sbh | R Documentation |
Main end-user function for fitting a Survival Bump Hunting (SBH) model
(or Group Survival Bump Hunting (GSBH)). It returns an object of class
sbh
, as generated by our Patient Recursive Survival Peeling (PRSP)
algorithm (or Patient Recursive Group Survival Peeling (PRGSP)), containing
cross-validated estimates of the target region (bump) of the input space with
end-points statistics of interest. See Dazard and Rao (2014, 2015, 2016, 2021a, 2021b)
for details, as well as Dazard et al. (2021c) ans Rao et al. (2020) for applications
in Patient Survival Subtyping and Survival Disparity Subtyping.
sbh(X, y, groups = NULL, delta, B = 30, K = 5, A = 1000, vs = TRUE, vstype = "ppl", vsarg = "alpha=1, nalpha=1, nlambda=100", cv = TRUE, cvtype = "combined", cvarg = "alpha=0.01, beta=0.10, peelcriterion=\"lrt\", cvcriterion=\"cer\"", pv = FALSE, control = sbh.control(vscons = 0.5, decimals = 2, onese = FALSE, probval = NULL, timeval = NULL, lag = 2, span = 0.10, degree = 2), parallel.vs = FALSE, parallel.rep = FALSE, parallel.pv = FALSE, conf = NULL, verbose = TRUE, seed = NULL)
X |
A |
y |
n- |
groups |
|
delta |
n- |
B |
Postitive |
K |
Postitive |
A |
Positive |
vs |
|
vstype |
|
vsarg |
PCQR:
PPL:
SPCA:
|
cv |
|
cvtype |
|
cvarg |
if |
pv |
|
control |
Optional function to set ancillary parameters for fitting the Survival Bump Hunting (SBH) model.
See |
parallel.vs |
|
parallel.rep |
|
parallel.pv |
|
conf |
|
verbose |
|
seed |
Positive |
The main function sbh
relies on an optional variable screening (pre-selection) procedure that is run
before the actual variable usage (selection) is done at the time of fitting the Survival Bump Hunting (SBH)
or Group Survival Bump Hunting (GSBH) model using our PRSP or PRGSP algorithm, respectively. The user can choose
between four possible variable screening (pre-selection) procedures (see Dazard and Rao (2021a) for details,
as well as Dazard et al. (2021c) for an application in Patient Survival Subtyping):
Patient Recursive Survival Peeling (PRSP) (by univariate screening of our algorithm)
Penalized Censored Quantile Regression (PCQR) (by Semismooth Newton Coordinate Descent fiting algorithm adapted from package hqreg)
Penalized Partial Likelihood (PPL) (by Elasticnet Regularization adapted from package glmnet)
Supervised Principal Component Analysis (SPCA) (by Supervised Principal Component adapted from package superpc)
NA
missing values are not allowed in PRIMsrc, because it depends on R package glmnet, which doesn't handle
missing values. In case of high-dimensional data (p >> n), the recommendation is to use PPL or SPCA because of computational
efficiency. Variable screening (pre-selection) is done by computing occurrence frequencies of top-ranking variables over the
cross-validation folds and replicates. The conservativeness of the procedure is controled by the argument vscons
.
The argument K
must be bigger than 2 for a regular K
-fold cross-validation procedure to work, and should be no less than 3
for a regular procedure to make sense; K
\in {5,...,10} is recommended; defaults to K
=5. Setting K
also
specifies the type of cross-validation to be done:
K
= 1 carries no cross-validation out, or set-value when cv
= FALSE
(see below).
K
\in {2,...,n-1} carries out K
-fold cross-validation.
K
= n carries out leave-one-out cross-validation.
If cross-validation is done (cv = TRUE
, the optimal number of peeling steps (optimal peeling sequence length),
and the optimal model size (cardinal of subset of top-screened variables) will be determined by cross-validation.
If cv = FALSE
, no cross-validation at all will be performed, and the values of K
and vscons
will both
be reset to 1.
The Patient Recursive Group Survival Peeling (PRGSP) algorithm is a derivation of our original Patient Recursive Survival Peeling (PRSP) algorithm to search for (or find an extreme of) outcome difference within existing (user-defined) fixed groups of observations. See Dazard and Rao (2021b) for details, as well as Rao et al. (2020) for an application in Survival Disparity Subtyping.
The argument object$cvarg$peelcriterion
is the peeling criterion that determines what type of bump hunting is done, that is,
either using the PRSP or PRGSP algorithm for building a SBH model or GSBH model, respectively. If a regular hunt of
bump difference is done (SBH model, peelcriterion
in {"lrt", "lhr", "chs"}), PRSP algorithm is used, and
cross-validated bumps are generated between observations from the higher-risk bump (in-bump) versus lower-risk bump (out-bump).
