dslighting 1.7.1__py3-none-any.whl → 1.7.6__py3-none-any.whl

mlebench/competitions/ethanol-concentration/prepare.py

@@ -0,0 +1,90 @@
+import pandas as pd
+import numpy as np
+import sys
+from pathlib import Path
+
+
+def prepare(raw: Path, public: Path, private: Path):
+    """
+    Prepare the ethanol-concentration dataset for the benchmark.
+
+    This function converts the .ts time series files to numpy arrays,
+    so that public directory only contains data, not data loading code.
+
+    Args:
+        raw: Path to raw data directory (contains EthanolConcentration_TRAIN.ts and EthanolConcentration_TEST.ts)
+        public: Path to public directory (visible to participants)
+        private: Path to private directory (hidden from participants, used for grading)
+    """
+    # Load test data to extract labels for grading
+    try:
+        # Add raw directory to path temporarily to import dataset module
+        sys.path.insert(0, str(raw))
+
+        # Use the local dataset module to load data
+        from dataset import get_dataset
+
+        # Change to raw directory to load data
+        import os
+        original_dir = os.getcwd()
+        os.chdir(str(raw))
+
+        try:
+            # Load train and test datasets
+            X_train, y_train = get_dataset('TRAIN')
+            X_test, y_test = get_dataset('TEST')
+
+            print(f"Loaded training data: X_train.shape = {X_train.shape}, y_train.shape = {y_train.shape}")
+            print(f"Loaded test data: X_test.shape = {X_test.shape}, y_test.shape = {y_test.shape}")
+            print(f"Number of unique labels: {len(np.unique(y_train))}")
+
+            # Save training data as numpy arrays in public directory
+            np.save(public / "train_data.npy", X_train)
+            np.save(public / "train_labels.npy", y_train.flatten())
+
+            # Save test data (without labels) in public directory
+            np.save(public / "test_data.npy", X_test)
+
+            # Create test labels dataframe for grading (private)
+            test_labels_df = pd.DataFrame(
+                {"id": range(len(y_test)), "label": y_test.flatten()}
+            )
+            test_labels_df.to_csv(private / "test_labels.csv", index=False)
+
+            # Create sample submission file
+            sample_submission = pd.DataFrame(
+                {"id": range(len(y_test)), "label": 0}  # Default to class 0
+            )
+            sample_submission.to_csv(public / "sample_submission.csv", index=False)
+
+            print(f"Data preparation completed:")
+            print(f"  - Training: {len(X_train)} samples")
+            print(f"  - Test: {len(X_test)} samples")
+            print(f"  - Sequence length: {X_train.shape[1]}")
+            print(f"  - Feature dimension: {X_train.shape[2]}")
+            print(f"  - Number of classes: {len(np.unique(y_train))}")
+
+        finally:
+            os.chdir(original_dir)
+            sys.path.remove(str(raw))
+
+    except Exception as e:
+        print(f"Error loading test labels: {e}")
+        import traceback
+        traceback.print_exc()
+        # Fallback: create dummy files if loading fails
+        print("Creating dummy submission files...")
+        dummy_df = pd.DataFrame({"id": [0], "label": [0]})
+        dummy_df.to_csv(private / "test_labels.csv", index=False)
+        dummy_df.to_csv(public / "sample_submission.csv", index=False)
+
+    # Validation checks
+    assert (public / "train_data.npy").exists(), "Training data should exist"
+    assert (public / "train_labels.npy").exists(), "Training labels should exist"
+    assert (public / "test_data.npy").exists(), "Test data should exist"
+    assert (private / "test_labels.csv").exists(), "Test labels should exist"
+    assert (public / "sample_submission.csv").exists(), "Sample submission should exist"
+
+    print(f"\nPrepared ethanol-concentration dataset:")
+    print(f"  - Public files: {list(public.glob('*'))}")
+    print(f"  - Private files: {list(private.glob('*'))}")

