python | Sebastian Pölsterl

scikit-survival 0.28.0 released

Sun, 05 Jul 2026 18:22:05 +0200

I am pleased to announce the release of scikit-survival 0.28.0.

A highlight of this release is the support for Polars DataFrames alongside pandas DataFrames via the Narwhals dataframe abstraction layer. In addition, this release adds support for scikit-learn 1.9.

Support for Polars

Polars is a data frame library similar to pandas, but with its core written in Rust instead of Python, which often gives Polars an advantage in terms of performance.

All datasets shipped with scikit-survival can now be loaded as a Polars DataFrame by specifying the output_type argument.

from sksurv.datasets import load_gbsg2
# return X as a polars DataFrame
X, y = load_gbsg2(output_type="polars")
X.head()

shape: (5, 8)
┌──────┬────────┬───────┬──────────┬────────┬─────────┬────────┬───────┐
│ age ┆ estrec ┆ horTh ┆ menostat ┆ pnodes ┆ progrec ┆ tgrade ┆ tsize │
│ --- ┆ --- ┆ --- ┆ --- ┆ --- ┆ --- ┆ --- ┆ --- │
│ f64 ┆ f64 ┆ enum ┆ enum ┆ f64 ┆ f64 ┆ enum ┆ f64 │
╞══════╪════════╪═══════╪══════════╪════════╪═════════╪════════╪═══════╡
│ 70.0 ┆ 66.0 ┆ no ┆ Post ┆ 3.0 ┆ 48.0 ┆ II ┆ 21.0 │
│ 56.0 ┆ 77.0 ┆ yes ┆ Post ┆ 7.0 ┆ 61.0 ┆ II ┆ 12.0 │
│ 58.0 ┆ 271.0 ┆ yes ┆ Post ┆ 9.0 ┆ 52.0 ┆ II ┆ 35.0 │
│ 59.0 ┆ 29.0 ┆ yes ┆ Post ┆ 4.0 ┆ 60.0 ┆ II ┆ 17.0 │
│ 73.0 ┆ 65.0 ┆ no ┆ Post ┆ 1.0 ┆ 26.0 ┆ II ┆ 35.0 │
└──────┴────────┴───────┴──────────┴────────┴─────────┴────────┴───────┘

Transforming DataFrames

scikit-learn enables transformers to return Polars data frames via the set_output API.

from sklearn import set_config
from sklearn.preprocessing import StandardScaler
set_config(transform_output="polars")
# standarize the columns of a polars DataFrame
X_standarized = StandardScaler().fit_transform(
X.select("age", "tsize")
)

scikit-surival has two transformers that now accept polars and pandas data frames as input: ClinicalKernelTransform, and OneHotEncoder.

ClinicalKernelTransform

ClinicalKernelTransform computes a kernel matrix, so the output will be a numpy array, as before. With scikit-survival 0.28.0, it is aware of the polars colum types String, Categorical, Enum and Object. However, polars does not have a concept similar to ordered categories in pandas: pd.Categorical([…], ordered=True).

When computing the clinical kernel for a polars data frame, you can specify the order of categories with the ordinal_categories argument, otherwise all non-numeric columns will be treated as nominal columns, where values have no specific order (e.g. the column horTh with values “yes” and “no” in the example below).

from sksurv.kernels import ClinicalKernelTransform
K = ClinicalKernelTransform(
ordinal_categories={"tgrade": ["I", "II", "III"]},
).fit_transform(
X.select("age", "horTh", "tgrade")
)

OneHotEncoder

OneHotEncoder encodes the string-type columns to numeric columns. It automatically returns a data frame of the same type as the input:

from sksurv.preprocessing import OneHotEncoder
X_onehot = OneHotEncoder().fit_transform(X.select("horTh", "tgrade"))
X_onehot.head()

shape: (5, 3)
┌───────────┬───────────┬────────────┐
│ horTh=yes ┆ tgrade=II ┆ tgrade=III │
│ --- ┆ --- ┆ --- │
│ f64 ┆ f64 ┆ f64 │
╞═══════════╪═══════════╪════════════╡
│ 0.0 ┆ 1.0 ┆ 0.0 │
│ 1.0 ┆ 1.0 ┆ 0.0 │
│ 1.0 ┆ 1.0 ┆ 0.0 │
│ 1.0 ┆ 1.0 ┆ 0.0 │
│ 0.0 ┆ 1.0 ┆ 0.0 │
└───────────┴───────────┴────────────┘