If a hunt of (user-specified) fixed group difference is done (GSBH model, peelcriterion
= {"grp"}),
PRGSP algorithm is used, and cross-validated bumps are generated between interacting subgroup from the fixed groups and bumps
(higher-risk (in-bump) versus lower-risk bump (out-bump)), that is, either between both groups within the higher-risk bump (in-bump),
or equivalently, between higher-risk (in-bump) versus lower-risk bump (out-bump) within a given group.
The argument groups
is to be specified only if a hunt of (user-specified) fixed group difference is to be done, i.e.
when option peelcriterion
= {"grp"} and PRGSP are used.
In the PRSP variable screening procedure (vsarg
of "prsp"), setting option msize
to a single non-NULL
value
within the allowable range [1,floor
(p)] will override the cross-validation setting within the variable screening
procedure. This could be recommended for high-dimensional data (p >> n) to reduce the computational burden. In this situation,
we suggest an arbitrary value of msize
within [1, floor
(p/5)]. Conversely, setting msize=NULL
will force the cross-validation within the variable screening procedure by automaticaly generating a vector of model sizes
(cardinals of subset of top-screened variables) within the restricted range [1, floor
(p/5)], which will be used to
determine the optimal value of model size.
In fitting the Survival Bump Hunting (SBH) model itself, note that the result contains initial step #0, which corresponds
to the entire set of the (training) data. Also, the number of peeling steps that is within the allowable range
[1,ceiling
(log
(1/n) / log
(1 - (1/n)))] is further restricted when either of the metaparameter
alpha
or beta
takes on values other than the smallest possible fraction of the (training) data, i.e. \frac{1}{n^t},
where n^t is the training sample size:
ceiling
(log
(beta
) / log
(1 - alpha
)) : alpha
and beta
fixed by user
ceiling
(log
(1/n^t) / log
(1 - alpha
)) : alpha
fixed by user and beta
fixed by data
ceiling
(log
(beta
) / log
(1 - (1/n^t))) : alpha
fixed by data and beta
fixed by user
ceiling
(log
(1/n^t) / log
(1 - (1/n^t))) : alpha
and beta
fixed by data
When cross-validation is requested (cv=TRUE
), the function performs a supervised (stratified) random splitting of the observations
accounting for the classes/strata provided by delta
(censoring). This is because it is desireable that the data splitting balances
the class distributions of the outcome within the cross-validation splits. For each screening method and for building the final
Survival Bump Hunting (SBH) model, all model tuning parameters are simultaneously estimated by cross-validation. The function offers a
number of options for the cross-validation to be perfomed: the number of replications B
; the type of technique; the peeling
criterion; and the optimization criterion.
The returned S3-class sbh
object contains cross-validated estimates of all the decision-rules of used (selected) covariates
and all other statistical quantities of interest at each iteration of the peeling sequence (inner loop of the PRSP algorithm).
This enables the graphical display of results of profiling curves for model tuning, peeling trajectories, covariate traces and survival
distributions (see plotting functions for more details).
In case replicated cross-validations are performed, a "summary report" of the outputs is done over the B
replicates as follows:
Even thought the PRSP algorithm uses only one covariate at a time at each peeling step, the reported matrix of
"Replicated CV" box decision rules may show more than one covariate being used in a given step depending on the replication.
In the end, the reported "Replicated CV" trace values are computed (at each peeling step) as a single modal trace value
of covariate usage over the B
replicates. This is also reflected in the "Replicated CV" importance and usage plots of
covariate traces.
Similarly, the reported "Replicated CV" box membership indicators are computed (at each peeling step) as the point-wise modal
membership value, that is majority vote, over the B
replicates (right-hand side of equation #22 in Dazard et al. 2016).
The reported "Replicated CV" box support and corresponding box sample size are computed (at each peeling step) based on the
above "Replicated CV" box membership indicators (i.e. not as equation #23 in Dazard et al. 2016).
All other reported "Replicated CV" box estimates are computed (at each peeling step) as average statistics over the B
replicates (i.e. as equation #21 in Dazard et al. 2016), that is, not as a single box estimate computed from the
"Replicated CV" box membership indicators. This includes the decision rules, the p-values, and all other box statistics.
This may result in some apparent discordance if these estimates are re-computed directly from the reported "Replicated CV"
box membership indicators.
