def test_load_features_duplicate_col_name():
df = pd.DataFrame()
df['a'] = np.arange(100).astype(float)
df['b'] = np.arange(100).astype(int)
df['c'] = np.arange(100).astype(int)
with get_temp_directory() as tmp:
fs.save_feature(df[['a', 'b']], 0, tmp)
fs.save_feature(df[['b', 'c']], 1, tmp)
fs.save_feature(df[['b', 'a']], 'X', tmp)
df_loaded = fs.load_features(None, [0, 1, 'X'], tmp, rename_duplicate=True)
assert list(df_loaded.columns) == ['a', 'b', 'b_1', 'c', 'b_X', 'a_X']
df_loaded = fs.load_features(None, [0, 1, 'X'], tmp, rename_duplicate=False)
assert list(df_loaded.columns) == ['a', 'b', 'b', 'c', 'b', 'a']
def test_load_features():
df = pd.DataFrame()
df['a'] = np.arange(100).astype(float)
df['b'] = np.arange(100).astype(int)
df['c'] = np.arange(100).astype(int)
with get_temp_directory() as tmp:
fs.save_feature(df[['b']], 0, tmp)
fs.save_feature(df[['c']], 1, tmp)
df_loaded = fs.load_features(df[['a']], [0, 1], tmp)
assert_frame_equal(df, df_loaded)
def test_load_features_no_base():
df = pd.DataFrame()
df['a'] = np.arange(100).astype(float)
df['b'] = np.arange(100).astype(int)
df['c'] = np.arange(100).astype(int)
with get_temp_directory() as tmp:
fs.save_feature(df[['b']], 0, tmp)
fs.save_feature(df[['c']], 1, tmp)
fs.save_feature(df[['a']], '2', tmp)
df_loaded = fs.load_features(None, [0, 1, '2'], tmp)
assert list(df_loaded.columns) == ['b', 'c', 'a']
def run_experiment(model_params: Dict[str, Any],
X_train: pd.DataFrame,
y: pd.Series,
X_test: Optional[pd.DataFrame] = None,
logging_directory: str = 'output/{time}',
if_exists: str = 'error',
eval_func: Optional[Callable] = None,
algorithm_type: Union[str, Type[BaseEstimator]] = 'lgbm',
fit_params: Optional[Union[Dict[str, Any],
Callable]] = None,
cv: Optional[Union[int, Iterable,
BaseCrossValidator]] = None,
groups: Optional[pd.Series] = None,
categorical_feature: Optional[List[str]] = None,
sample_submission: Optional[pd.DataFrame] = None,
submission_filename: Optional[str] = None,
type_of_target: str = 'auto',
feature_list: Optional[List[Union[int, str]]] = None,
feature_directory: Optional[str] = None,
inherit_experiment: Optional[Experiment] = None,
with_auto_hpo: bool = False,
with_auto_prep: bool = False,
with_mlflow: bool = False):
"""
Evaluate metrics by cross-validation and stores result
(log, oof prediction, test prediction, feature importance plot and submission file)
under the directory specified.
One of the following estimators are used (automatically dispatched by ``type_of_target(y)`` and ``gbdt_type``).
* LGBMClassifier
* LGBMRegressor
* CatBoostClassifier
* CatBoostRegressor
The output files are laid out as follows:
.. code-block:: none
<logging_directory>/
log.txt <== Logging file
importance.png <== Feature importance plot generated by nyaggle.util.plot_importance
oof_prediction.npy <== Out of fold prediction in numpy array format
test_prediction.npy <== Test prediction in numpy array format
submission.csv <== Submission csv file
metrics.json <== Metrics
params.json <== Parameters
models/
fold1 <== The trained model in fold 1
...
Args:
model_params:
Parameters passed to the constructor of the classifier/regressor object (i.e. LGBMRegressor).
X_train:
Training data. Categorical feature should be casted to pandas categorical type or encoded to integer.
y:
Target
X_test:
Test data (Optional). If specified, prediction on the test data is performed using ensemble of models.
logging_directory:
Path to directory where output of experiment is stored.
if_exists:
How to behave if the logging directory already exists.