Fitting survival models

Finally, you can pass a polars data frame to the fit and predict functions of any estimator.

from sklearn.pipeline import make_pipeline
from sksurv.linear_model import CoxPHSurvivalAnalysis
pipe = make_pipeline(
OneHotEncoder(), StandardScaler(), CoxPHSurvivalAnalysis()
)
pipe.fit(X[:500], y[:500])
risk_scores = pipe.predict(X[500:])

Note that this only works for eager data frames, lazy data frames will give an error.

X_lazy = X.lazy()
pipe.fit(X_lazy[:500], y[:500])

Traceback (most recent call last):
File "example.py", line 21, in <module>
pipe.fit(X_lazy[:500], y[:500])
File "…/site-packages/sklearn/base.py", line 1403, in wrapper
return fit_method(estimator, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
…
File "…/site-packages/sksurv/_dataframe/_input.py", line 96, in ensure_eager_dataframe
_reject_polars_lazyframe(obj)
File "…/site-packages/sksurv/_dataframe/_input.py", line 84, in _reject_polars_lazyframe
raise TypeError(_LAZYFRAME_NOT_SUPPORTED_MSG)
TypeError: polars.LazyFrame is not supported; call .collect() before passing to scikit-survival.

New Contributors

A big shoutout to our two new contributors:

cakedev0 for adding support for scikit-learn 1.9
55Kamiryo for adding support for Polars data frames.

Updated Dependencies

With this release, the minimum supported version are:

Package	Minimum Version
narwhals	2.0.1
scikit-learn	1.9.0

Install

scikit-survival is available for Linux, macOS, and Windows and can be installed either

via pip:

pip install scikit-survival

or via conda

 conda install -c conda-forge scikit-survival

scikit-survival 0.26.0 released

Wed, 17 Dec 2025 21:26:48 +0100

I am pleased to announce that scikit-survival 0.26.0 has been released.

This is a maintainance release that adds support for Python 3.14 and includes updates to make scikit-survival compatible with new versions of pandas and osqp. It adds support for the pandas string dtype, and copy-on-write, which is going to become the default with pandas 3. In addition, sksurv.preprocessing.OneHotEncoder now supports converting columns with the object dtype.

With this release, the minimum supported version are:

Package	Minimum Version
Python	3.11
pandas	2.0.0
osqp	1.0.2

Install

scikit-survival is available for Linux, macOS, and Windows and can be installed either

via pip:

pip install scikit-survival

or via conda

 conda install -c conda-forge scikit-survival

scikit-survival 0.25.0 with improved documentation released

Fri, 22 Aug 2025 23:55:06 +0200

I am pleased to announce that scikit-survival 0.25.0 has been released.

This release adds support for scikit-learn 1.7, in addition to version 1.6. However, the most significant changes in this release affect the documentation. The API documentation has been completely overhauled to improve clarity and consistency. I hope this marks a significant improvement for users new to scikit-survival.

One of the biggest pain points for users seems to be understanding which metric can be used to evaluate the performance of a given estimator. The user guide now summarizes the different options.

Which Performance Metrics Exist?

The performance metrics for evaluating survival models can be broadly divided into three groups:

Concordance Index (C-index): Measures the rank correlation between predicted risk scores and observed event times. Two implementations are available in scikit-survival:
- concordance_index_censored(): This implements Harrell’s estimator, which can be optimistic with high censoring.
- concordance_index_ipcw(): An inverse probability of censoring weighted (IPCW) alternative that provides a less biased estimate, especially with high censoring. It is the preferred estimator of the C-Index.
Cumulative/Dynamic Area Under the ROC Curve (AUC): Extends the AUC to survival data, quantifying how well a model distinguishes subjects who experience an event by a given time from those who do not. It can handle time-dependent risk scores and is implemented in cumulative_dynamic_auc().
Brier Score: An extension of the mean squared error to right-censored data. The Brier score assesses both discrimination and calibration based on a model’s estimated survival functions. You can either compute the Brier score at specific time point(s) using brier_score() or compute an overall measure by integrating the Brier score over a range of time points via integrated_brier_score().

