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https://github.com/eurobios-mews-labs/survival-trees
https://github.com/eurobios-mews-labs/survival-trees
Last synced: 6 days ago
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- Host: GitHub
- URL: https://github.com/eurobios-mews-labs/survival-trees
- Owner: eurobios-mews-labs
- License: other
- Created: 2022-04-06T15:02:05.000Z (over 2 years ago)
- Default Branch: master
- Last Pushed: 2024-06-24T13:50:35.000Z (5 months ago)
- Last Synced: 2024-06-24T15:32:54.093Z (5 months ago)
- Language: Python
- Size: 1.13 MB
- Stars: 5
- Watchers: 1
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# LTRC Survival Forest
### Install notice
To install the package you can run
```shell
python -m pip install git+https://eurobios-mews-labs/survival-trees.git
```
### Usage
```python
import numpy as np
from survival_trees import RandomForestLTRCFitter
from survival_trees.metric import time_dependent_auc
from lifelines import datasets
from sklearn.model_selection import train_test_split
# load dataset
data = datasets.load_larynx().dropna()
data["entry_date"] = data["age"]
data["time"] += data["entry_date"]
y = data[["entry_date", "time", "death"]]
X = data.drop(columns=y.columns.tolist())
# split dataset
x_train, x_test, y_train, y_test = train_test_split(
X, y, train_size=0.7)
# initialise and fit model
model = RandomForestLTRCFitter(
n_estimators=30,
min_impurity_decrease=0.0000001,
min_samples_leaf=3,
max_samples=0.89)
model.fit(
data.loc[x_train.index],
entry_col="entry_date",
duration_col="time",
event_col='death'
)
survival_function = - np.log(model.predict_cumulative_hazard(
x_test).astype(float)).T
auc_cd = time_dependent_auc(
- survival_function,
event_observed=y_test.loc[survival_function.index].iloc[:, 2],
censoring_time=y_test.loc[survival_function.index].iloc[:, 1])
```
## Benchmark
## References
* https://academic.oup.com/biostatistics/article/18/2/352/2739324
## Requirements
Having `R` compiler installed
## Project
This implementation come from an SNCF DTIPG project and is developped and maintained by Eurobios Scientific Computation
Branch and SNCF IR
## Authors
- Vincent LAURENT