If the computation of log-rank p-values is desired, then running with the parallelization option is strongly recommended. In case of large (p > n) or very large (p >> n) datasets, it is also highly recommended to use the parallelization option.
The function sbh
relies on the R package parallel to create a parallel backend within an R session. This enables access to a
cluster of compute cores and/or nodes on a local and/or remote machine(s) and scaling-up with the number of CPU cores available and
efficient parallel execution. To run a procedure in parallel (with parallel RNG), argument parallel
is to be set to TRUE
and argument conf
is to be specified (i.e. non NULL
). Argument conf
uses the options described in function
makeCluster
of the R packages parallel and snow. PRIMsrc supports two types of communication mechanisms
between master and worker processes: 'Socket' or 'Message-Passing Interface' ('MPI'). In PRIMsrc, parallel 'Socket' clusters
use sockets communication mechanisms only (no forking) and are therefore available on all platforms, including Windows, while parallel
'MPI' clusters use high-speed interconnects mechanism in networks of computers (with distributed memory) and are therefore available
only in these architectures. A parallel 'MPI' cluster also requires R package Rmpi to be installed. Value type
is used
to setup a cluster of type 'Socket' ("SOCKET") or 'MPI' ("MPI"), respectively. Depending on this type, values of spec
are to
be used alternatively:
For 'Socket' clusters (conf$type="SOCKET"
), spec
should be a character
vector
naming the hosts on
which to run the job; it can default to a unique local machine, in which case, one may use the unique host name "localhost".
Each host name can potentially be repeated to the number of CPU cores available on the local machine.
It can also be an integer
scalar specifying the number of processes to spawn on the local machine;
or a list of machine specifications if you have ssh installed (a character value named host specifying the name or address
of the host to use).
For 'MPI' clusters (conf$type="MPI"
), spec
should be an integer
scalar
specifying the total number of processes to be spawned across the network of available nodes, counting the workernodes and
masternode.
The actual creation of the cluster, its initialization, and closing are all done internally. For more details, see the reference manual of R package snow and examples below.
When random number generation is needed, the creation of separate streams of parallel RNG per node is done internally by distributing the stream states to the nodes. For more details, see the vignette of R package parallel. The use of a seed allows to reproduce the results within the same type of session: the same seed will reproduce the same results within a non-parallel session or within a parallel session, but it will not necessarily give the exact same results (up to sampling variability) between a non-parallelized and parallelized session due to the difference of management of the seed between the two (see parallel RNG and value of returned seed below).
Object of class
sbh
(Patient Recursive Survival Peeling)
list
containing the following 23 fields:
X |
|
y |
|
groups |
|
delta |
|
B |
positive |
K |
positive |
A |
positive |
vs |
|
vstype |
|
vsarg |
|
cv |
|
cvtype |
|
cvarg |
|
pv |
|
control |
|
vscons |
|
onese |
|
decimals |
|
probval |
|
timeval |
|
cvprofiles |
|
cvfit |
|
success |
|
seed |
User seed. An |
This work made use of the High Performance Computing Resource in the Core Facility for Advanced Research Computing at Case Western Reserve University. This project was partially funded by the National Institutes of Health NIH - National Cancer Institute (R01-CA160593) to J-E. Dazard and J.S. Rao.
Main end-user function for fitting the Survival Bump Hunting model.
"Jean-Eudes Dazard, Ph.D." jean-eudes.dazard@case.edu
"Michael Choe, M.D." mjc206@case.edu
"Michael LeBlanc, Ph.D." mleblanc@fhcrc.org
"Alberto Santana, MBA." ahs4@case.edu
"J. Sunil Rao, Ph.D." Rao@biostat.med.miami.edu
Maintainer: "Jean-Eudes Dazard, Ph.D." jean-eudes.dazard@case.edu
Dazard J-E. and Rao J.S. (2021a). "Variable Selection Strategies for High-Dimensional Recursive Peeling-Based Survival Bump Hunting Models." (in prep).
Dazard J-E. and Rao J.S. (2021b). "Group Bump Hunting by Recursive Peeling-Based Methods: Application to Survival/Risk Predictive Models." (in prep).
Dazard J-E., Choe M., Pawitan Y., and Rao J.S. (2021c). "Identification and Characterization of Informative Prognostic Subgroups by Survival Bump Hunting." (in prep).
Rao J.S., Huilin Y., and Dazard J-E. (2020). "Disparity Subtyping: Bringing Precision Medicine Closer to Disparity Science." Cancer Epidemiology Biomarkers & Prevention, 29(6 Suppl):C018.