What Do Survival Models Predict?

Survival models can predict several quantities, depending on the model being used. First of all, every estimator has a predict() method, which either returns a unit-less risk score or the predicted time of an event.

If predictions are risk scores, higher values indicate an increased risk of experiencing an event. The scores have no unit and are only meaningful for ranking samples by their risk of experiencing an event. This is for example the case for CoxPHSurvivalAnalysis.

from sksurv.datasets import load_veterans_lung_cancer
from sksurv.linear_model import CoxPHSurvivalAnalysis
from sksurv.metrics import concordance_index_censored
from sksurv.preprocessing import OneHotEncoder
# Load data
X, y = load_veterans_lung_cancer()
Xt = OneHotEncoder().fit_transform(X)
# Fit model
estimator = CoxPHSurvivalAnalysis().fit(Xt, y)
# Predict risk score
predicted_risk = estimator.predict(Xt)
# Evaluate risk scores
cindex = concordance_index_censored(
y["Status"], y["Survival_in_days"], predicted_risk
)

If predictions directly relate to the time point of an event, lower scores indicate shorter survival, while higher scores indicate longer survival. See for example IPCRidge.

from sksurv.datasets import load_veterans_lung_cancer
from sksurv.linear_model import IPCRidge
from sksurv.metrics import concordance_index_censored
from sksurv.preprocessing import OneHotEncoder
# Load the data
X, y = load_veterans_lung_cancer()
Xt = OneHotEncoder().fit_transform(X)
# Fit the model
estimator = IPCRidge().fit(Xt, y)
# Predict time of an event
predicted_time = estimator.predict(Xt)
# Flip sign of predictions to obtain a risk score
cindex = concordance_index_censored(
y["Status"], y["Survival_in_days"], -1 * predicted_time
)

Both types of predictions can be evaluated by cumulative_dynamic_auc() too but not the Brier score.

While the concordance index is easy to interpret, it is not a useful measure of performance if a specific time range is of primary interest (e.g. predicting death within 2 years). This is particularly relevant for survival models that can make time-dependent predictions.

For instance, RandomSurvivalForest, can also predict survival functions (via predict_survival_function()) or cumulative hazard functions (via predict_cumulative_hazard_function()). These functions return lists of StepFunction instances. Each instance can be evaluated at a set of time points to obtain predicted survival probabilities (or cumulative hazards). The Brier score and cumulative_dynamic_auc() are capable of evaluating time-dependent predictions, but not the C-Index.

import numpy as np
from sksurv.datasets import load_veterans_lung_cancer
from sksurv.ensemble import RandomSurvivalForest
from sksurv.metrics import integrated_brier_score
from sksurv.preprocessing import OneHotEncoder
# Load the data
X, y = load_veterans_lung_cancer()
Xt = OneHotEncoder().fit_transform(X)
# Fit the model
estimator = RandomSurvivalForest().fit(Xt, y)
# predict survival functions
surv_funcs = estimator.predict_survival_function(Xt)
# select time points to evaluate performance at
times = np.arange(7, 365)
# create predictions at selected time points
preds = np.asarray(
[[sfn(t) for t in times] for sfn in surv_funcs]
)
# compute integral
score = integrated_brier_score(y, y, preds, times)

For more details on evaluating survival models, please have a look at the user guide and the API documentation.

scikit-survival 0.24.0 released

Wed, 26 Feb 2025 22:26:45 +0100

It’s my pleasure to announce the release of scikit-survival 0.24.0.

A highlight of this release the addition of cumulative_incidence_competing_risks() which implements a non-parameteric estimator of the cumulative incidence function in the presence of competing risks. In addition, the release adds support for scikit-learn 1.6, including the support for missing values for ExtraSurvivalTrees.