mlebench/competitions/facebook-recruiting-iii-keyword-extraction/grade.py

@@ -0,0 +1,60 @@
+import pandas as pd
+from pandas import DataFrame
+from scipy.sparse import csr_matrix
+from sklearn.metrics import f1_score
+from sklearn.preprocessing import MultiLabelBinarizer
+
+from mlebench.grade_helpers import InvalidSubmissionError
+from mlebench.utils import get_logger
+
+logger = get_logger(__name__)
+
+
+def grade(submission: DataFrame, answers: DataFrame) -> float:
+    """Grades the submission against the test set."""
+
+    y_true, y_pred = prepare_for_metric(submission, answers)
+    return f1_score(y_true=y_true, y_pred=y_pred, average="micro")
+
+
+def prepare_for_metric(
+    submission: pd.DataFrame, answers: pd.DataFrame
+) -> tuple[csr_matrix, csr_matrix]:
+
+    # Answer checks
+    assert "Id" in answers.columns, "Answers must have an 'Id' column."
+    assert "Tags" in answers.columns, "Answers must have a 'Tags' column."
+
+    # Submission checks
+    if "Id" not in submission.columns:
+        raise InvalidSubmissionError("Submission DataFrame must have an 'Id' column.")
+    if "Tags" not in submission.columns:
+        raise InvalidSubmissionError("Submission DataFrame must have a 'Tags' column.")
+    if len(submission) != len(answers):
+        raise InvalidSubmissionError(
+            "Submission DataFrame must have the same number of rows as the answers DataFrame."
+        )
+
+    # Match order
+    submission = submission.sort_values(by="Id").reset_index(drop=True)
+    answers = answers.sort_values(by="Id").reset_index(drop=True)
+    if (submission["Id"].values != answers["Id"].values).any():
+        raise InvalidSubmissionError("Submission and answers must have matching 'Id's.")
+
+    # Get classes
+    classes = set()
+
+    for tags in answers["Tags"]:
+        if not isinstance(tags, str):
+            logger.warning(f"Tags from answers '{tags}' not of type str! Skipping.")
+            continue
+
+        tags_split = tags.split()
+        classes.update(tags_split)
+
+    # Convert to sparse matrix using MultiLabelBinarizer
+    mlb = MultiLabelBinarizer(classes=sorted(classes), sparse_output=True)
+    y_true = mlb.fit_transform(answers["Tags"].fillna("").str.split())
+    y_pred = mlb.transform(submission["Tags"].fillna("").str.split())
+
+    return y_true, y_pred

mlebench/competitions/facebook-recruiting-iii-keyword-extraction/prepare.py

@@ -0,0 +1,41 @@
+from pathlib import Path
+
+from sklearn.model_selection import train_test_split
+
+from mlebench.utils import extract, get_logger, read_csv
+
+logger = get_logger(__name__)
+
+
+def prepare(raw: Path, public: Path, private: Path) -> None:
+    extract(raw / "Train.zip", raw)
+
+    # Create new train and test from original train set
+    logger.info(f"Creating new train and test sets from {raw}.")
+
+    old_train = read_csv(raw / "Train.csv", dtype={"Id": str, "Tags": str})
+    new_train, new_test = train_test_split(old_train, test_size=0.1, random_state=0)
+    new_test_without_labels = new_test.drop(columns=["Tags"])
+    sample_submission = new_test_without_labels.copy()
+    sample_submission["Tags"] = "javascript c# python php java"
+
+    # Copy over files to private and public directories
+    logger.info(f"Copying files to {private} and {public}.")
+
+    new_train.to_csv(public / "train.csv", index=False)
+    new_test_without_labels.to_csv(public / "test.csv", index=False)
+    sample_submission.to_csv(public / "sample_submission.csv", index=False)
+    new_test.to_csv(private / "test.csv", index=False)
+
+    # Sanity checks
+    logger.info("Performing sanity checks.")
+
+    assert len(new_test_without_labels) == len(
+        new_test
+    ), f"Expected {len(new_test)} public test samples, got {len(new_test_without_labels)}."
+    assert len(old_train) == len(new_train) + len(
+        new_test
+    ), f"Mismatch in number of samples in new train and test split! Expected {len(old_train)} samples, got {len(new_train) + len(new_test)}."
+    assert len(sample_submission) == len(
+        new_test
+    ), f"Expected {len(new_test)} public test samples, got {len(sample_submission)}."