- error: Raise a ValueError.
- replace: Delete logging directory before logging.
- append: Append to exisitng experiment.
- rename: Rename current directory by adding "_1", "_2"... prefix
fit_params:
Parameters passed to the fit method of the estimator. If dict is passed, the same parameter except
eval_set passed for each fold. If callable is passed,
returning value of ``fit_params(fold_id, train_index, test_index)`` will be used for each fold.
eval_func:
Function used for logging and calculation of returning scores.
This parameter isn't passed to GBDT, so you should set objective and eval_metric separately if needed.
If ``eval_func`` is None, ``roc_auc_score`` or ``mean_squared_error`` is used by default.
gbdt_type:
Type of gradient boosting library used. "lgbm" (lightgbm) or "cat" (catboost)
cv:
int, cross-validation generator or an iterable which determines the cross-validation splitting strategy.
- None, to use the default ``KFold(5, random_state=0, shuffle=True)``,
- integer, to specify the number of folds in a ``(Stratified)KFold``,
- CV splitter (the instance of ``BaseCrossValidator``),
- An iterable yielding (train, test) splits as arrays of indices.
groups:
Group labels for the samples. Only used in conjunction with a “Group” cv instance (e.g., ``GroupKFold``).
sample_submission:
A sample dataframe alined with test data (Usually in Kaggle, it is available as sample_submission.csv).
The submission file will be created with the same schema as this dataframe.
submission_filename:
The name of submission file will be created under logging directory. If ``None``, the basename of the logging
directory will be used as a filename.
categorical_feature:
List of categorical column names. If ``None``, categorical columns are automatically determined by dtype.
type_of_target:
The type of target variable. If ``auto``, type is inferred by ``sklearn.utils.multiclass.type_of_target``.
Otherwise, ``binary``, ``continuous``, or ``multiclass`` are supported.
feature_list:
The list of feature ids saved through nyaggle.feature_store module.
feature_directory:
The location of features stored. Only used if feature_list is not empty.
inherit_experiment:
An experiment object which is used to log results. if not ``None``, all logs in this function are treated
as a part of this experiment.
with_auto_prep:
If True, the input datasets will be copied and automatic preprocessing will be performed on them.
For example, if ``gbdt_type = 'cat'``, all missing values in categorical features will be filled.
with_auto_hpo:
If True, model parameters will be automatically updated using optuna (only available in lightgbm).
with_mlflow:
If True, `mlflow tracking <https://www.mlflow.org/docs/latest/tracking.html>`_ is used.
One instance of ``nyaggle.experiment.Experiment`` corresponds to one run in mlflow.
Note that all output
mlflow's directory (``mlruns`` by default).
:return:
Namedtuple with following members
* oof_prediction:
numpy array, shape (len(X_train),) Predicted value on Out-of-Fold validation data.
* test_prediction:
numpy array, shape (len(X_test),) Predicted value on test data. ``None`` if X_test is ``None``
* metrics:
list of float, shape(nfolds+1) ``scores[i]`` denotes validation score in i-th fold.
``scores[-1]`` is overall score.
* models:
list of objects, shape(nfolds) Trained models for each folds.
* importance:
list of pd.DataFrame, feature importance for each fold (type="gain").
* time:
Training time in seconds.