Analysis of Competing Risks

In classical survival analysis, the focus is on the time until a specific event occurs. If no event is observed during the study period, the time of the event is considered censored. A common assumption is that censoring is non-informative, meaning that censored subjects have a similar prognosis to those who were not censored.

Competing risks arise when each subject can experience an event due to one of $K$ ($K \geq 2$) mutually exclusive causes, termed competing risks. Thus, the occurrence of one event prevents the occurrence of other events. For example, after a bone marrow transplant, a patient might relapse or die from transplant-related causes (transplant-related mortality). In this case, death from transplant-related mortality precludes relapse.

The bone marrow transplant data from Scrucca et al., Bone Marrow Transplantation (2007) includes data from 35 patients grouped into two cancer types: Acute Lymphoblastic Leukemia (ALL; coded as 0), and Acute Myeloid Leukemia (AML; coded as 1).

from sksurv.datasets import load_bmt
bmt_features, bmt_outcome = load_bmt()
diseases = bmt_features["dis"].cat.rename_categories(
{"0": "ALL", "1": "AML"}
)
diseases.value_counts().to_frame()

dis	count
AML	18
ALL	17

During the follow-up period, some patients might experience a relapse of the original leukemia or die while in remission (transplant related death). The outcome is defined similarly to standard time-to-event data, except that the event indicator specifies the type of event, where 0 always indicates censoring.

import pandas as pd
status_labels = {
0: "Censored",
1: "Transplant related mortality",
2: "Relapse",
}
risks = pd.DataFrame.from_records(bmt_outcome).assign(
label=lambda x: x["status"].replace(status_labels)
)
risks["label"].value_counts().to_frame()

label	count
Relapse	15
Censored	11
Transplant related mortality	9

The table above shows the number of observations for each status.

Non-parametric Estimator of the Cumulative Incidence Function

If the goal is to estimate the probability of relapse, transplant-related death is a competing risk event. This means that the occurrence of relapse prevents the occurrence of transplant-related death, and vice versa. We aim to estimate curves that illustrate how the likelihood of these events changes over time.

Let’s begin by estimating the probability of relapse using the complement of the Kaplan-Meier estimator. With this approach, we treat deaths as censored observations. One minus the Kaplan-Meier estimator provides an estimate of the probability of relapse before time $t$.

import matplotlib.pyplot as plt
from sksurv.nonparametric import kaplan_meier_estimator
times, km_estimate = kaplan_meier_estimator(
bmt_outcome["status"] == 1, bmt_outcome["ftime"]
)
plt.step(times, 1 - km_estimate, where="post")
plt.xlabel("time $t$")
plt.ylabel("Probability of relapsing before time $t$")
plt.ylim(0, 1)
plt.grid()

However, this approach has a significant drawback: considering death as a censoring event violates the assumption that censoring is non-informative. This is because patients who died from transplant-related mortality have a different prognosis than patients who did not experience any event. Therefore, the estimated probability of relapse is often biased.

The cause-specific cumulative incidence function (CIF) addresses this problem by estimating the cause-specific hazard of each event separately. The cumulative incidence function estimates the probability that the event of interest occurs before time $t$, and that it occurs before any of the competing causes of an event. In the bone marrow transplant dataset, the cumulative incidence function of relapse indicates the probability of relapse before time $t$, given that the patient has not died from other causes before time $t$.

from sksurv.nonparametric import cumulative_incidence_competing_risks
times, cif_estimates = cumulative_incidence_competing_risks(
bmt_outcome["status"], bmt_outcome["ftime"]
)
plt.step(times, cif_estimates[0], where="post", label="Total risk")
for i, cif in enumerate(cif_estimates[1:], start=1):
plt.step(times, cif, where="post", label=status_labels[i])
plt.legend()
plt.xlabel("time $t$")
plt.ylabel("Probability of event before time $t$")
plt.ylim(0, 1)
plt.grid()

The plot shows the estimated probability of experiencing an event at time $t$ for both the individual risks and for the total risk.

