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May 17, 2023 14:41
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Benchmarking random forest with missing values
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"""Instructions | |
1. Build this PR and run: | |
```bash | |
python bench_missing_rf.py bench ~/bench_results_rf pr | |
``` | |
2. On main run: | |
```bash | |
python bench_missing_rf.py bench ~/bench_results_rf main | |
``` | |
3. Plotting | |
```bash | |
python bench_missing_rf.py plot ~/bench_results_rf pr main results_image.png | |
``` | |
""" | |
from functools import partial | |
import argparse | |
from time import perf_counter | |
from statistics import mean, stdev | |
from itertools import product | |
import csv | |
from pathlib import Path | |
# from sklearn.tree import DecisionTreeRegressor, DecisionTreeClassifier | |
from sklearn.ensemble import RandomForestClassifier, RandomForestRegressor | |
from sklearn.datasets import make_classification, make_regression, make_low_rank_matrix | |
import numpy as np | |
from scipy.sparse import csc_matrix | |
def make_poisson_data(n_samples, n_features=50, random_state=0, has_missing=False): | |
rng = np.random.RandomState(random_state) | |
X = make_low_rank_matrix( | |
n_samples=n_samples, n_features=n_features, random_state=rng | |
) | |
coef = rng.uniform(low=-2, high=2, size=n_features) / np.max(X, axis=0) | |
y = rng.poisson(lam=np.exp(X @ coef)) | |
if has_missing: | |
missing_mask = rng.choice([True, False], size=X.shape, p=[0.1, 0.9]) | |
X[missing_mask] = np.nan | |
return X, y | |
def make_low_card_data(n_samples, n_features=50, random_state=0, has_missing=False): | |
rng = np.random.RandomState(random_state) | |
X = rng.choice([0.0, 1.0, 2.0], size=(n_samples, n_features)) | |
y = rng.choice([0, 1], size=n_samples) | |
if has_missing: | |
missing_mask = rng.choice([True, False], size=X.shape, p=[0.1, 0.9]) | |
X[missing_mask] = np.nan | |
return X, y | |
def make_regression_custom(*args, has_missing=False, random_state=None, **kwargs): | |
X, y = make_regression(*args, random_state=random_state, **kwargs) | |
rng = np.random.RandomState() | |
if has_missing: | |
rng = np.random.RandomState(random_state) | |
missing_mask = rng.choice([True, False], size=X.shape, p=[0.1, 0.9]) | |
X[missing_mask] = np.nan | |
return X, y | |
def make_classification_custom(*args, has_missing=False, random_state=None, **kwargs): | |
X, y = make_classification(*args, random_state=random_state, **kwargs) | |
rng = np.random.RandomState() | |
if has_missing: | |
rng = np.random.RandomState(random_state) | |
missing_mask = rng.choice([True, False], size=X.shape, p=[0.1, 0.9]) | |
X[missing_mask] = np.nan | |
return X, y | |
N_REPEATS = 20 | |
benchmark_config = [ | |
( | |
RandomForestRegressor, | |
list( | |
product( | |
["squared_error"], | |
[ | |
partial(make_regression_custom, n_targets=2), | |
make_low_card_data, | |
], | |
[40_000], | |
["dense"], | |
[False], | |
) | |
), | |
), | |
( | |
RandomForestRegressor, | |
list( | |
product( | |
["poisson"], | |
[make_poisson_data], | |
[40_000], | |
["dense"], | |
[False], | |
) | |
), | |
), | |
( | |
RandomForestClassifier, | |
list( | |
product( | |
["gini", "entropy"], | |
[ | |
partial(make_classification_custom, n_informative=10, n_classes=5), | |
make_low_card_data, | |
], | |
[40_000], | |
["dense"], | |
[False], | |
) | |
), | |
), | |
] | |
def bench(args): | |
bench_results, branch = args.bench_results, args.branch | |
