lambdas(augDat, lambda.min.ratio, penalty_fact, n.lambda)
# }
# trajAnneal <- anneal$theta
# if (not.only.timing) {
# inSampModels <- list("Binary Programming" = ip,
# "L2" = lassoSel,
# "Simulated Annealing" = anneal,
# "Stepwise" = step,
# "Hahn-Carvalho" = lassoHC)
# inSampModelsProj <- list("L2" = lassoProj,
# "L1" = PL1,
# "LInf" = PLInf,
# "Simulated Annealing" = Panneal,
# "Stepwise" = Pstep,
# "Hahn-Carvalho" = PlassoHC)
# rm("ip","lassoSel", "anneal","step","lassoHC")
# rm("lassoProj","PL1", "PLInf", "Panneal","Pstep","PlassoHC")
#
# cat("Calculating distances\n")
# if( calc_w2_post){
# W2_insamp <- distCompare(inSampModels, target = list(posterior = theta,
# mean = cond_mu),
# method = wp_alg,
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# mse_insamp <- distCompare(inSampModels, target = list(posterior = full_param,
# mean = true_mu),
# method = "mse",
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# PW2_insamp <- distCompare(inSampModelsProj, target = list(posterior = theta,
# mean = cond_mu),
# method = wp_alg,
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# Pmse_insamp <- distCompare(inSampModelsProj, target = list(posterior = full_param,
# mean = true_mu),
# method = "mse",
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# }
# else {
# W2_insamp <- distCompare(inSampModels, target = list(posterior = NULL,
# mean = cond_mu),
# method = wp_alg,
# quantity=c("mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# mse_insamp <- distCompare(inSampModels, target = list(posterior = NULL,
# mean = true_mu),
# method = "mse",
# quantity="mean",
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# PW2_insamp <- distCompare(inSampModelsProj, target = list(posterior = NULL,
# mean = cond_mu),
# method = wp_alg,
# quantity=c("mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# Pmse_insamp <- distCompare(inSampModelsProj, target = list(posterior = NULL,
# mean = true_mu),
# method = "mse",
# quantity="mean",
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# }
#
# rm(inSampModels)
# rm(inSampModelsProj)
#
# #### new X variable ####
# #mse on new outcome data from same paramters and different X
# #new method
# # augDatN <- augPseudo(X_new, cond_mu_new, theta, theta_norm, pseudo.obs, n, same=TRUE)
# # lambdas <- calc.lambdas(augDatN, lambda.min.ratio, penalty_fact, n.lambda)
# cat(paste0("Running methods, new X variable: ", date(),"\n"))
# cat(" Selection: IP")
# ipN <- W2IP(X = X_new, Y = cond_eta_new, theta = theta_new,
# display.progress=TRUE,
# transport.method = transport.method,
# model.size = ip_seq,
# infimum.maxit = 100, solution.method = "cone",
# parallel = NULL)
#
# cat(" Lasso")
# lassoSelN <- W2L1(X_new, cond_eta_new, theta_new, family="gaussian",
# penalty=penalty, alpha = 0.99, gamma = 1.1,
# penalty.factor=penalty_factN, nlambda = n.lambda,
# lambda.min.ratio = lambda.min.ratio, infimum.maxit=100,
# maxit = 1e5,
# transport.method = transport.method,
# display.progress=TRUE, method = "selection.variable")
# # trajSelN <- extractCoef(lassoSelN)
#
# cat(" HC, ")
# #carvalho method
# lassoHCN <- HC(X_new, cond_eta_new, theta = theta_new,
# family="gaussian", penalty=penalty, alpha = 0.99, gamma = 1.1,
# penalty.factor=HC_penalty_fact, nlambda = n.lambda,
# lambda.min.ratio = lambda.min.ratio, maxit = 1e5)
#
# cat(" SW")
# #stepwise
# stepN <- WPSW(X_new, cond_eta_new, theta_new, force=1, p=2,
# direction = "backward", method = "selection.variable",
# transport.method = transport.method,
# display.progress = TRUE)
#
# cat(" SA")
# annealN <- WPSA(X=X_new, Y=cond_eta_new, theta=theta_new,
# force = 1, p=2, model.size = sa_seq, iter = SAiter,
# temps = SAtemps,
# options = list(method = "selection.variable",
# energy.distribution = "boltzman",
# transport.method = transport.method,
# cooling.schedule="exponential",
# proposal.method = sa_prop),
# display.progress = TRUE, max.time = sa_max_time)
# cat(paste0(annealN$message,"\n"))
# cat("\n")
#
# cat(" Projection: Lasso")
# #projection
# lassoProjN <- W2L1(X_new, cond_eta_new, theta_new, family="gaussian", penalty=penalty,
# penalty.factor=proj_penalty_fact, nlambda = n.lambda,
# lambda.min.ratio = lambda.min.ratio, infimum.maxit=1,
# maxit=1e5, alpha = 0.99, gamma = 1.1,
# transport.method = transport.method,
# display.progress=TRUE, method = "projection")
#
# cat(" SW")
# #stepwise
# PstepN <- WPSW(X_new, cond_eta_new, theta_new, force=1, p=2,
# direction = "backward", method = "projection",
# transport.method = transport.method,
# display.progress = TRUE)
# cat(" HC, ")
# #HC
# PlassoHCN <- HC(X_new, cond_eta_new, theta = theta_new, alpha = 0.99, gamma = 1.1,
# family="gaussian", penalty=penalty, method = "projection",
# penalty.factor=HC_penalty_fact, nlambda = n.lambda,
# lambda.min.ratio = lambda.min.ratio, maxit = 1e5)
# cat(" SA")
# # anneal
# PannealN <- WPSA(X=X_new, Y=cond_eta_new, theta=theta_new,
# force = 1, p=2, model.size = sa_seq, iter = SAiter,
# temps = SAtemps,
# options = list(method = "projection",
# energy.distribution = "boltzman",
# transport.method = transport.method,
# cooling.schedule="exponential",
# proposal.method = sa_prop),
# display.progress = TRUE, max.time = sa_max_time)
# cat(paste0(PannealN$message,"\n"))
# cat("\n")
# # }
# # trajAnnealN <- annealCoef(annealN, theta)
# newXModels <- list("Binary Programming" = ipN,
# "Lasso" = lassoSelN,
# "Simulated Annealing" = annealN,
# "Stepwise" = stepN,
# "Hahn-Carvalho" = lassoHCN)
# rm("ipN","lassoSelN", "annealN","stepN","lassoHCN")
# newXModelsP <- list("Lasso" = lassoProjN,
# "Simulated Annealing" = PannealN,
# "Stepwise" = PstepN,
# "Hahn-Carvalho" = PlassoHCN)
# rm("lassoProjN",
# "PannealN", "PstepN","PlassoHCN")
#
# cat("Calculating distances\n")
# if( calc_w2_post){
# W2_newX <- distCompare(newXModels, target = list(posterior = theta_new,
# mean = cond_mu_new),
# method = wp_alg,
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# mse_newX <- distCompare(newXModels, target = list(posterior = full_param,
# mean = new_mu),
# method = "mse",
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# PW2_newX <- distCompare(newXModelsP, target = list(posterior = theta_new,
# mean = cond_mu_new),
# method = wp_alg,
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# Pmse_newX <- distCompare(newXModelsP, target = list(posterior = full_param,
# mean = new_mu),
# method = "mse",
# quantity=c("posterior","mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# }
# else {
# W2_newX <- distCompare(newXModels, target = list(posterior = NULL,
# mean = cond_mu_new),
# method = wp_alg,
# quantity=c("mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# mse_newX <- distCompare(newXModels, target = list(posterior = NULL,
# mean = new_mu),
# method = "mse",
# quantity="mean",
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# PW2_newX <- distCompare(newXModelsP, target = list(posterior = NULL,
# mean = cond_mu_new),
# method = wp_alg,
# quantity=c("mean"),
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# Pmse_newX <- distCompare(newXModelsP, target = list(posterior = NULL,
# mean = new_mu),
# method = "mse",
# quantity="mean",
# parallel=NULL,
# transform = data$invlink,
# epsilon = epsilon,
# niter = otmaxit)
# }
#
#
# rm(newXModels, newXModelsP)
#### generate output list ####
outList <- list (
W2_dist = list(inSamp = list(selection = W2_insamp,
projection = PW2_insamp),
# newX = list(selection = W2_newX,
# projection = PW2_newX),
single = list(selection = W2_single,
projection = PW2_single) ),
mse = list(inSamp = list(selection = mse_insamp,
projection = Pmse_insamp),
# newX = list(selection = mse_newX,
# projection = Pmse_newX),
single = list(selection = mse_single,
projection = Pmse_single) ),
importance = list(inSamp = imp_insamp,
# newX = imp_newX,
single = imp_single),
W2_r2 = list(expectation = list(
inSamp = list(selection = NULL,
projection = NULL),
single = list(selection = w2_r2_single,
projection = Pw2_r2_single) ),
null = list(
inSamp = list(selection = NULL,
projection = NULL),
single = list(selection = w2_r2_single_null,
projection = Pw2_r2_single_null) )
),
W1_r2 = list(expectation = list(
inSamp = list(selection = NULL,
projection = NULL),
single = list(selection = w1_r2_single,
projection = Pw1_r2_single) ),
null = list(
inSamp = list(selection = NULL,
projection = NULL),
single = list(selection = w1_r2_single_null,
projection = Pw1_r2_single_null) )
),
time = time, #,
data = list(test = list(
X = X_sing,
mean = new_mu_sing),
neighborhood = list(X = X_neighborhood,
mean = new_mu_neighb)
),
models = list(
selection = lapply(singleModels, function(s) s$theta),
projection = lapply(singleModelsP, function(s) s$theta),
estimation = list(boot = post_sample$test$eta[c(single_idx,neighb_idx),],
original = list(prediction = pred.orig,
derivatives = deriv.orig)
),
derivatives = derivative.test
))
return(outList)
}
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