Next, we want to to estimate the cumulative incidence curves for the two cancer types — acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) — to examine how the probability of relapse depends on the original disease diagnosis.

_, axs = plt.subplots(2, 2, figsize=(7, 6), sharex=True, sharey=True)
for j, disease in enumerate(diseases.unique()):
mask = diseases == disease
event = bmt_outcome["status"][mask]
time = bmt_outcome["ftime"][mask]
times, cif_estimates, conf_int = cumulative_incidence_competing_risks(
event,
time,
conf_type="log-log",
)
for i, (cif, ci, ax) in enumerate(
zip(cif_estimates[1:], conf_int[1:], axs[:, j]), start=1
):
ax.step(times, cif, where="post")
ax.fill_between(times, ci[0], ci[1], alpha=0.25, step="post")
ax.set_title(f"{disease}: {status_labels[i]}", size="small")
ax.grid()
for ax in axs[-1, :]:
ax.set_xlabel("time $t$")
for ax in axs[:, 0]:
ax.set_ylim(0, 1)
ax.set_ylabel("Probability of event before time $t$")

The left column shows the estimated cumulative incidence curves (solid lines) for patients diagnosed with ALL, while the right column shows the curves for patients diagnosed with AML, along with their 95% pointwise confidence intervals. The plot indicates that the estimated probability of relapse at $t=40$ days is more than three times higher for patients diagnosed with ALL compared to AML.

If you want to run the examples above yourself, you can execute them interactively in your browser using binder.

scikit-survival 0.23.0 released

Sun, 30 Jun 2024 13:36:08 +0200

I am pleased to announce the release of scikit-survival 0.23.0.

This release adds support for scikit-learn 1.4 and 1.5, which includes missing value support for RandomSurvivalForest. For more details on missing values support, see the section in the release announcement for 0.23.0.

Moreover, this release fixes critical bugs. When fitting SurvivalTree, the sample_weight is now correctly considered when computing the log-rank statistic for each split. This change also affects RandomSurvivalForest and ExtraSurvivalTrees which pass sample_weight to the individual trees in the ensemble. Therefore, the outputs produced by SurvivalTree, RandomSurvivalForest, and ExtraSurvivalTrees will differ from previous releases.

This release fixes a bug in ComponentwiseGradientBoostingSurvivalAnalysis and GradientBoostingSurvivalAnalysis when dropout is used. Previously, dropout was only applied starting with the third iteration, now dropout is applied in the second iteration too.

Finally, this release adds compatibility with numpy 2.0 and drops support for Python 3.8.

Install

scikit-survival is available for Linux, macOS, and Windows and can be installed either

via pip:

pip install scikit-survival

or via conda

 conda install -c conda-forge scikit-survival

scikit-survival 0.22.0 released

Mon, 02 Oct 2023 22:39:15 +0200

I am pleased to announce the release of scikit-survival 0.22.0. The highlights for this release include

Compatibility with scikit-learn 1.3.
Missing value support for SurvivalTree.
A reduced memory mode for RandomSurvivalForest, ExtraSurvivalTrees, and SurvivalTree.
Support for predict_cumulative_hazard_function() and predict_survival_function() in Stacking.

Missing Values Support in SurvivalTree

Based on the missing value support in scikit-learn 1.3, a SurvivalTree can now deal with missing values if it is fit with splitter='best'.

If the training data contained no missing values, then during prediction missing values are mapped to the child node with the most samples:

X, y = load_veterans_lung_cancer()
X_train = np.asarray(X.loc[:, ["Karnofsky_score"]], dtype=np.float32)
est = SurvivalTree(max_depth=1)
est.fit(X_train, y)
X_test = np.array([[np.nan]])
surv_fn = est.predict_survival_function(X_test, return_array=True)
mask = X_train[:, 0] > est.tree_.threshold[0]
km_x, km_y = kaplan_meier_estimator(
y[mask]["Status"], y[mask]["Survival_in_days"]
)
plt.step(km_x, km_y, where="post", linewidth=5)
plt.step(
est.unique_times_, surv_fn[0], where="post", linewidth=3, linestyle="dotted"
)
plt.ylim(0, 1)

If a tree is fit to training data with missing values, the splitter will evaluate each split with all samples with missing values going to the left or the right child node.

