Survival Priority Lasso Learner
mlr_learners_surv.priority_lasso.Rd
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()
:
$get("surv.priority_lasso")
mlr_learnerslrn("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
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.
Super classes
mlr3::Learner
-> mlr3proba::LearnerSurv
-> LearnerSurvPriorityLasso
Methods
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"