results_dir = Path(bench_results) | |
results_dir.mkdir(exist_ok=True) | |
results_path = results_dir / f"{branch}.csv" | |
with results_path.open("w") as f: | |
writer = csv.DictWriter( | |
f, | |
fieldnames=[ | |
"criterion", | |
"n_samples", | |
"make_data", | |
"container", | |
"splitter", | |
"has_missing", | |
"n_repeat", | |
"duration", | |
], | |
) | |
writer.writeheader() | |
for Klass, items in benchmark_config: | |
for config in items: | |
( | |
criterion, | |
make_data, | |
n_samples, | |
container, | |
has_missing, | |
) = config | |
if isinstance(make_data, partial): | |
make_data_str = make_data.func.__name__ | |
else: | |
make_data_str = make_data.__name__ | |
default_config = { | |
"criterion": criterion, | |
"n_samples": n_samples, | |
"make_data": make_data_str, | |
"container": container, | |
"has_missing": has_missing, | |
} | |
combine_config = " ".join(f"{k}={v}" for k, v in default_config.items()) | |
klass_results = [] | |
for n_repeat in range(N_REPEATS): | |
X, y = make_data( | |
n_samples=n_samples, | |
random_state=n_repeat, | |
n_features=100, | |
has_missing=has_missing, | |
) | |
tree = Klass(random_state=n_repeat, criterion=criterion, n_jobs=8) | |
if container == "sparse": | |
X = csc_matrix(X, dtype=np.float32) | |
start = perf_counter() | |
tree.fit(X, y) | |
duration = perf_counter() - start | |
klass_results.append(duration) | |
writer.writerow( | |
{ | |
**default_config, | |
**{ | |
"n_repeat": n_repeat, | |
"duration": duration, | |
}, | |
} | |
) | |
results_mean, results_stdev = mean(klass_results), stdev(klass_results) | |
print( | |
f"{combine_config} with {results_mean:.3f} +/- {results_stdev:.3f}" | |
) | |
def plot(args): | |
import matplotlib.pyplot as plt | |
import pandas as pd | |
import seaborn as sns | |
results_path = Path(args.bench_results) | |
pr_path = results_path / f"{args.pr_name}.csv" | |
main_path = results_path / f"{args.main_name}.csv" | |
image_path = results_path / args.image_path | |
df_pr = pd.read_csv(pr_path).assign(branch=args.pr_name) | |
df_main = pd.read_csv(main_path).assign(branch=args.main_name) | |
df_all = pd.concat((df_pr, df_main), ignore_index=True) | |
df_all = df_all.assign( | |
make_data=df_all["make_data"] | |
.str.replace("_custom", "") | |
.str.replace("make_", "") | |
.str.replace("_data", "") | |
) | |
gb = df_all.groupby(["criterion", "make_data"]) | |
groups = gb.groups | |
n_rows, n_cols = 2, 4 | |
fig, axes = plt.subplots(n_rows, n_cols, figsize=(12, 8), constrained_layout=True) | |
axes_flat = axes.ravel() | |
for i, (keys, idx) in enumerate(groups.items()): | |
ax = axes_flat[i] | |
ax.set_title(" | ".join(keys)) | |
sns.boxplot(data=df_all.loc[idx], y="duration", x="branch", ax=ax) | |
if i % n_cols != 0: | |
ax.set_ylabel("") | |
axes_flat[-1].set_visible(False) | |
fig.savefig(image_path) | |
print(f"Saved image to {image_path}") | |
if __name__ == "__main__": | |
parser = argparse.ArgumentParser() | |
subparsers = parser.add_subparsers() | |
bench_parser = subparsers.add_parser("bench") | |
bench_parser.add_argument("bench_results") | |
bench_parser.add_argument("branch") | |
bench_parser.set_defaults(func=bench) | |
plot_parser = subparsers.add_parser("plot") | |
plot_parser.add_argument("bench_results") | |
plot_parser.add_argument("pr_name") | |
plot_parser.add_argument("main_name") | |
plot_parser.add_argument("image_path") | |
plot_parser.set_defaults(func=plot) | |
args = parser.parse_args() | |
args.func(args) |
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