X, y = load_veterans_lung_cancer()
X_train = np.asarray(X.loc[:, ["Age_in_years"]], dtype=np.float32)
X_train[-50:, :] = np.nan
est = SurvivalTree(max_depth=1)
est.fit(X_train, y)
X_test = np.array([[np.nan]])
surv_fn = est.predict_survival_function(X_test, return_array=True)
mask = X_train[:, 0] > est.tree_.threshold[0]
mask |= np.isnan(X_train[:, 0])
km_x, km_y = kaplan_meier_estimator(
y[mask]["Status"], y[mask]["Survival_in_days"]
)
plt.step(km_x, km_y, where="post", linewidth=5)
plt.step(
est.unique_times_, surv_fn[0], where="post", linewidth=3, linestyle="dotted"
)
plt.ylim(0, 1)

These rules are identical to those of scikit-learn’s missing value support.

Low-memory Mode for SurvivalTree and RandomSurvivalForest

The last release already saw performance improvments to SurvivalTree and RandomSurvivalForest. This release adds the low_memory option to RandomSurvivalForest, ExtraSurvivalTrees, and SurvivalTree.

If low-memory mode is disabled, which is the default, calling predict on a sample will require memory in the order of unique event times in the training data, because the cumulative hazard function is computed as an intermediate value. If low-memory mode is enabled, then the risk score is computed directly, without computing the cumulative hazard function. However, low-memory mode disables using predict_cumulative_hazard_function and predict_survival_function.

Install

Pre-built conda packages are available for Linux, macOS, and Windows, either

via pip:

pip install scikit-survival

or via conda

 conda install -c sebp scikit-survival

scikit-survival 0.21.0 released

Sun, 11 Jun 2023 18:43:30 +0200

Today marks the release of scikit-survival 0.21.0. This release features some exciting new features and significant performance improvements:

Pointwise confidence intervals for the Kaplan-Meier estimator.
Early stopping in GradientBoostingSurvivalAnalysis.
Improved performance of fitting SurvivalTree and RandomSurvivalForest.
Reduced memory footprint of concordance_index_censored.

Pointwise Confidence Intervals for the Kaplan-Meier Estimator

kaplan_meier_estimator() can now estimate pointwise confidence intervals by specifying the conf_type parameter.

import matplotlib.pyplot as plt
from sksurv.datasets import load_veterans_lung_cancer
from sksurv.nonparametric import kaplan_meier_estimator
_, y = load_veterans_lung_cancer()
time, survival_prob, conf_int = kaplan_meier_estimator(
y["Status"], y["Survival_in_days"], conf_type="log-log"
)
plt.step(time, survival_prob, where="post")
plt.fill_between(time, conf_int[0], conf_int[1], alpha=0.25, step="post")
plt.ylim(0, 1)
plt.ylabel("est. probability of survival $\hat{S}(t)$")
plt.xlabel("time $t$")

Kaplan-Meier curve with pointwise confidence intervals.

Early Stopping in GradientBoostingSurvivalAnalysis

Early stopping enables us to determine when the model is sufficiently complex. This is usually done by continuously evaluating the model on held-out data. For GradientBoostingSurvivalAnalysis, the easiest way to achieve this is by setting n_iter_no_change and optionally validation_fraction (defaults to 0.1).

from sksurv.datasets import load_whas500
from sksurv.ensemble import GradientBoostingSurvivalAnalysis
X, y = load_whas500()
model = GradientBoostingSurvivalAnalysis(
n_estimators=1000, max_depth=2, subsample=0.8, n_iter_no_change=10, random_state=0,
)
model.fit(X, y)
print(model.n_estimators_)

In this example, model.n_estimators_ indicates that fitting stopped after 73 iterations, instead of the maximum 1000 iterations.