* submit_df:
The dataframe saved as submission.csv
"""
start_time = time.time()
cv = check_cv(cv, y)
if feature_list:
X = pd.concat([X_train, X_test]) if X_test is not None else X_train
X.reset_index(drop=True, inplace=True)
X = load_features(X, feature_list, directory=feature_directory)
ntrain = len(X_train)
X_train, X_test = X.iloc[:ntrain, :], X.iloc[ntrain:, :].reset_index(
drop=True)
_check_input(X_train, y, X_test)
if categorical_feature is None:
categorical_feature = [
c for c in X_train.columns
if X_train[c].dtype.name in ['object', 'category']
]
if type_of_target == 'auto':
type_of_target = multiclass.type_of_target(y)
model_type, eval_func, cat_param_name = _dispatch_models(
algorithm_type, type_of_target, eval_func)
if with_auto_prep:
assert algorithm_type in (
'cat', 'xgb', 'lgbm'), "with_auto_prep is only supported for gbdt"
X_train, X_test = autoprep_gbdt(algorithm_type, X_train, X_test,
categorical_feature)
logging_directory = logging_directory.format(
time=datetime.now().strftime('%Y%m%d_%H%M%S'))
if inherit_experiment is not None:
experiment = ExpeimentProxy(inherit_experiment)
else:
experiment = Experiment(logging_directory,
if_exists=if_exists,
with_mlflow=with_mlflow)
with experiment as exp:
exp.log('Algorithm: {}'.format(algorithm_type))
exp.log('Experiment: {}'.format(exp.logging_directory))
exp.log('Params: {}'.format(model_params))
exp.log('Features: {}'.format(list(X_train.columns)))
exp.log_param('algorithm_type', algorithm_type)
exp.log_param('num_features', X_train.shape[1])
if callable(fit_params):
exp.log_param('fit_params', str(fit_params))
else:
exp.log_dict('fit_params', fit_params)
exp.log_dict('model_params', model_params)
if feature_list is not None:
exp.log_param('features', feature_list)
if with_auto_hpo:
assert algorithm_type == 'lgbm', 'auto-tuning is only supported for LightGBM'
model_params = find_best_lgbm_parameter(
model_params,
X_train,
y,
cv=cv,
groups=groups,
type_of_target=type_of_target)
exp.log_param('model_params_tuned', model_params)
exp.log('Categorical: {}'.format(categorical_feature))
models = [model_type(**model_params) for _ in range(cv.get_n_splits())]
if fit_params is None:
fit_params = {}
if cat_param_name is not None and not callable(
fit_params) and cat_param_name not in fit_params:
fit_params[cat_param_name] = categorical_feature
if isinstance(fit_params, Dict):
exp.log_params(fit_params)
result = cross_validate(models,
X_train=X_train,
y=y,
X_test=X_test,
cv=cv,
groups=groups,
logger=exp.get_logger(),
eval_func=eval_func,
fit_params=fit_params,
type_of_target=type_of_target)
# save oof
exp.log_numpy('oof_prediction', result.oof_prediction)
exp.log_numpy('test_prediction', result.test_prediction)
for i in range(cv.get_n_splits()):
exp.log_metric('Fold {}'.format(i + 1), result.scores[i])
exp.log_metric('Overall', result.scores[-1])
# save importance plot
if result.importance:
importance = pd.concat(result.importance)
plot_file_path = os.path.join(exp.logging_directory,
'importance.png')
plot_importance(importance, plot_file_path)
exp.log_artifact(plot_file_path)
# save trained model
for i, model in enumerate(models):
_save_model(model, exp.logging_directory, i + 1, exp)
# save submission.csv
submit_df = None
if X_test is not None:
submit_df = make_submission_df(result.test_prediction,
sample_submission, y)
exp.log_dataframe(
submission_filename or os.path.basename(exp.logging_directory),
submit_df, 'csv')
elapsed_time = time.time() - start_time
return ExperimentResult(result.oof_prediction, result.test_prediction,
result.scores, models, result.importance,
elapsed_time, submit_df)
import pandas as pd
from nyaggle.experiment import run_experiment
from nyaggle.feature_store import load_features, load_feature
from sklearn.metrics import average_precision_score
from src.utils import prauc, get_folds
submission = pd.read_csv("input/atmaCup5__sample_submission.csv")
all_df = load_feature("all", "working")
data = load_features(
all_df,
feature_names=[
"fitting",
"peak_around",
"intensity_stats",
"savgol_peak",
"spec_percentile",
"fitting_combination",
],
ignore_columns=["spectrum_id", "spectrum_filename", "chip_id"],
)
train = data[data.target.notnull()].copy()
test = data[data.target.isnull()].copy()
target_col = "target"
drop_cols = ["spectrum_id", "spectrum_filename", "chip_id"]
X_train = train.drop(drop_cols + [target_col], axis=1)
y_train = train[target_col]
X_test = test.drop(drop_cols + [target_col], axis=1)