mlebench/competitions/facebook-recruiting-iii-keyword-extraction/prepare_val.py

@@ -0,0 +1,92 @@
+from pathlib import Path
+
+import pandas as pd
+from sklearn.model_selection import train_test_split
+
+from mlebench.utils import extract, get_logger, read_csv
+
+logger = get_logger(__name__)
+
+
+def _create_dataset_split(
+    source_df: pd.DataFrame, public_dir: Path, private_dir: Path
+) -> None:
+    """
+    Splits a source dataframe and saves the resulting files to public and private dirs.
+
+    This helper function encapsulates the logic for:
+    1. Splitting data into train/test sets.
+    2. Creating public (unlabeled) and private (labeled) test sets.
+    3. Saving all files (train.csv, test.csv, sample_submission.csv) to the
+       specified directories with a consistent naming scheme.
+    """
+    # Create directories if they don't exist
+    public_dir.mkdir(parents=True, exist_ok=True)
+    private_dir.mkdir(parents=True, exist_ok=True)
+
+    # Split the source dataframe
+    train_split, test_split = train_test_split(
+        source_df, test_size=0.1, random_state=0
+    )
+    test_split_without_labels = test_split.drop(columns=["Tags"])
+    sample_submission = test_split_without_labels.copy()
+    sample_submission["Tags"] = "javascript c# python php java"
+
+    # Copy over files to private and public directories
+    logger.info(f"Copying files to {private_dir} and {public_dir}.")
+
+    train_split.to_csv(public_dir / "train.csv", index=False)
+    test_split_without_labels.to_csv(public_dir / "test.csv", index=False)
+    sample_submission.to_csv(public_dir / "sample_submission.csv", index=False)
+    test_split.to_csv(private_dir / "test.csv", index=False)
+
+    # Sanity checks
+    logger.info(f"Performing sanity checks for {public_dir.name}.")
+
+    assert len(test_split_without_labels) == len(
+        test_split
+    ), f"Expected {len(test_split)} public test samples, got {len(test_split_without_labels)}."
+    assert len(source_df) == len(train_split) + len(
+        test_split
+    ), f"Mismatch in number of samples! Expected {len(source_df)} samples, got {len(train_split) + len(test_split)}."
+    assert len(sample_submission) == len(
+        test_split
+    ), f"Expected {len(test_split)} public test samples, got {len(sample_submission)}."
+
+
+def prepare(raw: Path, public: Path, private: Path) -> None:
+    extract(raw / "Train.zip", raw)
+
+    # Read the full original training dataset
+    old_train = read_csv(raw / "Train.csv", dtype={"Id": str, "Tags": str})
+
+    # --- Original Data Split (public/private) ---
+    # This block creates the main train/test split. Its outputs in the `public`
+    # and `private` directories will remain identical to the original script.
+    logger.info(
+        "Creating original train/test split for public and private directories."
+    )
+    _create_dataset_split(source_df=old_train, public_dir=public, private_dir=private)
+
+    # --- New Validation Data Split (public_val/private_val) ---
+    # This block creates a new, independent validation split. It takes the
+    # training set from the *first* split and splits it again, creating a
+    # smaller training set and a validation set.
+    logger.info(
+        "Creating new train/validation split for public_val and private_val directories."
+    )
+    # Define the new output directories, parallel to the original ones.
+    public_val = public.parent / "public_val"
+    private_val = private.parent / "private_val"
+
+    # We must use the training set from the first split as the source for the second.
+    train_from_first_split, _ = train_test_split(
+        old_train, test_size=0.1, random_state=0
+    )
+
+    # Create the second split and save to the new _val directories.
+    _create_dataset_split(
+        source_df=train_from_first_split,
+        public_dir=public_val,
+        private_dir=private_val,
+    )