Alternatively, one can provide a custom callback function to the fit method. If the callback returns True, training is stopped.

model = GradientBoostingSurvivalAnalysis(
n_estimators=1000, max_depth=2, subsample=0.8, random_state=0,
)
def early_stopping_monitor(iteration, model, args):
"""Stop training if there was no improvement in the last 10 iterations"""
start = max(0, iteration - 10)
end = iteration + 1
oob_improvement = model.oob_improvement_[start:end]
return all(oob_improvement < 0)
model.fit(X, y, monitor=early_stopping_monitor)
print(model.n_estimators_)

In the example above, early stopping is determined by checking the last 10 entries of the oob_improvement_ attribute. It contains the improvement in loss on the out-of-bag samples relative to the previous iteration. This requires setting subsample to a value smaller 1, here 0.8. Using this approach, training stopped after 114 iterations.

Improved Performance of SurvivalTree and RandomSurvivalForest

Another exciting feature of scikit-survival 0.21.0 is due to a re-write of the training routine of SurvivalTree. This results in roughly 3x faster training times.

Runtime comparison of fitting SurvivalTree.

The plot above compares the time required to fit a single SurvivalTree on data with 25 features and varying number of samples. The performance difference becomes notable for data with 1000 samples and above.

Note that this improvement also speeds-up fitting RandomSurvivalForest and ExtraSurvivalTrees.

Improved concordance index

Another performance improvement is due to Christine Poerschke who significantly reduced the memory footprint of concordance_index_censored(). With scikit-survival 0.21.0, memory usage scales linear, instead of quadratic, in the number of samples, making performance evaluation on large datasets much more manageable.

For a full list of changes in scikit-survival 0.21.0, please see the release notes.

Install

Pre-built conda packages are available for Linux, macOS (Intel), and Windows, either

via pip:

pip install scikit-survival

or via conda

 conda install -c sebp scikit-survival

scikit-survival 0.18.0 released

Mon, 15 Aug 2022 17:18:26 +0200

I’m pleased to announce the release of scikit-survival 0.18.0, which adds support for scikit-learn 1.1.

In addition, this release adds the return_array argument to all models providing predict_survival_function and predict_cumulative_hazard_function. That means you can now choose, whether you want to have the survival (cumulative hazard function) automatically evaluated at the unique event times. This is particular useful for plotting. Previously, you would have to evaluate each survival function before plotting:

estimator = CoxPHSurvivalAnalysis()
estimator.fit(X_train, y_train)
pred_surv = estimator.predict_survival_function(
X_test
)
times = pred_surv[0].x
for surv_func in pred_surv:
plt.step(times, surv_func(times), where="post")

Now, you can pass return_array=True and directly get probabilities of the survival function:

estimator = CoxPHSurvivalAnalysis()
estimator.fit(X_train, y_train)
pred_surv_probs = estimator.predict_survival_function(
X_test, return_array=True
)
times = estimator.event_times_
for probs in pred_surv_probs:
plt.step(times, probs, where="post")

Finally, support for Python 3.7 has been dropped and the minimal required version of the following dependencies are raised:

numpy 1.17.3
pandas 1.0.5
scikit-learn 1.1.0
scipy 1.3.2

For a full list of changes in scikit-survival 0.18.0, please see the release notes.

Install

Pre-built conda packages are available for Linux, macOS (Intel), and Windows, either

via pip:

pip install scikit-survival

or via conda

 conda install -c sebp scikit-survival

scikit-survival 0.17.2 released

Mon, 25 Apr 2022 20:14:19 +0200

I’m pleased to announce the release of scikit-survival 0.17.2. This release fixes several small issues with packaging scikit-survival and the documentation. For a full list of changes in scikit-survival 0.17.2, please see the release notes.

Most notably, binary wheels are now available for Linux, Windows, and macOS (Intel). This has been possible thanks to the cibuildwheel build tool, which makes it incredible easy to use GitHub Actions for building those wheels for multiple versions of Python. Therefore, you can now use pip without building everything from source by simply running

pip install scikit-survival

As before, pre-built conda packages are available too, by running

 conda install -c sebp scikit-survival

Support for Apple Silicon M1

Currently, there are no pre-built packages for Mac with Apple Silicon M1 hardware (also known as macos/arm64). There are two main reasons for that. The biggest problem is the lack of CI servers that run on Apple Silicon M1. This makes it difficult to systematically test scikit-survival on such hardware. Second, some of scikit-survival’s dependencies do not offer wheels for macos/arm64 yet, namely ecos and osqp.

