surv_net_benchmark.R

## select holdout as the resampling strategy
resampling <- rsmp("cv", folds = 3)

## add KM and CPH
learners <- c(learners, lrns(c("surv.kaplan", "surv.coxph")))
design <- benchmark_grid(tasks, learners, resampling)
bm <- benchmark(design)
               
## Aggreggate with Harrell's C and Integrated Graf Score
msrs <- msrs(c("surv.cindex", "surv.graf"))
bm$aggregate(msrs)[, c(3, 4, 7, 8)]

Ah apologies I saw the warning not the error. The error is saying that the predictions from your model are not valid survival probabilities. Unfortunately without access to your data I can't tell if the error is in my software, your code, or your data. I suggest you open an issue in the survivalmodels repo so we can figure it out properly

Hi Raphael, first thanks for you work. It just what I needed. However, I'm encountering the error as follows. Do you know what's the reason? Thanks!

INFO [10:53:55.224] [bbotk] Evaluating 1 configuration(s)
INFO [10:53:55.254] [mlr3] Running benchmark with 1 resampling iterations
INFO [10:53:55.259] [mlr3] Applying learner 'surv.pchazard' on task 'lung' (iter 1/1)
INFO [10:53:55.300] [mlr3] Applying learner 'surv.kaplan' on task 'lung' (iter 1/3)
INFO [10:53:55.314] [mlr3] Applying learner 'surv.kaplan' on task 'lung' (iter 2/3)
INFO [10:53:55.328] [mlr3] Applying learner 'surv.kaplan' on task 'lung' (iter 3/3)
INFO [10:53:55.342] [mlr3] Applying learner 'surv.coxph' on task 'lung' (iter 1/3)
INFO [10:53:55.374] [mlr3] Applying learner 'surv.coxph' on task 'lung' (iter 2/3)
INFO [10:53:55.397] [mlr3] Applying learner 'surv.coxph' on task 'lung' (iter 3/3)
Error in py_call_impl(callable, dots$args, dots$keywords) :
RuntimeError: CUDA error: unspecified launch failure
CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.
For debugging consider passing CUDA_LAUNCH_BLOCKING=1.
Compile with TORCH_USE_CUDA_DSA to enable device-side assertions.

Hey @lxtpvt this is an error on the pyrthon side, I think possibly you might just need to restart your session and the error will clear itself. Does this issue help? There's lots of other similar ones associated with pytorch if you Google "RuntimeError: CUDA error: unspecified launch failure"

Thanks Raphael, I fixed this problem by upgrading the ''mlr3proba" package. However, this is another error from the "coxtime" model as follows.

Error in py_call_impl(callable, dots$args, dots$keywords) :
AttributeError: 'Series' object has no attribute 'iteritems'

This happened PipeOp surv.coxtime.tuned's $train()

When I remove the "coxtime" model from the learners list, everything is OK.

Great! Strange I've never seen that error before... Looks like it's in the underlying {pycox} implementation. Maybe try reinstalling pycox?