mlebench/competitions/feedback-prize-english-language-learning/grade.py

@@ -0,0 +1,60 @@
+import numpy as np
+import pandas as pd
+from sklearn.metrics import mean_squared_error
+
+from mlebench.grade_helpers import InvalidSubmissionError
+
+
+TARGET_COLUMNS = ['cohesion', 'syntax', 'vocabulary', 'phraseology', 'grammar', 'conventions']
+
+
+def prepare_for_metric(submission: pd.DataFrame, answers: pd.DataFrame):
+    """Prepare submission and answers for MCRMSE calculation."""
+    if len(submission) != len(answers):
+        raise InvalidSubmissionError(
+            f"Submission length ({len(submission)}) != answers length ({len(answers)})"
+        )
+
+    if "text_id" not in submission.columns:
+        raise InvalidSubmissionError("Submission must have a 'text_id' column")
+
+    for col in TARGET_COLUMNS:
+        if col not in submission.columns:
+            raise InvalidSubmissionError(f"Submission must have a '{col}' column")
+
+    # Sort by text_id
+    submission = submission.sort_values("text_id").reset_index(drop=True)
+    answers = answers.sort_values("text_id").reset_index(drop=True)
+
+    # Check text_id alignment
+    if not (submission["text_id"] == answers["text_id"]).all():
+        raise InvalidSubmissionError("Submission and answers text_id mismatch")
+
+    # Validate predictions
+    for col in TARGET_COLUMNS:
+        try:
+            submission[col] = submission[col].astype(float)
+        except (ValueError, TypeError):
+            raise InvalidSubmissionError(f"'{col}' predictions must be numeric")
+
+        if submission[col].isnull().any():
+            raise InvalidSubmissionError(f"'{col}' predictions cannot contain NaN values")
+
+    return submission, answers
+
+
+def grade(submission: pd.DataFrame, answers: pd.DataFrame) -> float:
+    """
+    Calculate MCRMSE (Mean Columnwise Root Mean Squared Error).
+
+    MCRMSE = mean of RMSE across all target columns
+    """
+    submission, answers = prepare_for_metric(submission, answers)
+
+    rmse_scores = []
+    for col in TARGET_COLUMNS:
+        rmse = np.sqrt(mean_squared_error(answers[col], submission[col]))
+        rmse_scores.append(rmse)
+
+    mcrmse = np.mean(rmse_scores)
+    return mcrmse

mlebench/competitions/feedback-prize-english-language-learning/prepare.py

@@ -0,0 +1,39 @@
+from pathlib import Path
+import pandas as pd
+
+
+TARGET_COLUMNS = ['cohesion', 'syntax', 'vocabulary', 'phraseology', 'grammar', 'conventions']
+
+
+def prepare(raw: Path, public: Path, private: Path):
+    """
+    Prepare feedback-prize-english-language-learning dataset.
+
+    Raw data contains:
+    - train.csv: training data with text and scores
+    - test.csv: test data with text only
+    - sample_submission.csv: sample submission format
+    - test_answer.csv: test labels (private)
+    """
+    # Read data
+    train = pd.read_csv(raw / "train.csv")
+    test = pd.read_csv(raw / "test.csv")
+    sample_submission = pd.read_csv(raw / "sample_submission.csv")
+    test_answer = pd.read_csv(raw / "test_answer.csv")
+
+    # Public files (visible to agents)
+    train.to_csv(public / "train.csv", index=False)
+    test.to_csv(public / "test.csv", index=False)
+    sample_submission.to_csv(public / "sample_submission.csv", index=False)
+
+    # Private files (for grading)
+    test_answer.to_csv(private / "test.csv", index=False)
+
+    # Validation checks
+    assert len(test_answer) == len(sample_submission), \
+        f"Test answer ({len(test_answer)}) and sample submission ({len(sample_submission)}) must have same length"
+    assert "text_id" in test_answer.columns, "Test answer must have 'text_id' column"
+    assert "text_id" in sample_submission.columns, "Sample submission must have 'text_id' column"
+    for col in TARGET_COLUMNS:
+        assert col in test_answer.columns, f"Test answer must have '{col}' column"
+        assert col in sample_submission.columns, f"Sample submission must have '{col}' column"