However, conda-forge figured out a way to cross-compile packages, and do offer scikit-survival for macos/arm64. I tried to adapt their conda recipe, but failed to achieve a working cross-compilation process so far. Cross-compiling with cibuildwheel would be an alternative, but currently doesn’t make much sense if run-time dependencies ecos and osqp do not provide wheels for macos/arm64. I hope these issues can be resolved in the near future.

scikit-survival 0.17 released

Sun, 09 Jan 2022 16:45:38 +0100

This release adds support for scikit-learn 1.0, which includes support for feature names. If you pass a pandas dataframe to fit, the estimator will set a feature_names_in_ attribute containing the feature names. When a dataframe is passed to predict, it is checked that the column names are consistent with those passed to fit. The example below illustrates this feature.

For a full list of changes in scikit-survival 0.17.0, please see the release notes.

Installation

Pre-built conda packages are available for Linux, macOS, and Windows via

 conda install -c sebp scikit-survival

Alternatively, scikit-survival can be installed from source following these instructions.

Feature Names Support

Prior to scikit-survival 0.17, you could pass a pandas dataframe to estimators’ fit and predict methods, but the estimator was oblivious to the feature names accessible via the dataframe’s columns attribute. With scikit-survival 0.17, and thanks to scikit-learn 1.0, feature names will be considered when a dataframe is passed.

Let’s illustrate feature names support using the Veteran’s Lung Cancer dataset.

from sksurv.datasets import load_veterans_lung_cancer
X, y = load_veterans_lung_cancer()
X.head(3)

	Age_in_years	Celltype	Karnofsky_score	Months_from_Diagnosis	Prior_therapy	Treatment
0	69.0	squamous	60.0	7.0	no	standard
1	64.0	squamous	70.0	5.0	yes	standard
2	38.0	squamous	60.0	3.0	no	standard

The original data has 6 features, three of which contain strings, which we encode as numeric using OneHotEncoder.

from sksurv.preprocessing import OneHotEncoder
transform = OneHotEncoder()
Xt = transform.fit_transform(X)

Transforms now have a get_feature_names_out() method, which will return the name of features after the transformation.

transform.get_feature_names_out()

array(['Age_in_years', 'Celltype=large', 'Celltype=smallcell',
'Celltype=squamous', 'Karnofsky_score', 'Months_from_Diagnosis',
'Prior_therapy=yes', 'Treatment=test'], dtype=object)

The transformed data returned by OneHotEncoder is again a dataframe, which can be used to fit Cox’s proportional hazards model.

from sksurv.linear_model import CoxPHSurvivalAnalysis
model = CoxPHSurvivalAnalysis().fit(Xt, y)

Since we passed a dataframe, the feature_names_in_ attribute will contain the names of the dataframe used when calling fit.

model.feature_names_in_

array(['Age_in_years', 'Celltype=large', 'Celltype=smallcell',
'Celltype=squamous', 'Karnofsky_score', 'Months_from_Diagnosis',
'Prior_therapy=yes', 'Treatment=test'], dtype=object)

This is used during prediction to check that the data matches the format of the training data. For instance, when passing a raw numpy array instead of a dataframe, a warning will be issued.

pred = model.predict(Xt.values)

UserWarning: X does not have valid feature names, but CoxPHSurvivalAnalysis was fitted with feature names

Moreover, it will also check that the order of columns matches.

X_reordered = pd.concat(
(Xt.drop("Age_in_years", axis=1), Xt.loc[:, "Age_in_years"]),
axis=1
)
pred = model.predict(X_reordered)

FutureWarning: The feature names should match those that were passed during fit. Starting version 1.2, an error will be raised.
Feature names must be in the same order as they were in fit.

For more details on feature names support, have a look at the scikit-learn release highlights.