Survival analysis is a task dealing with time-to-event prediction. Aside from the well-understood models like CPH, many more complex models have recently emerged, but most lack interpretability. Due to a functional type of prediction, either in the form of survival function or cumulative hazard function, standard model-agnostic explanations cannot be applied directly.

The `survex`

package provides model-agnostic explanations for machine learning survival models. It is based on the `DALEX`

package. If you’re unfamiliar with explainable machine learning, consider referring to the Explanatory Model Analysis book – most of the methods included in `survex`

extend these described in EMA and implemented in `DALEX`

but to models with functional output.

The main `explain()`

function uses a model and data to create a standardized `explainer`

object, which is further used as an interface for calculating predictions. We automate creating explainers from the following packages: `mlr3proba`

, `censored`

, `ranger`

, `randomForestSRC`

, and `survival`

. **Raise an Issue on GitHub if you find models from other packages that we can incorporate into the explain() interface.**

Note that an explainer can be created for **any** survival model, using the `explain_survival()`

function by passing `model`

, `data`

, `y`

, and `predict_survival_function`

arguments.

The package is available on CRAN:

`install.packages("survex")`

The latest development version can be installed from GitHub using `devtools::install_github()`

:

`devtools::install_github("https://github.com/ModelOriented/survex")`

```
library("survex")
library("survival")
library("ranger")
# create a model
model <- ranger(Surv(time, status) ~ ., data = veteran)
# create an explainer
explainer <- explain(model,
data = veteran[, -c(3, 4)],
y = Surv(veteran$time, veteran$status))
# evaluate the model
model_performance(explainer)
# visualize permutation-based feature importance
plot(model_parts(explainer))
# explain one prediction with SurvSHAP(t)
plot(predict_parts(explainer, veteran[1, -c(3, 4)]))
```

Existing functionalities: - [x] unified prediction interface using the explainer object - `predict()`

- [x] calculation of performance metrics (Brier Score, Time-dependent C/D AUC, metrics from `mlr3proba`

) - `model_performance()`

- [x] calculation of feature importance (Permutation Feature Importance - PFI) - `model_parts()`

- [x] calculation of partial dependence (Partial Dependence Profiles - PDP, Accumulated Local Effects - ALE) - `model_profile()`

- [x] calculation of 2-dimensional partial dependence (2D PDP, 2D ALE) - `model_profile_2d()`

- [x] calculation of local feature attributions (SurvSHAP(t), SurvLIME) - `predict_parts()`

- [x] calculation of local ceteris paribus explanations (Ceteris Paribus profiles - CP/ Individual Conditional Expectations - ICE) - `predict_profile()`

- [x] calculation of global feature attributions using SurvSHAP(t) - `model_survshap()`

Currently in develompment: - [ ] …

Future plans: - [ ] … (raise an Issue on GitHub if you have any suggestions) - [ ] examples for sursvm and survboost (https://github.com/ModelOriented/survex/issues/88)

If you use `survex`

, please cite our article:

M. Spytek, M. Krzyziński, S. H. Langbein, H. Baniecki, M. N. Wright, P. Biecek.

survex: an R package for explaining machine learning survival models.Bioinformatics, Volume 39, Issue 12, btad723, 2023.

```
@article{spytek2023survex,
author = {Mikołaj Spytek and Mateusz Krzyziński and Sophie Hanna Langbein and
Hubert Baniecki and Marvin N Wright and Przemysław Biecek},
title = {survex: an {R} package for explaining machine learning survival models},
journal = {Bioinformatics},
volume = {39},
number = {12},
pages = {btad723},
year = {2023},
month = {12},
doi = {10.1093/bioinformatics/btad723}
}
```

`survex`

H. Baniecki, B. Sobieski, P. Bombiński, P. Szatkowski, P. Biecek. Hospital Length of Stay Prediction Based on Multi-modal Data towards Trustworthy Human-AI Collaboration in Radiomics.

*International Conference on Artificial Intelligence in Medicine*, 2023.W. Chen, B. Zhou, C. Y. Jeon, F. Xie, Y.-C. Lin, R. K. Butler, Y. Zhou, T. Q. Luong, E. Lustigova, J. R. Pisegna, B. U. Wu. Machine learning versus regression for prediction of sporadic pancreatic cancer.

*Pancreatology*, 2023.M. Nachit, Y. Horsmans, R. M. Summers, I. A. Leclercq, P. J. Pickhardt. AI-based CT Body Composition Identifies Myosteatosis as Key Mortality Predictor in Asymptomatic Adults.

*Radiology*, 2023.R. Passera, S. Zompi, J. Gill, A. Busca. Explainable Machine Learning (XAI) for Survival in Bone Marrow Transplantation Trials: A Technical Report.

*BioMedInformatics*, 2023.P. Donizy, M. Spytek, M. Krzyziński, K. Kotowski, A. Markiewicz, B. Romanowska-Dixon, P. Biecek, M. P. Hoang. Ki67 is a better marker than PRAME in risk stratification of BAP1-positive and BAP1-loss uveal melanomas.

*British Journal of Ophthalmology*, 2023.X. Qi, Y. Ge, A. Yang, Y. Liu, Q. Wang, G. Wu. Potential value of mitochondrial regulatory pathways in the clinical application of clear cell renal cell carcinoma: a machine learning-based study.

*Journal of Cancer Research and Clinical Oncology*, 2023.C. C. Lee, S. Y. Su, S. F. Sung. Machine learning-based survival analysis approaches for predicting the risk of pneumonia post-stroke discharge.

*International Journal of Medical Informatics*, 2024.P. Wang, X. Qian, W. Jiang, H. Wang, Y. Wang, Y. Zhou, Y. Zhang, Y. Huang, X. Zhai. Cord Blood Transplantation for Very Early‑Onset Inflammatory Bowel Disease Caused by Interleukin‑10 Receptor Deficiency.

*Journal of Clinical Immunology*, 2024.E. Ruiz, J. Honles, R. Fernández, K. Uribe, J. P. Cerapio, K. Cancino, J. Contreras-Mancilla, S. Casavilca-Zambrano, F. Berrospi, P. Pineau, S. Bertani. A preoperative risk score based on early recurrence for estimating outcomes after resection of hepatocellular carcinoma in the non-cirrhotic liver.

*HPB*, 2024.Share it with us!

- H. Ishwaran, U. B. Kogalur, E. H. Blackstone, M. S. Lauer. Random survival forests.
*Annals of Applied Statistics*, 2008. - A. Grudziąż, A. Gosiewska, P. Biecek. survxai: an R package for structure-agnostic explanations of survival models.
*Journal of Open Source Software*, 2018. - M. S. Kovalev, L. V. Utkin, E. M. Kasimov. SurvLIME: A method for explaining machine learning survival models.
*Knowledge-Based Systems*, 2020. - R. Sonabend, F. J. Király, A. Bender, B. Bischl, M. Lang. mlr3proba: an R package for machine learning in survival analysis.
*Bioinformatics*, 2021. - E. Hvitfeldt, H. Frick. censored: ‘parsnip’ Engines for Survival Models.
*CRAN v0.1.0*, 2022. - M. Krzyziński, M. Spytek, H. Baniecki, P. Biecek. SurvSHAP(t): Time-dependent explanations of machine learning survival models.
*Knowledge-Based Systems*, 2023.