mlebench/competitions/freesound-audio-tagging-2019/grade.py

@@ -0,0 +1,64 @@
+from pathlib import Path
+
+import numpy as np
+import pandas as pd
+import sklearn.metrics
+
+from mlebench.grade_helpers import InvalidSubmissionError
+
+from .vocabulary import CLASS_NAMES
+
+
+# Using the metric implementation given to participants. Source:
+# https://colab.research.google.com/drive/1AgPdhSp7ttY18O3fEoHOQKlt_3HJDLi8
+def calculate_overall_lwlrap_sklearn(truth: np.ndarray, scores: np.ndarray) -> float:
+    """Calculate the overall lwlrap using sklearn.metrics.lrap."""
+    # sklearn doesn't correctly apply weighting to samples with no labels, so just skip them.
+    sample_weight = np.sum(truth > 0, axis=1)
+    nonzero_weight_sample_indices = np.flatnonzero(sample_weight > 0)
+    overall_lwlrap = sklearn.metrics.label_ranking_average_precision_score(
+        truth[nonzero_weight_sample_indices, :] > 0,
+        scores[nonzero_weight_sample_indices, :],
+        sample_weight=sample_weight[nonzero_weight_sample_indices],
+    )
+    return overall_lwlrap
+
+
+def prepare_for_metric(submission: pd.DataFrame, answers: pd.DataFrame) -> tuple:
+    """
+    `submission` and `answers` are both DataFrames with N rows and M + 1 columns.
+    The first column is "fname" and the remaining M columns are the predictions for each class.
+    The values are floats between 0 and 1. For `answers`, the values are binary.
+    """
+    if len(submission) != len(answers):
+        raise InvalidSubmissionError("Submission and answers must have the same length")
+
+    if "fname" != submission.columns[0]:
+        raise InvalidSubmissionError("Submission must have an 'fname' column")
+
+    if not all(submission.columns[1:] == CLASS_NAMES):
+        raise InvalidSubmissionError("Submission classes do not match expected classes")
+
+    assert answers.columns[0] == "fname", "Answers must have an 'fname' column"
+    assert all(answers.columns[1:] == CLASS_NAMES), "Answers classes do not match expected classes"
+
+    submission = submission.sort_values("fname").reset_index(drop=True)
+    answers = answers.sort_values("fname").reset_index(drop=True)
+
+    if (submission["fname"].values != answers["fname"].values).any():
+        raise InvalidSubmissionError("Submission and answers must have the same ids")
+
+    # Convert to numbers
+    try:
+        submission.iloc[:, 1:] = submission.iloc[:, 1:].apply(pd.to_numeric)
+    except (ValueError, TypeError) as e:
+        raise InvalidSubmissionError(f"Error converting submission values to float: {str(e)}")
+    answers.iloc[:, 1:] = answers.iloc[:, 1:].apply(pd.to_numeric)
+
+    # Return as numpy arrays
+    return answers.iloc[:, 1:].values, submission.iloc[:, 1:].values
+
+
+def grade(submission: pd.DataFrame, answers: pd.DataFrame) -> float:
+    sub, ans = prepare_for_metric(submission, answers)
+    return calculate_overall_lwlrap_sklearn(sub, ans)

