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[dask] Allow empty data matrix in AFT survival (#6379)

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* [dask] Allow empty data matrix in AFT survival

* Add unit test
This commit is contained in:
Philip Hyunsu Cho 2020-11-12 17:49:58 -08:00 committed by GitHub
parent 5a33c2f3a0
commit e5193c21a1
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3 changed files with 11 additions and 6 deletions
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4
src/metric/survival_metric.cu
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@ -206,10 +206,6 @@ struct EvalEWiseSurvivalBase : public Metric {
bst_float Eval(const HostDeviceVector<bst_float>& preds, bst_float Eval(const HostDeviceVector<bst_float>& preds,
const MetaInfo& info, const MetaInfo& info,
bool distributed) override { bool distributed) override {
CHECK_NE(info.labels_lower_bound_.Size(), 0U)
<< "labels_lower_bound cannot be empty";
CHECK_NE(info.labels_upper_bound_.Size(), 0U)
<< "labels_upper_bound cannot be empty";
CHECK_EQ(preds.Size(), info.labels_lower_bound_.Size()); CHECK_EQ(preds.Size(), info.labels_lower_bound_.Size());
CHECK_EQ(preds.Size(), info.labels_upper_bound_.Size()); CHECK_EQ(preds.Size(), info.labels_upper_bound_.Size());

10
tests/python/test_survival.py
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@ -52,6 +52,16 @@ def test_aft_survival_toy_data():
for tree in model_json: for tree in model_json:
assert gather_split_thresholds(tree).issubset({2.5, 3.5, 4.5}) assert gather_split_thresholds(tree).issubset({2.5, 3.5, 4.5})
def test_aft_empty_dmatrix():
X = np.array([]).reshape((0, 2))
y_lower, y_upper = np.array([]), np.array([])
dtrain = xgb.DMatrix(X)
dtrain.set_info(label_lower_bound=y_lower, label_upper_bound=y_upper)
bst = xgb.train({'objective': 'survival:aft', 'tree_method': 'hist'},
dtrain, num_boost_round=2, evals=[(dtrain, 'train')])
@pytest.mark.skipif(**tm.no_pandas()) @pytest.mark.skipif(**tm.no_pandas())
def test_aft_survival_demo_data(): def test_aft_survival_demo_data():
import pandas as pd import pandas as pd

3
tests/python/test_with_dask.py
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@ -594,7 +594,6 @@ def test_predict_with_meta(client):
def run_aft_survival(client, dmatrix_t): def run_aft_survival(client, dmatrix_t):
# survival doesn't handle empty dataset well.
df = dd.read_csv(os.path.join(tm.PROJECT_ROOT, 'demo', 'data', df = dd.read_csv(os.path.join(tm.PROJECT_ROOT, 'demo', 'data',
'veterans_lung_cancer.csv')) 'veterans_lung_cancer.csv'))
y_lower_bound = df['Survival_label_lower_bound'] y_lower_bound = df['Survival_label_lower_bound']
@ -632,7 +631,7 @@ def run_aft_survival(client, dmatrix_t):
def test_aft_survival(): def test_aft_survival():
with LocalCluster(n_workers=1) as cluster: with LocalCluster(n_workers=kWorkers) as cluster:
with Client(cluster) as client: with Client(cluster) as client:
run_aft_survival(client, DaskDMatrix) run_aft_survival(client, DaskDMatrix)