Yi C. and Huang J. (2017). "Semismooth Newton Coordinate Descent Algorithm for Elastic-Net Penalized Huber Loss Regression and Quantile Regression." J. Comp Graph. Statistics, 26(3):547-557.
Dazard J-E., Choe M., LeBlanc M., and Rao J.S. (2016). "Cross-validation and Peeling Strategies for Survival Bump Hunting using Recursive Peeling Methods." Statistical Analysis and Data Mining, 9(1):12-42.
Dazard J-E., Choe M., LeBlanc M., and Rao J.S. (2015). "R package PRIMsrc: Bump Hunting by Patient Rule Induction Method for Survival, Regression and Classification." In JSM Proceedings, Statistical Programmers and Analysts Section. Seattle, WA, USA. American Statistical Association IMS - JSM, p. 650-664.
Dazard J-E., Choe M., LeBlanc M., and Rao J.S. (2014). "Cross-Validation of Survival Bump Hunting by Recursive Peeling Methods." In JSM Proceedings, Survival Methods for Risk Estimation/Prediction Section. Boston, MA, USA. American Statistical Association IMS - JSM, p. 3366-3380.
sbh.control
makeCluster
(R package parallel)
glmnet
, cv.glmnet
(R package glmnet)
hqreg
, cv.hqreg
(R package hqreg)
superpc.cv
(R package superpc)
#=================================================== # Loading the library and its dependencies #=================================================== library("PRIMsrc") ## Not run: #=================================================== # PRIMsrc Package news #=================================================== PRIMsrc.news() #=================================================== # PRIMsrc Package citation #=================================================== citation("PRIMsrc") #=================================================== # Demo with a synthetic dataset # Use help for descriptions #=================================================== data("Synthetic.1", package="PRIMsrc") ?Synthetic.1 ## End(Not run) #=================================================== # Simulated dataset #1 (n=250, p=3) # Peeling criterion = LRT # Cross-Validation criterion = LRT # With Combined Cross-Validation (RCCV) # Without Replications (B = 1) # Without variable screening (pre-selection) # Without computation of log-rank \eqn{p}-values # Without parallelization #=================================================== data("Synthetic.1", package="PRIMsrc") synt1 <- sbh(X = Synthetic.1[ , -c(1,2), drop=FALSE], y = Synthetic.1[ ,1, drop=TRUE], groups = NULL, delta = Synthetic.1[ ,2, drop=TRUE], B = 1, K = 3, vs = FALSE, cv = TRUE, cvtype = "combined", cvarg = "alpha=0.05, beta=0.10, peelcriterion=\"lrt\", cvcriterion=\"lrt\"", pv = FALSE, control = sbh.control(probval = 0.5), parallel.vs = FALSE, parallel.rep = FALSE, parallel.pv = FALSE, conf = NULL, verbose = TRUE, seed = 123) summary(object = synt1) print(x = synt1) n <- 100 p <- length(synt1$cvfit$cv.used) x <- matrix(data = runif(n = n*p, min = 0, max = 1), nrow = n, ncol = p, byrow = FALSE, dimnames = list(1:n, paste("X", 1:p, sep=""))) synt1.pred <- predict(object = synt1, newdata = x, steps = synt1$cvfit$cv.nsteps) plot(x = synt1, main = paste("Scatter plot for model #1", sep=""), proj = synt1$cvfit$cv.used[c(1,2)], steps = synt1$cvfit$cv.nsteps, pch = 16, cex = 0.5, col = c(1,2), boxes = TRUE, col.box = 2, lty.box = 2, lwd.box = 1, add.caption.box = TRUE, text.caption.box = paste("Step: ", synt1$cvfit$cv.nsteps, sep=""), device = NULL) plot_profile(object = synt1, main = "Cross-validated tuning profiles for model #1", pch = 20, col = 1, lty = 1, lwd = 0.5, cex = 0.5, add.sd = TRUE, add.profiles = TRUE, add.caption = TRUE, text.caption = c("Mean","Std. Error"), device = NULL) plot_traj(object = synt1, main = paste("Cross-validated peeling trajectories for model #1", sep=""), col = 1, lty = 1, lwd = 0.5, cex = 0.5, toplot = synt1$cvfit$cv.used, device = NULL) plot_trace(object = synt1, main = paste("Cross-validated trace plots for model #1", sep=""), xlab = "Box Support", ylab = "Covariate Range (centered)", col = 1, lty = 1, lwd = 0.5, cex = 0.5, toplot = synt1$cvfit$cv.used, center = TRUE, scale = FALSE, device = NULL) plot_km(object = synt1, main = paste("Cross-validated probability curves for model #1", sep=""), xlab = "Time", ylab = "Probability", ci = TRUE, col = c(1,2), lty = 1, lwd = 0.5, cex = 0.5, steps = 1:synt1$cvfit$cv.nsteps, plot.type = "bumps", bump.reference = "in-bump", group.reference = levels(synt1$groups)[1], add.caption = TRUE, text.caption = c("out-bump","in-bump"), device = NULL) ## Not run: #=================================================== # Examples of parallel backend parametrization #=================================================== if (require("parallel")) { cat("'parallel' is attached correctly \n") } else { stop("'parallel' must be attached first \n") } #=================================================== # Ex. #1 - Multicore PC # Running WINDOWS # SOCKET communication cluster # Shared memory parallelization #=================================================== cpus <- parallel::detectCores(logical = TRUE) conf <- list("spec" = rep("localhost", cpus), "type" = "SOCKET", "homo" = TRUE, "verbose" = TRUE, "outfile" = "") #=================================================== # Ex. #2 - Master node + 3 Worker nodes cluster # All nodes equipped with identical setups of multicores # (8 core CPUs per machine for a total of 32) # SOCKET communication cluster # Distributed memory parallelization #=================================================== masterhost <- Sys.getenv("HOSTNAME") slavehosts <- c("compute-0-0", "compute-0-1", "compute-0-2") nodes <- length(slavehosts) + 1 cpus <- 8 conf <- list("spec" = c(rep(masterhost, cpus), rep(slavehosts, cpus)), "type" = "SOCKET", "homo" = TRUE, "verbose" = TRUE, "outfile" = "") #=================================================== # Ex. #3 - Enterprise Multinode Cluster w/ multicore/node # Running LINUX with SLURM scheduler # MPI communication cluster # Distributed memory parallelization # Below, variable 'cpus' is the total number of requested # tasks (threads/CPUs), which is specified from within a # SLURM script. #================================================== if (require("Rmpi")) { print("Rmpi is loaded correctly \n") } else { stop("Rmpi must be installed first to use MPI\n") } cpus <- as.numeric(Sys.getenv("SLURM_NTASKS")) conf <- list("spec" = cpus, "type" = "MPI", "homo" = TRUE, "verbose" = TRUE, "outfile" = "") #=================================================== # Simulated dataset #1 (n=250, p=3) # Peeling criterion = LRT # Cross-Validation criterion = LRT # With Combined Cross-Validation (RCCV) # With Replications (B = 30) # With PPL variable screening (pre-selection) # With computation of log-rank \eqn{p}-values # With parallelization #=================================================== data("Synthetic.1", package="PRIMsrc") synt1 <- sbh(X = Synthetic.1[ , -c(1,2), drop=FALSE], y = Synthetic.1[ ,1, drop=TRUE], groups = NULL, delta = Synthetic.1[ ,2, drop=TRUE], B = 30, K = 5, A = 1000, vs = TRUE, vstype = "ppl", vsarg = "alpha=1, nalpha=1, nlambda=100", cv = TRUE, cvtype = "combined", cvarg = "alpha=0.01, beta=0.10, peelcriterion=\"lrt\", cvcriterion=\"lrt\"", pv = TRUE, control = sbh.control(probval = 0.5, vscons = 0.5), parallel.vs = FALSE, parallel.rep = TRUE, parallel.pv = TRUE, conf = conf, verbose = TRUE, seed = 123) #=================================================== # Simulated dataset #4 (n=100, p=1000) # Peeling criterion = LRT # Cross-Validation criterion = CER # With Combined Cross-Validation (RCCV) # With Replications (B = 30) # With PRSP variable screening (pre-selection) # With computation of log-rank \eqn{p}-values # With parallelization #=================================================== data("Synthetic.4", package="PRIMsrc") synt4 <- sbh(X = Synthetic.4[ , -c(1,2), drop=FALSE], y = Synthetic.4[ ,1, drop=TRUE], groups = NULL, delta = Synthetic.4[ ,2, drop=TRUE], B = 30, K = 5, A = 1000, vs = TRUE, vstype = "prsp", vsarg = "alpha=0.01, beta=0.10, msize=NULL, peelcriterion=\"lrt\", cvcriterion=\"cer\"", cv = TRUE, cvtype = "combined", cvarg = "alpha=0.01, beta=0.10, peelcriterion=\"lrt\", cvcriterion=\"cer\"", pv = TRUE, control = sbh.control(probval = 0.5, vscons = 0.5), parallel.vs = FALSE, parallel.rep = TRUE, parallel.pv = TRUE, conf = conf, verbose = TRUE, seed = 123) ## End(Not run)
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