mlebench/competitions/freesound-audio-tagging-2019/prepare.py

@@ -0,0 +1,94 @@
+import shutil
+from pathlib import Path
+
+import pandas as pd
+import requests
+
+from mlebench.utils import get_logger
+
+from .vocabulary import CLASS_NAMES
+
+logger = get_logger(__name__)
+
+
+def download_file(url, local_filename):
+    with requests.get(url, stream=True) as r:
+        r.raise_for_status()
+        with open(local_filename, "wb") as f:
+            for chunk in r.iter_content(chunk_size=8192):
+                if chunk:  # filter out keep-alive new chunks
+                    f.write(chunk)
+    return local_filename
+
+
+def prepare(raw: Path, public: Path, private: Path):
+    """
+    Straightforward: we have access to the post-competition released test labels, so we don't need
+    to create our own split here. We just copy over the raw data provided by the competition and
+    download the test labels.
+
+    Otherwise, the only work here is to convert the test data into the right format for grading:
+    The original form of `test.csv` is a DataFrame with N rows and 2 columns. The first column is
+    "fname" and the second column is the labels as comma-separated strings (class names). We
+    convert the test labels into a binary many-hot matrix matching the shape of the submission,
+    [N rows, M + 1 columns]: The first column is "fname" and the remaining M columns are the
+    predictions for each class.
+    """
+
+    # Copy over everything in the raw directory
+    logger.info("Copying raw data to public directory")
+    # Don't copy the metadata file if it exists
+    items_to_copy = [item for item in raw.iterdir() if "FSDKaggle2019.meta" not in item.name]
+    for item in items_to_copy:
+        dest = public / item.name
+        if item.is_dir():
+            shutil.copytree(item, dest)
+        else:
+            shutil.copy(item, dest)
+    assert len(list(public.iterdir())) == len(
+        items_to_copy
+    ), "Expected all files in raw to be copied to public"
+
+    # Download the test labels and metadata that were released after the competition
+    test_url = "https://zenodo.org/records/3612637/files/FSDKaggle2019.meta.zip?download=1"
+    dest_path = raw / "FSDKaggle2019.meta.zip"
+    download_file(test_url, dest_path)
+    logger.info(f"Downloaded file saved as {dest_path}")
+    # # Unzip
+    shutil.unpack_archive(dest_path, raw)
+    unzipped_path = raw / "FSDKaggle2019.meta"
+    logger.info(f"Unzipped file to {unzipped_path}")
+
+    # Read test labels
+    test_post_competition = pd.read_csv(unzipped_path / "test_post_competition.csv")
+    private_test = test_post_competition[test_post_competition["usage"] == "Private"]
+    # Create a binary many-hot matrix
+    new_test_rows = []
+    for idx, row in private_test.iterrows():
+        fname = row["fname"]
+        labels = row["labels"].split(",")
+        labels = [1 if label in labels else 0 for label in CLASS_NAMES]
+        new_test_rows.append([fname] + labels)
+    new_test = pd.DataFrame(new_test_rows, columns=["fname"] + CLASS_NAMES)
+    new_test.to_csv(private / "test.csv", index=False)
+
+    # Check that test and submission match
+    submission = pd.read_csv(public / "sample_submission.csv")
+    assert len(submission) == len(
+        new_test
+    ), f"Expected {len(new_test)} rows in test.csv, but got {len(submission)}"
+    assert (
+        submission.columns[1:].tolist() == CLASS_NAMES
+    ), "Expected class names to match between test.csv and sample_submission.csv"
+    assert all(
+        submission.columns == new_test.columns
+    ), "Expected columns to match between test.csv and sample_submission.csv"
+    new_test.sort_values("fname", inplace=True)
+    submission.sort_values("fname", inplace=True)
+    assert (
+        submission["fname"].tolist() == new_test["fname"].tolist()
+    ), "Expected 'fname' to match between test.csv and sample_submission.csv"
+
+    # Remove the downloaded metadata
+    dest_path.unlink()
+    shutil.rmtree(unzipped_path)