Survival Priority Lasso Learner

Patient outcome prediction based on multi-omics data taking practitioners’ preferences into account. Calls prioritylasso::prioritylasso() from prioritylasso.

Dictionary

This Learner can be instantiated via the dictionary mlr_learners or with the associated sugar function lrn():

mlr_learners$get("surv.priority_lasso")
lrn("surv.priority_lasso")

Meta Information

• Task type: “surv”

• Predict Types: “lp”, “response”

• Feature Types: “logical”, “integer”, “numeric”

• Required Packages: mlr3, mlr3proba, prioritylasso

Parameters

Id	Type	Default	Levels	Range
blocks	untyped			-
max.coef	untyped			-
block1.penalization	logical	TRUE	TRUE, FALSE	-
lambda.type	character	lambda.min	lambda.min, lambda.1se	-
standardize	logical	TRUE	TRUE, FALSE	-
nfolds	integer	5		\([1, \infty)\)
foldid	untyped			-
cvoffset	logical	FALSE	TRUE, FALSE	-
cvoffsetnfolds	integer	10		\([1, \infty)\)
alignment	character	lambda	lambda, fraction	-
alpha	numeric	1		\([0, 1]\)
big	numeric	9.9e+35		\((-\infty, \infty)\)
devmax	numeric	0.999		\([0, 1]\)
dfmax	integer	-		\([0, \infty)\)
eps	numeric	1e-06		\([0, 1]\)
epsnr	numeric	1e-08		\([0, 1]\)
exclude	untyped	-		-
exmx	numeric	250		\((-\infty, \infty)\)
fdev	numeric	1e-05		\([0, 1]\)
gamma	untyped	-		-
grouped	logical	TRUE	TRUE, FALSE	-
intercept	logical	TRUE	TRUE, FALSE	-
keep	logical	FALSE	TRUE, FALSE	-
lambda	untyped	-		-
lambda.min.ratio	numeric	-		\([0, 1]\)
lower.limits	untyped	- , Inf		-
maxit	integer	100000		\([1, \infty)\)
mnlam	integer	5		\([1, \infty)\)
mxit	integer	100		\([1, \infty)\)
mxitnr	integer	25		\([1, \infty)\)
nlambda	integer	100		\([1, \infty)\)
offset	untyped			-
parallel	logical	FALSE	TRUE, FALSE	-
penalty.factor	untyped	-		-
pmax	integer	-		\([0, \infty)\)
pmin	numeric	1e-09		\([0, 1]\)
prec	numeric	1e-10		\((-\infty, \infty)\)
predict.gamma	numeric	gamma.1se		\((-\infty, \infty)\)
relax	logical	FALSE	TRUE, FALSE	-
s	numeric	lambda.1se		\([0, 1]\)
standardize.response	logical	FALSE	TRUE, FALSE	-
thresh	numeric	1e-07		\([0, \infty)\)
trace.it	integer	0		\([0, 1]\)
type.gaussian	character	-	covariance, naive	-
type.logistic	character	Newton	Newton, modified.Newton	-
type.multinomial	character	ungrouped	ungrouped, grouped	-
upper.limits	untyped	Inf		-

References

Simon K, Vindi J, Roman H, Tobias H, Anne-Laure B (2018). “Priority-Lasso: a simple hierarchical approach to the prediction of clinical outcome using multi-omics data.” BMC Bioinformatics, 19. doi:10.1186/s12859-018-2344-6 .

See also

• Dictionary of Learners: mlr3::mlr_learners.

• as.data.table(mlr_learners) for a table of available Learners in the running session (depending on the loaded packages).

• Chapter in the mlr3book: https://mlr3book.mlr-org.com/basics.html#learners

• mlr3learners for a selection of recommended learners.

• mlr3cluster for unsupervised clustering learners.

• mlr3pipelines to combine learners with pre- and postprocessing steps.

• mlr3tuning for tuning of hyperparameters, mlr3tuningspaces for established default tuning spaces.

Author

HarutyunyanLiana

Super classes

mlr3::Learner -> mlr3proba::LearnerSurv -> LearnerSurvPriorityLasso

Methods

Public methods

• LearnerSurvPriorityLasso$new()

• LearnerSurvPriorityLasso$selected_features()

• LearnerSurvPriorityLasso$clone()

Inherited methods

• mlr3::Learner$base_learner()
• mlr3::Learner$format()
• mlr3::Learner$help()
• mlr3::Learner$predict()
• mlr3::Learner$predict_newdata()
• mlr3::Learner$print()
• mlr3::Learner$reset()
• mlr3::Learner$train()

---

Method new()

Creates a new instance of this R6 class.

Usage

LearnerSurvPriorityLasso$new()

---

Method selected_features()

Selected features, i.e. those where the coefficient is positive.

Usage

LearnerSurvPriorityLasso$selected_features()

Returns

character().

---

Method clone()

The objects of this class are cloneable with this method.

Usage

LearnerSurvPriorityLasso$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

learner = mlr3::lrn("surv.priority_lasso")
print(learner)
#> <LearnerSurvPriorityLasso:surv.priority_lasso>: Priority Lasso
#> * Model: -
#> * Parameters: list()
#> * Packages: mlr3, mlr3proba, prioritylasso
#> * Predict Types:  lp, [response]
#> * Feature Types: logical, integer, numeric
#> * Properties: selected_features, weights

# available parameters:
learner$param_set$ids()
#>  [1] "blocks"               "max.coef"             "block1.penalization" 
#>  [4] "lambda.type"          "standardize"          "nfolds"              
#>  [7] "foldid"               "cvoffset"             "cvoffsetnfolds"      
#> [10] "alignment"            "alpha"                "big"                 
#> [13] "devmax"               "dfmax"                "eps"                 
#> [16] "epsnr"                "exclude"              "exmx"                
#> [19] "fdev"                 "gamma"                "grouped"             
#> [22] "intercept"            "keep"                 "lambda"              
#> [25] "lambda.min.ratio"     "lower.limits"         "maxit"               
#> [28] "mnlam"                "mxit"                 "mxitnr"              
#> [31] "nlambda"              "offset"               "parallel"            
#> [34] "penalty.factor"       "pmax"                 "pmin"                
#> [37] "prec"                 "predict.gamma"        "relax"               
#> [40] "s"                    "standardize.response" "thresh"              
#> [43] "trace.it"             "type.gaussian"        "type.logistic"       
#> [46] "type.multinomial"     "upper.limits"